WO2006006948A2 - METHODS AND COMPOSITIONS FOR SELECTING siRNA OF IMPROVED FUNCTIONALITY - Google Patents

METHODS AND COMPOSITIONS FOR SELECTING siRNA OF IMPROVED FUNCTIONALITY Download PDF

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Publication number
WO2006006948A2
WO2006006948A2 PCT/US2004/014885 US2004014885W WO2006006948A2 WO 2006006948 A2 WO2006006948 A2 WO 2006006948A2 US 2004014885 W US2004014885 W US 2004014885W WO 2006006948 A2 WO2006006948 A2 WO 2006006948A2
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WO
WIPO (PCT)
Prior art keywords
base
sense strand
sirna
value
seq
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Application number
PCT/US2004/014885
Other languages
French (fr)
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WO2006006948A3 (en
Inventor
Devin Leake
Angela Reynolds
Anastasia Khvorova
William Marshall
Yuriy Fedorov
Steven Read
Original Assignee
Dharmacon, Inc.
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Filing date
Publication date
Priority claimed from US10/714,333 external-priority patent/US8090542B2/en
Application filed by Dharmacon, Inc. filed Critical Dharmacon, Inc.
Priority to PCT/US2004/014885 priority Critical patent/WO2006006948A2/en
Priority to US10/940,892 priority patent/US20120052487A9/en
Publication of WO2006006948A2 publication Critical patent/WO2006006948A2/en
Priority to US11/593,100 priority patent/US7615541B2/en
Priority to US11/594,530 priority patent/US7608706B2/en
Priority to US11/594,666 priority patent/US20070128641A1/en
Priority to US11/598,179 priority patent/US7541453B2/en
Priority to US11/595,698 priority patent/US7598369B2/en
Priority to US11/595,112 priority patent/US7605250B2/en
Priority to US11/726,245 priority patent/US20070207491A1/en
Priority to US11/729,388 priority patent/US20070185317A1/en
Priority to US11/729,924 priority patent/US20080015114A1/en
Priority to US11/731,843 priority patent/US7569684B2/en
Priority to US11/731,894 priority patent/US7521191B2/en
Priority to US11/731,890 priority patent/US20080045703A1/en
Priority to US11/731,875 priority patent/US20070299253A1/en
Priority to US11/732,457 priority patent/US7638621B2/en
Priority to US11/732,413 priority patent/US20070238868A1/en
Priority to US11/732,810 priority patent/US20070219362A1/en
Priority to US11/732,809 priority patent/US20070255046A1/en
Priority to US11/784,559 priority patent/US20070213520A1/en
Priority to US11/784,536 priority patent/US20070179286A1/en
Priority to US11/784,752 priority patent/US20070213521A1/en
Priority to US11/784,755 priority patent/US7550572B2/en
Priority to US11/784,756 priority patent/US20070232797A1/en
Priority to US11/807,530 priority patent/US20070255047A1/en
Priority to US11/807,486 priority patent/US7745610B2/en
Priority to US11/807,577 priority patent/US20070260048A1/en
Priority to US11/807,836 priority patent/US7619081B2/en
Priority claimed from US11/807,836 external-priority patent/US7619081B2/en
Priority to US11/809,909 priority patent/US20070255048A1/en
Priority to US11/810,074 priority patent/US20070276135A1/en
Priority to US11/810,383 priority patent/US7595388B2/en
Priority to US11/810,381 priority patent/US20080221316A1/en
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Priority to US11/980,263 priority patent/US7632939B2/en
Priority to US11/980,300 priority patent/US7592443B2/en
Publication of WO2006006948A3 publication Critical patent/WO2006006948A3/en
Priority to US12/157,151 priority patent/US7582747B2/en
Priority to US12/157,152 priority patent/US20080268457A1/en
Priority to US12/157,137 priority patent/US7642349B2/en
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Priority to US12/584,352 priority patent/US8222395B2/en
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Priority to US12/928,950 priority patent/US20110105363A1/en
Priority to US13/135,336 priority patent/US8293887B2/en
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Priority to US13/199,001 priority patent/US20110319474A1/en
Priority to US13/199,240 priority patent/US20110319297A1/en
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Priority to US13/531,657 priority patent/US8445667B2/en
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Priority to US13/539,630 priority patent/US20120270751A1/en
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Priority to US13/551,794 priority patent/US8658784B2/en
Priority to US13/613,910 priority patent/US20130023446A1/en
Priority to US13/632,519 priority patent/US20130059760A1/en
Priority to US13/647,869 priority patent/US8658785B1/en
Priority to US13/764,825 priority patent/US8937172B2/en
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Priority to US13/867,175 priority patent/US20130225447A1/en
Priority to US13/867,168 priority patent/US20130225667A1/en
Priority to US14/097,551 priority patent/US9228186B2/en
Priority to US14/099,339 priority patent/US8907077B2/en
Priority to US14/936,403 priority patent/US10011836B2/en
Priority to US14/936,395 priority patent/US9839649B2/en
Priority to US14/937,607 priority patent/US9879266B2/en
Priority to US14/965,816 priority patent/US9777270B2/en
Priority to US15/254,524 priority patent/US9771586B2/en
Priority to US15/255,973 priority patent/US9719094B2/en
Priority to US15/255,829 priority patent/US9719092B2/en
Priority to US15/679,097 priority patent/US20170349904A1/en
Priority to US15/705,650 priority patent/US10233449B2/en
Priority to US15/823,415 priority patent/US10765695B2/en
Priority to US15/862,479 priority patent/US10696968B2/en
Priority to US16/038,029 priority patent/US20180320182A1/en
Priority to US16/171,166 priority patent/US10920226B2/en
Priority to US16/256,933 priority patent/US20190316139A1/en
Priority to US16/378,629 priority patent/US10421970B2/en
Priority to US16/379,273 priority patent/US20190270995A1/en
Priority to US16/680,340 priority patent/US20200123550A1/en
Priority to US16/782,976 priority patent/US11198870B2/en
Priority to US17/520,530 priority patent/US20220315922A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • C—CHEMISTRY; METALLURGY
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    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1135—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against oncogenes or tumor suppressor genes
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/10—Applications; Uses in screening processes
    • C12N2320/11—Applications; Uses in screening processes for the determination of target sites, i.e. of active nucleic acids

Definitions

  • Applicant submits a compact disc of tables related to sequences and hereby incorporates by reference the material submitted herewith, on the compact disk labeled COPY 1 - TABLES PART DISK 1/1 , TABLES XII and XIII (provided in triplicate, which copies are identical), in files entitled table-xii.txt, date of creation 26 April 2004, with a size of 110,486 kb, and table-xiii.txt, date of creation 26 April 2004, with a size of 23,146 kb; and in accordance with PCT Administrative Instructions Section 801(a)(i) on the compact disk labeled CRF (with three further copies, which copies are identical) in a file entitled 13608PCT.txt, date of creation 26 April 2004, with a size of 556,776 kb.
  • RNA interference RNA interference
  • dsRNA double stranded RNA
  • Double stranded RNA induced gene silencing can occur on at least three different levels: (i) transcription inactivation, which refers to RNA guided DNA or histone methylation; (ii) siRNA induced rnRNA degradation; and (iii) mRNA induced transcriptional attenuation.
  • RNAi RNA induced silencing
  • siRNAs small inhibitory RNAs
  • Dicer a Type III endonuclease known as Dicer.
  • Dicer a ribonuclease-III-like enzyme, processes the dsRNA into 19-23 base pair short interfering RNAs with characteristic two base 3' overhangs. Bernstein, Caudy, Hammond, & Harmon, Role for a bidentate ribonuclease in the initiation step of RNA interference, Nature 2001, 409:363.
  • RNA-induced silencing complex RISC
  • one or more helicases unwind the siRNA duplex, enabling the complementary antisense strand to guide target recognition.
  • Nykanen, Haley, & Zamore ATP requirements and small interfering RNA structure in the RNA interference pathway, Cell 2001, 107:309.
  • one or more endonucleases within the RISC cleaves the target to induce silencing.
  • Elbashir, Lendeckel, & Tuschl RNA interference is mediated by 21- and 22 -nucleotide RNAs 1 Genes Dev 2001, 15:188, Figure 1.
  • RNAi exhibits sequence specificity, Kisielow, M. et al. (2002) Isoform-specific knockdown and expression of adaptor protein ShcA using small interfering RNA, J. of Biochemistry 363: 1-5.
  • the RNAi machinery can specifically knock down one type of transcript, while not affecting closely related mRNA.
  • siRNAs are potentially useful as therapeutic agents against: (1) diseases that are caused by over-expression or misexpression of genes; and (2) diseases brought about by expression of genes that contain mutations.
  • RNAi One of the most contentious issues in RNAi is the question of the necessity of siRNA design, i.e., considering the sequence of the siRNA used.
  • long dsRNA see, for instance, Fire, A. et al. (1998) Nature 391:806-811).
  • long dsRNA molecules are cleaved into siRNA by Dicer, thus generating a diverse population of duplexes that can potentially cover the entire transcript. While some fraction of these molecules are non-functional (i.e., induce little or no silencing) one or more have the potential to be highly functional, thereby silencing the gene of interest and alleviating the need for siRNA design.
  • siRNA design is not a crucial element of RNAi.
  • others in the field have begun to explore the possibility that RNAi can be made more efficient by paying attention to the design of the siRNA.
  • none of the reported methods have provided a satisfactory scheme for reliably selecting siRNA with acceptable levels of functionality. Accordingly, there is a need to develop rational criteria by which to select siRNA with an acceptable level of functionality, and to identify siRNA that have this improved level of functionality, as well as to identify siRNAs that are hyperfunctional.
  • the present invention is directed to increasing the efficiency of RNAi, particularly in mammalian systems. Accordingly, the present invention provides kits, siRNAs and methods for increasing siRNA efficacy.
  • the present invention provides a kit for gene silencing, wherein said kit is comprised of a pool of at least two siRNA duplexes, each of which is comprised of a sequence that is complementary to a portion of the sequence of one or more target messenger RNA, and each of which is selected using non-target specific criteria.
  • the present invention provides a method for selecting an siRNA, said method comprising applying selection criteria to a set of , potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; and determining the relative functionality of the at least two siRNAs.
  • the present invention also provides a method wherein said selection criteria are embodied in a formula comprising:
  • G 1 1 if G is the base at position 1 on the sense strand, otherwise its value is 0;
  • G 2 1 if G is the base at position 2 of the sense strand, otherwise its value is 0;
  • G 8 1 if G is the base at position 8 on the sense strand, otherwise its value is 0;
  • G 1O 1 if G is the base at position 10 on the sense strand, otherwise its value is 0;
  • G 13 1 if G is the base at position 13 on the sense strand, otherwise its value is 0;
  • G ⁇ g 1 if G is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
  • U 1 1 if U is the base at position 1 on the sense strand, otherwise its value is 0;
  • U 2 1 if U is the base at position 2 on the sense strand, otherwise its value is 0;
  • U 3 1 if U is the base at position 3 on the sense strand, otherwise its value is 0;
  • U 4 1 if U is the base at position 4 on the sense strand, otherwise its value is 0;
  • U 7 1 if U is the base at position 7 on the sense strand, otherwise its value is 0;
  • U 9 1 if U is the base at position 9 on the sense strand, otherwise its value is 0;
  • U 10 1 if U is the base at position 10 on the sense strand, otherwise its value is 0;
  • U 15 1 if U is the base at position 15 on the sense strand, otherwise its value is 0;
  • U 16 1 if U is the base at position 16 on the sense strand, otherwise its value is 0;
  • U 17 1 if U is the base at position 17 on the sense strand, otherwise its value is 0;
  • U 1S 1 if U is the base at position 18 on the sense strand, otherwise its value is 0.
  • GQ 5 - 49 the number of G and C bases within positions 15 - 19 of the sense strand, or within positions 15 -18 if the sense strand is only 18 base pairs in length; GCtotai - the number of G and C bases in the sense strand;
  • Tm 100 if the siRNA oligo has the internal repeat longer then 4 base pairs, otherwise its value is 0;
  • the invention provides a method for developing an algorithm for selecting siRNA, said method comprising: (a) selecting a set of siRNA; (b) measuring gene silencing ability of each siRNA from said set; (c) determining relative functionality of each siRNA; (d) determining improved functionality by the presence or absence of at least one variable selected from the group consisting of the presence or absence of a particular nucleotide at a particular position, the total number of As and Us in positions 15-19, the number of times that the same nucleotide repeats within a given sequence, and the total number of Gs and Cs; and (e) developing an algorithm using the information of step (d).
  • the present invention provides a kit, wherein said kit is comprised of at least two siRNAs, wherein said at least two siRNAs comprise a first optimized siRNA and a second optimized siRNA, wherein said first optimized siRNA and said second optimized siRNA are optimized according a formula comprising Formula X.
  • the present invention provides a method for identifying a hyperfunctional siRNA, comprising applying selection criteria to a set of potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; determining the relative functionality of the at least two siRNAs and assigning each of the at least two siRNAs a functionality score; and selecting siRNAs from the at least two siRNAs that have a functionality score that reflects greater than 80 percent silencing at a concentration in the picomolar range, wherein said greater than 80 percent silencing endures for greater than 120 hours.
  • the present invention provides a hyperfunctional siRNA that is capable of silencing Bcl2.
  • the present invention provides a method for developing an siRNA algorithm for selecting functional and hyperfunctional siRNAs for a given sequence.
  • the method comprises: (a) selecting a set of siRNAs;
  • step (e) developing an algorithm using the information of step (d).
  • the set of siRNAs comprises at least 90 siRNAs from at least one gene, more preferably at least 180 siRNAs from at least two different genes, and most preferably at least 270 and 360 siRNAs from at least three and four different genes, respectively. Additionally, in step (d) the determination is made with preferably at least two, more preferably at least three, even more preferably at least four, and most preferably all of the variables. The resulting algorithm is not target sequence specific.
  • the present invention provides rationally designed siRNAs identified using the formulas above.
  • the present invention is directed to hyperfunctional siRNA.
  • FIGURES Figure 1 shows a model for siRNA-RISC interactions.
  • RISC has the ability to interact with either end of the siRNA or miRNA molecule. Following binding, the duplex is unwound, and the relevant target is identified, cleaved, and released.
  • Figure 2 is a representation of the functionality of two hundred and seventy siRNA duplexes that were generated to target human cyclophilin, human diazepam-binding inhibitor (DB), and firefly luciferase.
  • Figure 3a is a representation of the silencing effect of 30 siRNAs in three different cells lines, HEK293, DU 145, and HeIa.
  • Figure 3b shows the frequency of different functional groups (>95% silencing (black), >80% silencing (gray), >50% silencing (dark gray), and ⁇ 50% silencing (white)) based on GC content. In cases where a given bar is absent from a particular GC percentage, no siRNA were identified for that particular group.
  • Figure 3c shows the frequency of different functional groups based on melting temperature (Tm).
  • Figure 4 is a representation of a statistical analysis that revealed correlations between silencing and five sequence-related properties of siRNA: (A) an A at position 19 of the sense strand, (B) an A at position 3 of the sense strand, (C) a U at position 10 of the sense strand, (D) a base other than G at position 13 of the sense strand, and (E) a base other than C at position 19 of the sense strand. All variables were correlated with siRNA silencing of firefly luciferase and human cyclophilin. siRNAs satisfying the criterion are grouped on the left (Selected) while those that do not, are grouped on the right (Eliminated). Y-axis is "% Silencing of Control.” Each position on the X- axis represents a unique siRNA.
  • Figures 5 A and 5 B are representations of firefly luciferase and cyclophilin siRNA panels sorted according to functionality and predicted values using Formula VIII.
  • the siRNA found within the circle represent those that have Formula VIII values (SMARTscoresTM) above zero.
  • siRNA outside the indicated area have calculated Formula VIII values that are below zero.
  • Y-axis is "Expression (% Control)." Each position on the X-axis represents a unique siRNA.
  • Figure 6 A is a representation of the average internal stability profile (AISP) derived from 270 siRNAs taken from three separate genes (cyclophilin B, DBI and firefly luciferase). Graphs represent AISP values of highly functional, functional, and non ⁇ functional siRNA.
  • Figure 6B is a comparison between the AISP of naturally derived GFP siRNA (filled squares) and the AISP of siRNA from cyclophilin B, DBI, and luciferase having >90% silencing properties (no fill) for the antisense strand.
  • "DG" is the symbol for ⁇ G, free energy.
  • Figure 7 is a histogram showing the differences in duplex functionality upon introduction of basepair mismatches.
  • the X-axis shows the mismatch introduced in the siRNA and the position it is introduced (e.g., 8C >A reveals that position 8 (which normally has a C) has been changed to an A).
  • the Y-axis is "% Silencing (Normalized to Control)."
  • Figure 8a is histogram that shows the effects of 5 'sense and antisense strand modification with 2'-O-methylation on functionality.
  • Figure 8b is an expression profile showing a comparison of sense strand off-target effects for IGF1R-3 and 2'-O- methyl IGF1R-3.
  • Sense strand off-targets (lower box) are not induced when the 5' end of the sense strand is modified with 2'-O-methyl groups (top box).
  • Figure 9 shows a graph of SMARTscoresTM versus RNAi silencing values for more than 360 siRNA directed against 30 different genes.
  • siRNA to the right of the vertical bar represent those siRNA that have desirable SMARTscoresTM.
  • Figures 1OA - E compare the RNAi of five different genes (SEAP 5 DBI, PLK 5 Firefly Luciferase, and Renila Luciferase) by varying numbers of randomly selected siRNA and four rationally designed (SMART-selected) siRNA chosen using the algorithm described in Formula VIII.
  • RNAi induced by a pool of the four SMART-selected siRNA is reported at two different concentrations (100 and 40OnM).
  • 1OF is a comparison between a pool of randomly selected EGFR siRNA (Pool 1) and a pool of SMART selected EGFR siRNA (Pool 2). Pool 1, Sl- S4 and Pool 2 Sl- S4 represent the individual members that made up each respective pool. Note that numbers for random siRNAs represent the position of the 5' end of the sense strand of the duplex.
  • the Y-axis represents the % expression of the control(s).
  • the X-axis is the percent expression of the control.
  • Figure 11 shows the Western blot results from cells treated with siRNA directed against twelve different genes involved in the clathrin-dependent endocytosis pathway (CHC, DynII, CALM, CLCa, CLCb, Epsl5, Epsl5R, Rab5a, Rab5b, Rab5c, ⁇ 2 subunit of AP-2 and EEA.l).
  • siRNA were selected using Formula VIII.
  • Figure 12 is a representation of the gene silencing capabilities of rationally-selected siRNA directed against ten different genes (human and mouse cyclophilin, C-myc, human lamin AJC, QB (ubiquinol-cytochrome c reductase core protein I), MEKl and MEK2, ATEl (arginyl-tRNA protein transferase), GAPDH, and Eg5).
  • the Y-axis is the percent expression of the control. Numbers 1, 2, 3 and 4 represent individual rationally selected siRNA. "Pool” represents a mixture of the four individual siRNA.
  • Figure 13 is the sequence of the top ten Bcl2 siRNAs as determined by Formula VIII. Sequences are listed 5' to 3'.
  • Figure 14 is the knockdown by the top ten Bcl2 siRNAs at 10OnM concentrations.
  • the Y-axis represents the amount of expression relative to the non-specific (ns) and transfection mixture control.
  • Figure 15 represents a functional walk where siRNA beginning on every other base pair of a region of the luciferase gene are tested for the ability to silence the luciferase gene.
  • the Y-axis represents the percent expression relative to a control.
  • the X-axis represents the position of each individual siRNA.
  • Figure 16 is a histogram demonstrating the inhibition of target gene expression by pools of 2 and 3 siRNAs duplexes taken from the walk described in Figure 15.
  • the Y-axis represents the percent expression relative to control.
  • the X-axis represents the position of the first siRNA in paired pools, or trios of siRNA. For instance, the first paired pool contains siRNA 1 and 3.
  • the second paired pool contains siRNA 3 and 5. Pool 3 (of paired pools) contains siRNA 5 and 7, and so on.
  • Figure 17 is a histogram demonstrating the inhibition of target gene expression by pools of 4 and 5 siRNA duplexes.
  • the Y-axis represents the percent expression relative to a control.
  • the X-axis represents the position of the first siRNA in each pool.
  • Figure 18 is a histogram demonstrating the inhibition of target gene expression by siRNAs that are ten and twenty basepairs apart.
  • the Y-axis represents the percent expression relative to a control.
  • the X-axis represents the position of the first siRNA in each pool.
  • Figure 19 shows that pools of siRNAs (dark gray bar) work as well (or better) than the best siRNA in the pool (light gray bar).
  • the Y-axis represents the percent expression relative to a control.
  • The-X axis represents the position of the first siRNA in each pool.
  • Figure 20 shows that the combination of several semifunctional siRNAs (dark gray) result in a significant improvement of gene expression inhibition over individual (semi-functional; light gray) siRNA.
  • the Y-axis represents the percent expression relative to a control.
  • Figure 21 shows both pools (Library, Lib) and individual siRNAs in inhibition of gene expression of Beta-Galactosidase, Renilla Luciferase and SEAP (alkaline phosphatase). Numbers on the X-axis indicate the position of the 5'-most nucleotide of the sense strand of the duplex. The Y-axis represents the percent expression of each gene relative to a control.
  • Libraries contain 19 nucleotide long siRNAs (not including overhangs) that begin at the following nucleotides: SEAP: Lib 1 : 206, 766, 812,923, Lib 2: 1117, 1280, 1300, 1487, Lib 3: 206, 766, 812, 923, 1117, 1280, 1300,1487, Lib 4: 206, 812, 1117, 1300, Lib 5: 766, 923, 1280, 1487, Lib 6: 206, 1487; Bgal: Lib 1: 979, 1339, 2029, 2590, Lib 2: 1087,1783,2399,3257, Lib 3: 979, 1783, 2590, 3257, Lib 4: 979, 1087, 1339, 1783, 2029, 2399,2590,3257, Lib 5: 979, 1087, 1339, 1783, Lib 6: 2029,2399,2590,3257; Renilla: Lib 1:
  • Figure 22 shows the results of an EGFR and TfiiR internalization assay when single gene knockdowns are performed.
  • the Y-axis represents percent internalization relative to control.
  • Figure 23 shows the results of an EGFR and TfnR internalization assay when multiple genes are knocked down ⁇ e.g., Rab5a, b, c).
  • the Y-axis represents the percent internalization relative to control.
  • Figure 24 shows the simultaneous knockdown of four different genes.
  • siRNAs directed against G6PD, GAPDH, PLK 5 and UQC were simultaneously introduced into cells. Twenty-four hours later, cultures were harvested and assayed for mRNA target levels for each of the four genes. A comparison is made between cells transfected with individual siRNAs vs. a pool of siRNAs directed against all four genes.
  • Figure 25 shows the functionality often siRNAs at 0.3nM concentrations.
  • siRNA refers to small inhibitory RNA duplexes that induce the
  • RNA interference (RNAi) pathway RNA interference pathway. These molecules can vary in length (generally 18-30 basepairs) and contain varying degrees of complementarity to their target mRNA in the antisense strand. Some, but not all, siRNA have unpaired overhanging bases on the 5' or 3' end of the sense strand and/or the antisense strand.
  • siRNA includes duplexes of two separate strands, as well as single strands that can form hairpin structures comprising a duplex region.
  • siRNA may be divided into five (5) groups (non-functional, semi-functional, functional, highly functional, and hyper-functional) based on the level or degree of silencing that they induce in cultured cell lines. As used herein, these definitions are based on a set of conditions where the siRNA is transfected into said cell line at a concentration of 10OnM and the level of silencing is tested at a time of roughly 24 hours after transfection, and not exceeding 72 hours after transfection. hi this context, "non-functional siRNA” are defined as those siRNA that induce less than 50%
  • siRNA ( ⁇ 50%) target silencing.
  • “Semi-functional siRNA” induce 50-79% target silencing.
  • “Functional siRNA” are molecules that induce 80-95% gene silencing.
  • “Highly- functional siRNA” are molecules that induce greater than 95% gene silencing.
  • “Hyperfunctional siRNA” are a special class of molecules. For purposes of this document, hyperfunctional siRNA are defined as those molecules that: (1) induce greater than 95% silencing of a specific target when they are transfected at subnanomolar concentrations (i.e., less than one nanomolar); and/or (2) induce functional (or better) levels of silencing for greater than 96 hours. These relative functionalities (though not intended to be absolutes) may be used to compare siRNAs to a particular target for applications such as functional genomics, target identification and therapeutics.
  • microRNA refers to microRNA.
  • gene silencing refers to a process by which the expression of a specific gene product is lessened or attenuated. Gene silencing can take place by a variety of pathways. Unless specified otherwise, as used herin, gene silencing refers to decreases in gene product expression that results from RNA interference (RNAi), a defined, though partially characterized pathway whereby small inhibitory RNA (siRNA) act in concert with host proteins (e.g., the RNA induced silencing complex, RISC) to degrade messenger RNA (mRNA) in a sequence-dependent fashion.
  • RNAi RNA interference
  • host proteins e.g., the RNA induced silencing complex, RISC
  • the level of gene silencing can be measured by a variety of means, including, but not limited to, measurement of transcript levels by Northern Blot Analysis, B-DNA techniques, transcription-sensitive reporter constructs, expression profiling (e.g., DNA chips), and related technologies.
  • the level of silencing can be measured by assessing the level of the protein encoded by a specific gene. This can be accomplished by performing a number of studies including Western Analysis, measuring the levels of expression of a reporter protein that has e.g., fluorescent properties (e.g., GFP) or enzymatic activity (e.g., alkaline phosphatases), or several other procedures.
  • fluorescent properties e.g., GFP
  • enzymatic activity e.g., alkaline phosphatases
  • filter refers to one or more procedures that are performed on sequences that are identified by the algorithm.
  • filtering includes in silico procedures where sequences identified by the algorithm can be screened to identify duplexes carrying desirable or undesirable motifs. Sequences carrying such motifs can be selected for, or selected against, to obtain a final set with the preferred properties.
  • filtering includes wet lab experiments. For instance, sequences identified by one or more versions of the algorithm can be screened using any one of a number of procedures to identify duplexes that have hyperfunctional traits (e.g., they exhibit a high degree of silencing at subnanomolar concentrations and/or exhibit high degrees of silencing longevity).
  • transfection refers to a process by which agents are introduced into a cell.
  • the list of agents that can be transfected is large and includes, but is not limited to, siRNA, sense and/or anti-sense sequences, DNA encoding one or more genes and organized into an expression plasmid, proteins, protein fragments, and more.
  • methods for transfecting agents into a cell including, but not limited to, electroporation, calcium phosphate-based transfections, DEAE-dextran- based transfections, lipid-based transfections, molecular conjugate-based transfections (e.g., polylysine-DNA conjugates), microinjection and others.
  • target is used in a variety of different forms throughout this document and is defined by the context in which it is used.
  • “Target rnRNA” refers to a messenger RNA to which a given siRNA can be directed against.
  • target sequence and “target site” refer to a sequence within the mRNA to which the sense strand of an siRNA shows varying degrees of homology and the antisense strand exhibits varying degrees of complementarity.
  • siRNA target can refer to the gene, mRNA, or protein against which an siRNA is directed.
  • target silencing can refer to the state of a gene, or the corresponding mRNA or protein.
  • off-target silencing and “off-target interference” are defined as degradation of mRNA other than the intended target mRNA due to overlapping and/or partial homology with secondary mRNA messages.
  • SMARTscoreTM refers to a number determined by applying any of the Formulas I - Formula X to a given siRNA sequence.
  • SMART- selected or “rationally selected” or “rational selection” refer to siRNA that have been selected on the basis of their SMARTscoresTM.
  • Complementary refers to the ability of polynucleotides to form base pairs with one another. Base pairs are typically formed by hydrogen bonds between nucleotide units in antiparallel polynucleotide strands. Complementary polynucleotide strands can base pair in the Watson-Crick manner ⁇ e.g., A to T, A to U, C to G), or in any other manner that allows for the formation of duplexes.
  • uracil rather than thymine is the base that is considered to be complementary to adenosine.
  • a U is denoted in the context of the present invention, the ability to substitute a T is implied, unless otherwise stated.
  • Perfect complementarity or 100% complementarity refers to the situation in which each nucleotide unit of one polynucleotide strand can hydrogen bond with a nucleotide unit of a second polynucleotide strand.
  • Less than perfect complementarity refers to the situation in which some, but not all, nucleotide units of two strands can " hydrogen bond with each other. For example, for two 20-mers, if only two base pairs on each strand can hydrogen bond with each other, the polynucleotide strands exhibit 10% complementarity. In the same example, if 18 base pairs on each strand can hydrogen bond with each other, the polynucleotide strands exhibit 90% complementarity.
  • Substantial complementarity refers to polynucleotide strands exhibiting 79% or greater complementarity, excluding regions of the polynucleotide strands, such as overhangs, that are selected so as to be noncomplementary.
  • Substantial similarity refers to polynucleotide strands exhibiting 79% or greater similarity, excluding regions of the polynucleotide strands, such as overhangs, that are selected so as not to be similar.
  • two polynucleotides of 29 nucleotide units each, wherein each comprises a di-dT at the 3' terminus such that the duplex region spans 27 bases, and wherein 26 of the 27 bases of the duplex region on each strand are complementary are substantially complementary since they are 96.3% complementary when excluding the di-dT overhangs.
  • deoxynucleotide refers to a nucleotide or polynucleotide lacking a hydroxyl group (OH group) at the 2' and/or 3' position of a sugar moiety. Instead, it has a hydrogen bonded to the 2' and/or 3' carbon.
  • deoxynucleotide refers to the lack of an OH group at the T position of the sugar moiety, having instead a hydrogen bonded directly to the 2' carbon.
  • deoxvribonucleotide and “DNA” refer to a nucleotide or polynucleotide comprising at least one sugar moiety that has an H 5 rather than an OH, at its 2' and/or 3 'position.
  • substantially similar refers to a similarity of at least 90% with respect to the identity of the bases of the sequence.
  • duplex region refers to the region in two complementary or substantially complementary polynucleotides that form base pairs with one another, either by Watson-Crick base pairing or any other manner that allows for a stabilized duplex between polynucleotide strands that are complementary or substantially complementary.
  • a polynucleotide strand having 21 nucleotide units can base pair with another polynucleotide of 21 nucleotide units, yet only 19 bases on each strand are complementary or substantially complementary, such that the "duplex region” has 19 base pairs. The remaining bases may, for example, exist as 5' and 3' overhangs.
  • 100% complementarity is not required; substantial complementarity is allowable within a duplex region.
  • Substantial complementarity refers to 79% or greater complementarity. For example, a mismatch in a duplex region consisting of 19 base pairs results in 94.7% complementarity, rendering the duplex region substantially complementary.
  • nucleotide refers to a ribonucleotide or a deoxyribonucleotide or modified form thereof, as well as an analog thereof.
  • Nucleotides include species that comprise purines, e.g., adenine, hypoxanthine, guanine, and their derivatives and analogs, as well as pyrimidines, e.g., cytosine, uracil, thymine, and their derivatives and analogs.
  • Nucleotide analogs include nucleotides having modifications in the chemical structure of the base, sugar and/or phosphate, including, but not limited to, 5-position pyrimidine modifications, 8-position purine modifications, modifications at cytosine exocyclic amines, and substitution of 5-bromo-uracil; and 2'-position sugar modifications, including but not limited to, sugar-modified ribonucleotides in which the 2'-OH is replaced by a group such as an H, OR, R, halo, SH, SR, NH 2 , NHR, NR 2 , or CN, wherein R is an alkyl moiety.
  • Nucleotide analogs are also meant to include nucleotides with bases such as inosine, queuosine, xanthine, sugars such as 2'-methyl ribose, non-natural phosphodiester linkages such as methylphosphonates, phosphorothioates and peptides.
  • Modified bases refer to nucleotide bases such as, for example, adenine, guanine, cytosine, thymine, uracil, xanthine, inosine, and queuosine that have been modified by the replacement or addition of one or more atoms or groups.
  • nucleotide bases such as, for example, adenine, guanine, cytosine, thymine, uracil, xanthine, inosine, and queuosine that have been modified by the replacement or addition of one or more atoms or groups.
  • Some examples of types of modifications that can comprise nucleotides that are modified with respect to the base moieties include but are not limited to, alkylated, halogenated, thiolated, aminated, amidated, or acetylated bases, individually or in combination.
  • More specific examples include, for example, 5-propynyluridine, 5-propynylcytidine, 6-methyladenine, 6-metliylguanine, N,N,-dimethyladenine, 2 -propyl adenine, 2- propylguanine, 2-aminoadenine, 1-methylinosine, 3-methyluridine, 5-methylcytidine, 5-methyluridine and other nucleotides having a modification at the 5 position, 5-(2- amino)propyl uridine, 5-halocytidine, 5-halouridine, 4-acetylcytidine, 1- methyladenosine, 2-methyladenosine, 3-methylcytidine, 6-methyluridine, 2- methylguanosine, 7-methylguanosine, 2,2-dimethylguanosine, 5- methylaminoethyluridine, 5-methyloxyuridine, deazanucleotides such as 7-deaza- adenosine, 6-azour
  • Modified nucleotides also include those nucleotides that are modified with respect to the sugar moiety, as well as nucleotides having sugars or analogs thereof that are not ribosyl.
  • the sugar moieties may be, or be based on, mannoses, arabinoses, glucopyranoses, galactopyranoses, 4'- thioribose, and other sugars, heterocycles, or carbocycles.
  • nucleotide is also meant to include what are known in the art as universal bases.
  • universal bases include but are not limited to 3- nitropyrrole, 5-nitroindole, or nebularine.
  • nucleotide is also meant to include the N3' to P5' phosphoramidate, resulting from the substitution of a ribosyl 3' oxygen with an amine group.
  • nucleotide also includes those species that have a detectable label, such as for example a radioactive or fluorescent moiety, or mass label attached to the nucleotide.
  • polynucleotide refers to polymers of nucleotides, and includes but is not limited to DNA, RNA, DNA/RNA hybrids including polynucleotide chains of regularly and/or irregularly alternating deoxyribosyl moieties and ribosyl moieties
  • polyribonucleotide refers to a polynucleotide comprising two or more modified or unmodified ribonucleotides and/or their analogs.
  • polyribonucleotide is used interchangeably with the term “oligoribonucleotide.”
  • ribonucleotide and the phrase “ribonucleic acid” (RNA), refer to a modified or unmodified nucleotide or polynucleotide comprising at least one ribonucleotide unit.
  • a ribonucleotide unit comprises an hydroxyl group attached to the 2' position of a ribosyl moiety that has a nitrogenous base attached in N- glycosidic linkage at the 1' position of a ribosyl moiety, and a moiety that either allows for linkage to another nucleotide or precludes linkage.
  • the present invention is directed to improving the efficiency of gene silencing by siRNA. Through the inclusion of multiple siRNA sequences that are targeted to a particular gene and/or selecting an siRNA sequence based on certain defined criteria, improved efficiency may be achieved.
  • the present invention is directed to increasing the efficiency of RNAi, particularly in mammalian systems. Accordingly, the present invention provides kits, siRNAs and methods for increasing siRNA efficacy.
  • the present invention provides a kit for gene silencing, wherein said kit is comprised of apool of at least two siRNA duplexes, each of which is comprised of a sequence that is complementary to a portion of the sequence of one or more target messenger RNA, and each of which is selected using non-target specific criteria.
  • Each of the at least two siRNA duplexes of the kit complementary to a portion of the sequence of one or more target mRNAs is preferably selected using Formula X.
  • the present invention provides a method for selecting an siRNA, said method comprising applying selection criteria to a set of potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; and determining the relative functionality of the at least two siRNAs.
  • the present invention also provides a method wherein said selection criteria are embodied in a formula comprising:
  • G 1 1 if G is the base at position 1 on the sense strand, otherwise its value is 0;
  • G 2 1 if G is the base at position 2 of the sense strand, otherwise its value is 0;
  • G 8 1 if G is the base at position 8 on the sense strand, otherwise its value is 0;
  • G 10 1 if G is the base at position 10 on the sense strand, otherwise its value is 0;
  • G 13 1 if G is the base at position 13 on the sense strand, otherwise its value is 0;
  • G 19 1 if G is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
  • U 1 1 if U is the base at position 1 on the sense strand, otherwise its value is 0;
  • U 2 1 if U is the base at position 2 on the sense strand, otherwise its value is 0;
  • U 3 1 if U is the base at position 3 on the sense strand, otherwise its value is 0;
  • U 4 1 if U is the base at position 4 on the sense strand, otherwise its value is 0;
  • U 7 1 if U is the base at position 7 on the sense strand, otherwise its value is 0;
  • U 9 1 if U is the base at position 9 on the sense strand, otherwise its value is 0;
  • U 1O 1 if U is the base at position 10 on the sense strand, otherwise its value is 0;
  • U 15 1 if U is the base at position 15 on the sense strand, otherwise its value is 0;
  • U 16 1 if U is the base at position 16 on the sense strand, otherwise its value is 0;
  • GC 15 _ !9 the number of G and C bases within positions 15 - 19 of the sense strand, or within positions 15 -18 if the sense strand is only 18 base pairs in length;
  • GQot a i the number of G and C bases in the sense strand;
  • Tm 100 if the siRNA oligo has the internal repeat longer then 4 base pairs, otherwise its value is 0;
  • X the number of times that the same nucleotide repeats four or more times in a row.
  • any of the methods of selecting siRNA in accordance with the invention can further comprise comparing the internal stability profiles of the siRNAs to be selected, and selecting those siRNAs with the most favorable internal stability profiles. Any of the methods of selecting siRNA can further comprise selecting either for or against sequences that contain motifs that induce cellular stress. Such motifs include, for example, toxicity motifs. Any of the methods of selecting siRNA can further comprise either selecting for or selecting against sequences that comprise stability motifs.
  • the present invention provides a method of gene silencing, comprising introducing into a cell at least one siRNA selected according to any of the methods of the present invention.
  • the siRNA can be introduced by allowing passive uptake of siRNA, or through the use of a vector.
  • the invention provides a method for developing an algorithm for selecting siRNA, said method comprising: (a) selecting a set of siRNA; (b) measuring gene silencing ability of each siRNA from said set; (c) determining relative functionality of each siRNA; (d) determining improved functionality by the presence or absence of at least one variable selected from the group consisting of the presence or absence of a particular nucleotide at a particular position, the total number of As and Us in positions 15-19, the number of times that the same nucleotide repeats within a given sequence, and the total number of Gs and Cs; and (e) developing an algorithm using the information of step (d).
  • the invention provides a method for selecting an siRNA with improved functionality, comprising using the above-mentioned algorithm to identify an siRNA of improved functionality.
  • the present invention provides a kit, wherein said kit is comprised of at least two siRNAs, wherein said at least two siRNAs comprise a first optimized siRNA and a second optimized siRNA, wherein said first optimized siRNA and said second optimized siRNA are optimized according a formula comprising Formula X.
  • the present invention provides a method for identifying a hyperfunctional siRNA, comprising applying selection criteria to a set of potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; determining the relative functionality of the at least two siRNAs and assigning each of the at least two siRNAs a functionality score; and selecting siRNAs from the at least two siRNAs that have a functionality score that reflects greater than 80 percent silencing at a concentration in the picomolar range, wherein said greater than 80 percent silencing endures for greater than 120 hours.
  • the invention provides kits and/or methods wherein the siRNA are comprised of two separate polynucleotide strands; wherein the siRNA are comprised of a single contiguous molecule such as, for example, a unimolecular siRNA (comprising, for example, either a nucleotide or non-nucleotide loop); wherein the siRNA are expressed from one or more vectors; and wherein two or more genes are silenced by a single administration of siRNA.
  • a unimolecular siRNA comprising, for example, either a nucleotide or non-nucleotide loop
  • the present invention provides a hyperfunctional siRNA that is capable of silencing BcI 2.
  • the present invention provides a method for developing an siRNA algorithm for selecting functional and hyperfunctional siRNAs for a given sequence.
  • the method comprises:
  • each siRNA determines the relative functionality of each siRNA; (d) determining the amount of improved functionality by the presence or absence of at least one variable selected from the group consisting of the total GC content, melting temperature of the siRNA, GC content at positions 15 -19, the presence or absence of a particular nucleotide at a particular position, relative thermodynamic stability at particular positions in a duplex, and the number of times that the same nucleotide repeats within a given sequence; and
  • step (e) developing an algorithm using the information of step (d).
  • the set of siRNAs comprises at least 90 siRNAs from at least one gene, more preferably at least 180 siRNAs from at least two different genes,.and most preferably at least 270 and 360 siRNAs from at least three and four different genes, respectively.
  • the determination is made with preferably at least two, more preferably at least three, even more preferably at least four, and most preferably all of the variables.
  • the resulting algorithm is not target sequence specific.
  • the present invention provides rationally designed siRNAs identified using the formulas above.
  • the present invention is directed to hyperfunctional siRNA.
  • the methods disclosed herein can be used in conjunction with comparing internal stability profiles of selected siRNAs, and designing an siRNA with a desireable internal stability profile; and/or in conjunction with a selection either for or against sequences that contain motifs that induce cellular stress, for example, cellular toxicity. Any of the methods disclosed herein can be used to silence one or more genes by introducing an siRNA selected, or designed, in accordance with any of the methods disclosed herein.
  • the siRNA(s) can be introduced into the cell by any method known in the art, including passive uptake or through the use of one or more vectors.
  • any of the methods and kits disclosed herein can employ either unimolecular siRNAs, siRNAs comprised of two separate polynucleotide strands, or combinations thereof. Any of the methods disclosed herein can be used in gene silencing, where two or more genes are silenced by a single administration of siRNA(s).
  • the siRNA(s) can be directed against two or more target genes, and administered in a single dose or single transfection, as the case may be.
  • the present invention provides a method for improving the effectiveness of gene silencing for use to silence a particular gene through the selection of an optimal siRNA.
  • An siRNA selected according to this method may be used individually, or in conjunction with the first embodiment, i.e., with one or more other siRNAs, each of which may or may not be selected by this criteria in order to maximize their efficiency.
  • an siRNA is selected for a given gene by using a rational design. That said, rational design can be described in a variety of ways. Rational design is, in simplest terms, the application of a proven set of criteria that enhance the probability of identifying a functional or hyperfunctional siRNA. hi one method, rationally designed siRNA can be identified by maximizing one or more of the following criteria:
  • a low GC content preferably between about 30 -52%.
  • a Tm which refers to the character of the internal repeat that results in inter- or intramolecular structures for one strand of the duplex, that is preferably not stable at greater than 50°C, more preferably not stable at . greater than 37 0 C, even more preferably not stable at greater than 3O 0 C and most preferably not stable at greater than 20°C.
  • a base other than an A at position 1 of the sense strand 12.
  • a base other than an A at position 2 of the sense strand 14.
  • a base other than a U at position 2 of the sense strand is a base other than a U at position 2 of the sense strand.
  • a base other than a U at position 14 of the sense strand is a base other than a U at position 14 of the sense strand.
  • a base other than a C at position 5 of the sense strand is a base other than a C at position 5 of the sense strand.
  • a base other than a C at position 15 of the sense strand is a base other than a C at position 15 of the sense strand.
  • a C base at position 10 of the sense strand makes a minor contribution to duplex functionality.
  • the absence of a C at position 3 of the sense strand is very important. Accordingly, preferably an siRNA will satisfy as many of the aforementioned criteria as possible.
  • GC content as well as a high number of AU in positions 15-19 of the sense strand, maybe important for easement of the unwinding of double stranded siRNA duplex.
  • Duplex unwinding has been shown to be crucial for siRNA functionality in vivo.
  • the internal structure is measured in terms of the melting temperature of the single strand of siRNA, which is the temperature at which 50% of the molecules will become denatured.
  • the positions refer to sequence positions on the sense strand, which is the strand that is identical to the mRNA. In one preferred embodiment, at least criteria 1 and 8 are satisfied. In another preferred embodiment, at least criteria 7 and 8 are satisfied. In still another preferred embodiment, at least criteria 1, 8 and 9 are satisfied.
  • the base pair that is not present is the base pair that is located at the 3' of the sense strand.
  • additional bases are added at the 5' end of the sense chain and occupy positions " 1 to ⁇ 11.
  • SEQ. ID NO. 0001 NNANANNNNUCNAANNNNA and SEQ. ID NO. 0028 GUCNNANANNNNUCNAANNNNA both would have A at position 3, A at position 5, U at position 10, C at position 11, A and position 13, A and position 14 and A at position 19.
  • SEQ. ID NO. 0028 would also have C at position -1 , U at position —2 and G at position -3.
  • N is any base, A, C, G, or U:
  • the sequence used as an siRNA is selected by choosing the siRNA that score highest according to one of the following seven algorithms that are represented by Formulas I - VII:
  • G 13 1 if G is the base at position 13 on the sense strand, otherwise its value is
  • C 19 1 if C is the base at position 19 of the sense strand, otherwise its value is 0;
  • GC the number of G and C bases in the entire sense strand
  • Tm 20° c 1 if the Tm is greater than 20°C;
  • a 3 1 if A is the base at position 3 on the sense strand, otherwise its value is
  • a 11 1 if A is the base at position 11 of the sense strand, otherwise its value is 0.
  • Formulas I -VII provide relative information regarding functionality. When the values for two sequences are compared for a given formula, the relative functionality is ascertained; a higher positive number indicates a greater functionality. For example, in many applications a value of 5 or greater is beneficial.
  • formulas V and VI might provide greater insights into duplex functionality.
  • formula II might by used in situations where hairpin structures are not observed in duplexes, and formula IV might be applicable for sequences that have higher AU content.
  • application of a given algorithim may identify an unususally large number of potential siRNA sequences, and in those cases, it may be appropriate to re-analyze that sequence with a second algorithm that is, for instance, more stringent.
  • analysis of a sequence with a given formula yields no acceptable siRNA sequences (i.e., low SMARTscoresTM). In this instance, it may be appropriate to re-analyze that sequences with a second algorithm that is, for instance, less stringent.
  • analysis of a single sequence with two separate formulas may give rise to conflicting results (i.e., one formula generates a set of siRNA with high SMARTscoresTM while the other formula identifies a set of siRNA with low SMARTscoresTM).
  • weighted factor(s) e.g., GC content
  • the sequence could be analyzed by a third, fourth, or fifth algorithm to identify a set of rationally designed siRNA.
  • siRNAs that produce ⁇ 70% silencing drops from 23% to 8% and the number of siRNA duplexes that produce >80% silencing rises from 50% to 88.5%.
  • siRNA duplexes with >80% silencing a larger portion of these siRNAs actually silence >95% of the target expression (the new criteria increases the portion from 33% to 50%).
  • the new criteria increases the portion from 33% to 50%.
  • Table II similarly shows the particularly beneficial results of pooling in combination with the aforementioned criteria. However, Table II, which takes into account each of the aforementioned variables, demonstrates even a greater degree of improvement in functionality.
  • the above-described algorithms may be used with or without a computer program that allows for the inputting of the sequence of the mRNA and automatically outputs the optimal siRNA.
  • the computer program may, for example, be accessible from a local terminal or personal computer, over an internal network or over the Internet.
  • RNA duplex of 18-30 base pairs is selected such that it is optimized according a formula selected from:
  • a 1 1 if A is the base at position 1 of the sense strand, otherwise its value is 0;
  • a 2 1 if A is the base at position 2 of the sense strand, otherwise its value is 0;
  • a 3 1 if A is the base at position 3 of the sense strand, otherwise its value is 0;
  • a 4 1 if A is the base at position 4 of the sense strand, otherwise its value is 0;
  • a 5 1 if A is the base at position 5 of the sense strand, otherwise its value is 0;
  • a 6 1 if A is the base at position 6 of the sense strand, otherwise its value is 0;
  • a 7 1 if A is the base at position 7 of the sense strand, otherwise its value is 0;
  • a 1O 1 if A is the base at position 10 of the sense strand, otherwise its value is 0;
  • a 11 1 if A is the base at position 11 of the sense strand, otherwise its value is 0;
  • a 13 1 if A is the base at position 13 of the sense strand, otherwise its value is 0;
  • G 1 1 if G is the base at position 1 on the sense strand, otherwise its value is 0;
  • G 2 1 if G is the base at position 2 of the sense strand, otherwise its value is 0;
  • G 8 1 if G is the base at position 8 on the sense strand, otherwise its value is 0;
  • G 1O 1 if G is the base at position 10 on the sense strand, otherwise its value is 0;
  • G 13 1 if G is the base at position 13 on the sense strand, otherwise its value is 0;
  • G 19 1 if G is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
  • U 1 1 if U is the base at position 1 on the sense strand, otherwise its value is 0;
  • U 2 1 if U is the base at position 2 on the sense strand, otherwise its value is 0;
  • U 3 1 if U is the base at position 3 on the sense strand, otherwise its value is 0;
  • U 4 1 if U is the base at position 4 on the sense strand, otherwise its value is 0;
  • U 7 1 if U is the base at position 7 on the sense strand, otherwise its value is 0;
  • U 9 1 if U is the base at position 9 on the sense strand, otherwise its value is 0;
  • U 10 1 if U is the base at position 10 on the sense strand, otherwise its value is 0;
  • U 15 1 if U is the base at position 15 on the sense strand, otherwise its value is 0;
  • U 16 1 if U is the base at position 16 on the sense strand, otherwise its value is 0;
  • U 17 1 if U is the base at position 17 on the sense strand, otherwise its value is 0;
  • U 18 1 if U is the base at position 18 on the sense strand, otherwise its value is 0;
  • Tm 100 if the siRNA oligo has the internal repeat longer then 4 base pairs, otherwise its value is 0;
  • X the number of times that the same nucleotide repeats four or more times in a row.
  • formulas VIII, IX, and X provide methods for selecting siRNA in order to increase the efficiency of gene silencing.
  • a subset of variables of any of the formulas may be used, though when fewer variables are used, the optimization hierarchy becomes less reliable.
  • a single letter of A or C or G or U followed by a subscript refers to a binary condition.
  • the binary condition is that either the particular base is present at that particular position (wherein the value is “1") or the base is not present (wherein the value is "0").
  • any base with a subscript of 19 in the formulas above would have a zero value for that parameter.
  • each variable is a number followed by *, which indicates that the value of the variable is to be multiplied or weighed by that number.
  • the numbers preceding the variables A, or G, or C, or U in Formulas VIII, IX, and X were determined by comparing the difference in the frequency of individual bases at different positions in functional siRNA and total siRNA. Specifically, the frequency in which a given base was observed at a particular position in functional groups was compared with the frequency that that same base was observed in the total, randomly selected siRNA set. If the absolute value of the difference between the functional and total values was found to be greater than 6%, that parameter was included in the equation.
  • the inventors When developing a means to optimize siRNAs, the inventors observed that a bias toward low internal thermodynamic stability of the duplex at the 5'-antisense (AS) end is characteristic of naturally occurring miRNA precursors. The inventors extended this observation to siRNAs for which functionality had been assessed in tissue culture.
  • AS 5'-antisense
  • a value of 0 - 5 will be ascribed depending on the number of G or C bases at positions 15 to 19. If there are only 18 base pairs, the value is between 0 and 4.
  • GC tota i content a number from 0 - 30 will be ascribed, which correlates to the total number of G and C nucleotides on the sense strand, excluding overhangs.
  • significance of the GC content (as well as AU content at positions 15-19, which is a parameter for formulas III - VII) relates to the easement of the unwinding of a double-stranded siRNA duplex.
  • Duplex unwinding is believed to be crucial for siRNA functionality in vivo and overall low internal stability, especially low internal stability of the first unwound base pair is believed to be important to maintain sufficient processivity of RISC complex-induced duplex unwinding. If the duplex has 19 base pairs, those at positions 15-19 on the sense strand will unwind first if the molecule exhibits a sufficiently low internal stability at that position.
  • RISC is a complex of approximately twelve proteins; Dicer is one, but not the only, helicase within this complex. Accordingly, although the GC parameters are believed to relate to activity with Dicer, they are also important for activity with other RISC proteins.
  • the value of the parameter Tm is 0 when there are no internal repeats longer than (or equal to) four base pairs present in the siRNA duplex; otherwise the value is 1.
  • the value will be one (1).
  • the value will be zero (0).
  • RNA the "target RNA” or “target molecule”
  • a computer program to evaluate the criteria for every sequence of 18 - 30 base pairs or only sequences of a fixed length, e.g., 19 base pairs.
  • the computer program is designed such that it provides a report ranking of all of the potential siRNAs 18-30 base pairs, ranked according to which sequences generate the highest value. A higher value refers to a more efficient siRNA for a particular target gene.
  • the computer program that may be used may be developed in any computer language that is known to be useful for scoring nucleotide sequences, or it may be developed with the assistance of commercially available product such as Microsoft's product.net.
  • BLAST Basic Local Alignment Search Tool
  • Formulas I - VII either Formula VIII, Formula IX, or Formula X may be used for a given mRNA target sequence. However, it is possible that according to one or the other formula more than one siRNA will have the same value. Accordingly, it is beneficial to have a second formula by which to differentiate sequences.
  • Formulas IX and X were derived in a similar fashion as Formula VIII, yet used a larger data set and thus yields sequences with higher statistical correlations to highly functional duplexes.
  • the sequence that has the highest value ascribed to it may be referred to as a "first optimized duplex.”
  • the sequence that has the second highest value ascribed to it may be referred to as a "second optimized duplex.”
  • the sequences that have the third and fourth highest values ascribed to them may be referred to as a third optimized duplex and a fourth optimized duplex, respectively.
  • each of them may, for example, be referred to as first optimized duplex sequences or co-first optimized duplexes.
  • Formula X is similar to Formula IX, yet uses a greater numbers of variables and for that reason, identifies sequences on the basis of slightly different criteria.
  • siRNA sequences identified using Formula VIII and Formula X are contained within the enclosed compact disks.
  • the data included on the enclosed compact disks is described more fully below.
  • the sequences identified by Formula VIII and Formula X that are disclosed in the compacts disks may be used in gene silencing applications. It should be noted that for Formulas VIII, IX, and X all of the aforementioned criteria are identified as positions on the sense strand when oriented in the 5' to 3' direction as they are identified in connection with Formulas I — VII unless otherwise specified.
  • Formulas I - X may be used to select or to evaluate one, or more than one, siRNA in order to optimize silencing.
  • at least two optimized siRNAs that have been selected according to at least one of these formulas are used to silence a gene, more preferably at least three and most preferably at least four.
  • the siRNAs may be used individually or together in a pool or kit. Further, they may be applied to a cell simultaneously or separately. Preferably, the at least two siRNAs are applied simultaneously. Pools are particularly beneficial for many research applications. However, for therapeutics, it may be more desirable to employ a single hyperfunctional siRNA as described elsewhere in this application.
  • siRNAs When planning to conduct gene silencing, and it is necessary to choose between two or more siRNAs, one should do so by comparing the relative values when the siRNA are subjected to one of the formulas above. In general a higher scored siRNA should be used.
  • Useful applications include, but are not limited to, target validation, gene functional analysis, research and drug discovery, gene therapy and therapeutics. Methods for using siRNA in these applications are well known to persons of skill in the art.
  • the present invention is applicable across a broad range of species, including but not limited to all mammalian species, such as humans, dogs, horses, cats, cows, mice, hamsters, chimpanzees and gorillas, as well as other species and organisms such as bacteria, viruses, insects, plants and C. elegans.
  • the present invention is also applicable for use for silencing a broad range of genes, including but not limited to the roughly 45,000 genes of a human genome, and has particular relevance in cases where those genes are associated with diseases such as diabetes, Alzheimer's, cancer, as well as all genes in the genomes of the aforementioned organisms.
  • siRNA selected according to the aforementioned criteria or one of the aforementioned algorithms are also, for example, useful in the simultaneous screening and functional analysis of multiple genes and gene families using high throughput strategies, as well as in direct gene suppression or silencing.
  • siRNA panel consisting of 270 siRNAs targeting three genes, Human Cyclophilin, Firefly Luciferase, and Human DBI. In all three cases, siRNAs were directed against specific regions of each gene. For Human Cyclophilin and Firefly Luciferase, ninety siRNAs were directed against a 199 bp segment of each respective mRNA. For DBI, 90 siRNAs were directed against a smaller, 109 base pair region of the mRNA. The sequences to which the siRNAs were directed are provided below.
  • t is present. This is because many databases contain information in this manner. However, the t denotes a uracil residue in mRNA and siRNA. Any algorithm will, unless otherwise specified, process a t in a sequence as a u.
  • SEQ. ID NO. 0031 acgggcaaggccaagtgggatgcctggaatgagctgaaagggacttccaaggaagatgccatgaaagcttacatcaaca aagtagaagagctaaagaaaaatacggg
  • the set of duplexes was analyzed to identify correlations between siRNA functionality and other biophysical or thermodynamic properties.
  • siRNA panel was analyzed in functional and non-functional subgroups, certain nucleotides were much more abundant at certain positions in functional or non-functional groups. More specifically, the frequency of each nucleotide at each position in highly functional siRNA duplexes was compared with that of nonfunctional duplexes in order to assess the preference for or against any given nucleotide at every position.
  • the data set was also analyzed for distinguishing biophysical properties of siRNAs in the functional group, such as optimal percent of GC content, propensity for internal structures and regional thermodynamic stability. Of the presented criteria, several are involved in duplex recognition, RISC activation/duplex unwinding, and target cleavage catalysis.
  • each x-axis tick-mark represents an individual siRNA, with each subsequent siRNA differing in target position by two nucleotides for Human Cyclophilin B and Firefly Luciferase, and by one nucleotide for Human DBI.
  • the y-axis denotes the level of target expression remaining after transfection of the duplex into cells and subsequent silencing of the target.
  • siRNA identified and optimized in this document work equally well in a wide range of cell types.
  • Figure 3a shows the evaluation of thirty siRNAs targeting the DBI gene in three cell lines derived from different tissues. Each DBI siRNA displays very similar functionality in HEK293 (ATCC, CRL-1573, human embryonic kidney), HeLa (ATCC, CCL-2, cervical epithelial adenocarcinoma) and DU 145 (HTB-81, prostate) cells as deterimined by the B-DNA assay.
  • siRNA functionality is determined by the primary sequence of the siRNA and not by the intracellular environment.
  • the present invention provides for a determination of the functionality of siRNA for a given target, the same siRNA may silence more than one gene.
  • the complementary sequence of the silencing siRNA may be present in more than one gene. Accordingly, in these circumstances, it may be desirable not to use the siRNA with highest SMARTscoreTM. In such circumstances, it may be desirable to use the siRNA with the next highest SMARTscoreTM.
  • the G/C content of each duplex in the panel was calculated and the functional classes of siRNAs ( ⁇ F50, > F50, > F80, > F95 where F refers to the percent gene silencing) were sorted accordingly.
  • the group with extremely low GC content (26% or less) contained a higher proportion of non-functional siRNAs and no highly- functional siRNAs.
  • the G/C content range of 30% — 52% was therefore selected as Criterion I for siRNA functionality, consistent with the observation that a G/C range 30% — 70% promotes efficient RNAi targeting.
  • the siRNA panel presented here permitted a more systematic analysis and quantification of the importance of this criterion than that used previously.
  • a relative measure of local internal stability is the A/U base pair (bp) content; therefore, the frequency of A/U bp was determined for each of the five terminal positions of the duplex (5' sense (S)/5' antisense (AS)) of all siRNAs in the panel. Duplexes were then categorized by the number of A/U bp in positions 1 — 5 and 15 — 19 of the sense strand. The thermodynamic flexibility of the duplex 5'-end (positions 1 — 5; S) did not appear to correlate appreciably with silencing potency, while that of the 3'-end (positions 15 — 19; S) correlated with efficient silencing. No duplexes lacking A/U bp in positions 15 — 19 were functional.
  • the complementary strands of siRNAs that contain internal repeats or palindromes may form internal fold-back structures. These hairpin-like structures exist in equilibrium with the duplexed form effectively reducing the concentration of functional duplexes.
  • the propensity to form internal hairpins and their relative stability can be estimated by predicted melting temperatures. High Tm reflects a tendency to form hairpin structures. Lower Tm values indicate a lesser tendency to form hairpins.
  • duplexes are further sorted from most functional to least functional with the y-axis of Figure 4a-e representing the % expression i.e., the amount of silencing that is elicited by the duplex (Note: each position on the X-axis represents a different duplex).
  • Statistical analysis revealed correlations between silencing and several sequence-related properties of siRNAs.
  • Figure 4 and Table IV show quantitative analysis for the following five sequence-related properties of siRNA: (A) an A at position 19 of the sense strand; (B) an A at position 3 of the sense strand; (C) a U at position 10 of the sense strand; (D) a base other than G at position 13 of the sense strand; and (E) a base other than C at position 19 of the sense strand.
  • the difference in the frequency of a given attribute e.g., GC content, base preference
  • individual functional groups e.g., ⁇ F50
  • the total siRNA population studied e.g., 270 siRNA molecules selected randomly.
  • Criterion I (30%-52% GC content) members of the ⁇ F50 group were observed to have GC contents between 30-52% in 16.4% of the cases.
  • the total group of 270 siRNAs had GC contents in this range, 20% of the time.
  • the >F95 group contained a "U” at this position 41.7% of the time.
  • the total group of 270 siRNAs had a "U” at this position 21.7% of the time, thus the improvement over random is calculated to be 20% (or 41.7%-21.7%).
  • RNAi The Average Internal Stability Profile of Strong siRNA
  • 270 different siRNAs derived from the cyclophilin B, the diazepam binding inhibitor (DBI), and the luciferase gene were individually transfected into HEK293 cells and tested for their ability to induce RNAi of the respective gene. Based on their performance in the in vivo assay, the sequences were then subdivided into three groups, (i) >95% silencing; (ii) 80-95% silencing; and (iii) less than 50% silencing. Sequences exhibiting 51-84% silencing were eliminated from further consideration to reduce the difficulties in identifying relevant thermodynamic patterns.
  • siRNA duplex stability Following the division of siRNA into three groups, a statistical analysis was performed on each member of each group to determine the average internal stability profile (AISP) of the siRNA. To accomplish this the Oligo 5.0 Primer Analysis Software and other related statistical packages ⁇ e.g., Excel) were exploited to determine the internal stability of pentamers using the nearest neighbor method described by Freier et al., (1986) Improved fi'ee-energy parameters for predictions of RNA duplex stability, Proc Natl. Acad. Sci. U. S. A. 83(24): 9373-7.
  • ALSP average internal stability profile
  • siRNA molecules that were critical for successful gene silencing.
  • highly functional siRNA >95% gene silencing, see Figure 6a, >F95
  • INP of position 19 ⁇ -7.6kcal/mol
  • hi contrast low- efficiency siRNA i.e., those exhibiting less than 50% silencing, ⁇ F50
  • siRNAs with poor silencing capabilities show a distinctly different profile. While the AISP value at position 12 is nearly identical with that of strong siRNAs, the values at positions 7 and 8 rise considerably, peaking at a high of- -9.0 kcal/mol. In addition, at the 5' end of the molecule the AISP profile of strong and weak siRNA differ dramatically. Unlike the relatively strong values exhibited by siRNA in the >95% silencing group, siRNAs that exhibit poor silencing activity have weak AISP values (-7.6, -7.5, and -7.5 kcal/mol for positions 1, 2 and 3 respectively).
  • siRNA that have strong or even stronger gene-specific silencing effects might have exaggerated ⁇ G values (either higher or lower) at key positions.
  • ⁇ G values either higher or lower
  • the 5 '-most position of the sense strand position 19
  • position 12 and position 7 could have values above 8.3 kcal/mol and below 7.7 kcal/mole, respectively, without abating the silencing effectiveness of the molecule.
  • a stabilizing chemical modification e.g., a chemical modification of the 2' position of the sugar backbone
  • a stabilizing chemical modification e.g., a chemical modification of the 2' position of the sugar backbone
  • mismatches similar to those described previously could be introduced that would lower the ⁇ G values at that position.
  • non-functional siRNA are defined as those siRNA that induce less than 50% ( ⁇ 50%) target silencing
  • siRNA induce 50-79% target silencing
  • functional siRNA are molecules that induce 80- 95% gene silencing
  • highly-functional siRNA are molecules that induce great than 95% gene silencing.
  • siRNA that reduces gene activity by only 30%. While this level of gene silencing may be "non-functional" for, e.g., therapeutic needs, it is sufficient for gene mapping purposes and is, under these uses and conditions, "functional.” For these reasons, functional siRNA can be defined as those molecules having greater than 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% silencing capabilities at 10OnM transfection conditions. Similarly, depending upon the needs of the study and/or application, non-functional and semi-functional siRNA can be defined as having different parameters.
  • semi-functional siRNA can be defined as being those molecules that induce 20%, 30%, 40%, 50%, 60%, or 70% silencing at 10OnM transfection conditions.
  • non-functional siRNA can be defined as being those molecules that silence gene expression by less than 70%, 60%, 50%, 40%, 30%, or less. Nonetheless, unless otherwise stated, the descriptions stated in the "Definitions" section of this text should be applied.
  • Functional attributes can be assigned to each of the key positions in the AISP of strong siRNA.
  • the low 5' (sense strand) AISP values of strong siRNAs maybe necessary for determining which end of the molecule enters the RISC complex.
  • the high and low AISP values observed in the central regions of the molecule may be critical for siRNA-target niRNA interactions and product release, respectively.
  • siRNA functionality is likely influenced by specific biophysical and molecular properties that promote efficient interactions within the context of the multi-component complexes. Indeed, the systematic analysis of the siRNA test set identified multiple factors that correlate well with functionality. When combined into a single algorithm, they proved to be very effective in selecting active siRNAs.
  • the fadtors described here may also be predictive of key functional associations important for each step in RNAi.
  • the potential formation of internal hairpin structures correlated negatively with siRNA functionality.
  • Complementary strands with stable internal repeats are more likely to exist as stable hairpins thus decreasing the effective concentration of the functional duplex form.
  • the duplex is the preferred conformation for initial pre-RISC association.
  • the effective concentration required is at least two orders of magnitude higher than that of the duplex form.
  • siRNA-pre-RISC complex formation is followed by an ATP-dependent duplex unwinding step and "activation" of the RISC.
  • the siRNA functionality was shown to correlate with overall low internal stability of the duplex and low internal stability of the 3' sense end (or differential internal stability of the 3' sense compare to the 5' sense strand), which may reflect strand selection and entry into the RISC.
  • Overall duplex stability and low internal stability at the 3' end of the sense strand were also correlated with siRNA functionality.
  • siRNAs with very high and very low overall stability profiles correlate strongly with non-functional duplexes.
  • One interpretation is that high internal stability prevents efficient unwinding while very low stability reduces siRNA target affinity and subsequent mRNA cleavage by the RISC.
  • Base preferences for A at position 19 of the sense strand but not C are particularly interesting because they reflect the same base preferences observed for naturally occurring miRNA precursors. That is, among the reported miRNA precursor sequences 75% contain a U at position 1 which corresponds to an A in position 19 of the sense strand of siRNAs, while G was under- represented in this same position for miRNA precursors.
  • the functional interpretation of the predominance of a U/A base pair is that it promotes flexibility at the 5'antisense ends of both siRNA duplexes and miRNA precursors and facilitates efficient unwinding and selective strand entrance into an activated RISC.
  • RISC preferentially cleaves target mRNA between nucleotides 10 and 11 relative to the 5' end of the complementary targeting strand. Therefore, it may be that U, the preferred base for most endoribonucleases, at this position supports more efficient cleavage.
  • a U/A bp between the targeting siRNA strand and its cognate target mRNA may create an optimal conformation for the RISC-associated "'slicing" activity.
  • the output of any one of the formulas previously listed can be filtered to remove or select for siRNAs containing undesirable or desirable motifs or properties, respectively.
  • sequences identified by any of the formulas can be filtered to remove any and all sequences that induce toxicity or cellular stress.
  • Introduction of an siRNA containing a toxic motif into a cell can induce cellular stress and/or cell death (apoptosis) which in turn can mislead researchers into associating a particular (e.g., nonessential) gene with, e.g., an essential function.
  • sequences generated by any of the before mentioned formulas can be filtered to identify and retain duplexes that contain toxic motifs.
  • duplexes may be valuable from a variety of perspectives including, for instance, uses as therapeutic molecules.
  • a variety of toxic motifs exist and can exert their influence on the cell through RNAi and non-RNAi pathways. Examples of toxic motifs are explained more fully in commonly assigned U.S. Provisional Patent Application Serial No. 60/538,874, entitled “Identification of Toxic Sequences," filed January 23, 2004. Briefly, toxic motifs include A/G UUU A/G/U, G/C AAA G/C, and GCCA, or a complement of any of the foregoing.
  • sequences identified by any of the before mentioned formulas can be filtered to identify duplexes that contain motifs (or general properties) that provide serum stability or induce serum instability.
  • duplexes targeting disease-associated genes will be introduced into patients intravenously.
  • post-algorithm filters designed to select molecules that contain motifs that enhance duplex stability in the presence of serum and/or (conversely) eliminate duplexes that contain motifs that destabilize siRNA in the presence of serum, would be beneficial.
  • sequences identified by any of the before mentioned formulas can be filtered to identify duplexes that are hyperfunctional.
  • Hyperfunctional sequences are defined as those sequences that (1) induce greater than 95% silencing of a specific target when they are transfected at subnanomolar concentrations (i.e., less than one nanomolar); and/or (2) induce functional (or better) levels of silencing for greater than 96 hours.
  • Filters that identify hyperfunctional molecules can vary widely. In one example, the top ten, twenty, thirty, or forty siRNA can be assessed for the ability to silence a given target at, e.g. , concentrations of InM and 0.5nM to identify hyperfunctional molecules.
  • the present invention provides a pool of at least two siRNAs, preferably in the form of a kit or therapeutic reagent, wherein one strand of each of the siRNAs, the sense strand comprises a sequence that is substantially similar to a sequence within a target mRNA.
  • the opposite strand, the antisense strand will preferably comprise a sequence that is substantially complementary to that of the target mRNA.
  • one strand of each siRNA will comprise a sequence that is identical to a sequence that is contained in the target mRNA.
  • each siRNA will be 19 base pairs in length, and one strand of each of the siRNAs will be 100% complementary to a portion of the target mRNA.
  • siRNAs directed to a particular target By increasing the number of siRNAs directed to a particular target using a pool or kit, one is able both to increase the likelihood that at least one siRNA with satisfactory functionality will be included, as well as to benefit from additive or synergistic effects. Further, when two or more siRNAs directed against a single gene do not have satisfactory levels of functionality alone, if combined, they may satisfactorily promote degradation of the target messenger RNA and successfully inhibit translation. By including multiple siRNAs in the system, not only is the probability of silencing increased, but the economics of operation are also improved when compared to adding different siRNAs sequentially. This effect is contrary to the conventional wisdom that the concurrent use of multiple siRNA will negatively impact gene silencing ⁇ e.g., Holen, T. et al. (2003) "Similar behavior of single strand and double strand siRNAs suggests they act through a common RNAi pathway.” NAR 31: 2401-21407).
  • the kit is comprised of at least three siRNAs, wherein one strand of each siRNA comprises a sequence that is substantially similar to a sequence of the target mRNA and the other strand comprises a sequence that is substantially complementary to the region of the target mRNA.
  • one strand will comprise a sequence that is identical to a sequence that is contained in the mRNA and another strand that is 100% complementary to a sequence that is contained in the mRNA.
  • the kit is comprised of at least four siRNAs, wherein one strand of each siRNA comprises a sequence that is substantially similar to a region of the sequence of the target mRNA, and the other strand comprises a sequence that is substantially complementary to the region of the target mRNA.
  • one strand of each of the siRNA duplexes will comprise a sequence that is identical to a sequence that is contained in the mRNA, and another strand that is 100% complementary to a sequence that is contained in the mRNA.
  • kits and pools with at least five, at least six, and at least seven siRNAs may also be useful with the present invention.
  • pools of five siRNA induced 95% gene silencing with 77% probability and 80% silencing with 98.8% probability.
  • pooling of siRNAs together can result in the creation of a target-specific silencing reagent with almost a 99% probability of being functional.
  • the fact that such high levels of success are achievable using such pools of siRNA, enables one to dispense with costly and time-consuming target-specific validation procedures.
  • each of the siRNAs within a pool will preferably comprise 18-30 base pairs, more preferably 18-25 base pairs, and most preferably 19 base pairs.
  • at least 18 contiguous bases of the antisense strand will be 100% complementary to the target mRNA. More preferably, at least 19 contiguous bases of the antisense strand will be 100% complementary to the target mRNA.
  • there may be overhangs on either the sense strand or the antisense strand and these overhangs may be at either the 5' end or the 3' end of either of the strands, for example there may be one or more overhangs of 1-6 bases.
  • overhangs When overhangs are present, they are not included in the calculation of the number of base pairs.
  • the two nucleotide 3' overhangs mimic natural siRNAs and are commonly used but are not essential.
  • the overhangs should consist of two nucleotides, most often dTdT or UU at the 3' end of the sense and antisense strand that are not complementary to the target sequence.
  • the siRNAs may be produced by any method that is now known or that comes to be known for synthesizing double stranded RNA that one skilled in the art would appreciate would be useful in the present invention.
  • the siRNAs will be produced by Dharmacon's proprietary ACE® technology.
  • siRNAs are well known to persons skilled in the art and include, but are not limited to, any chemical synthesis of RNA oligonucleotides, ligation of shorter oligonucleotides, in vitro transcription of RNA oligonucleotides, the use of vectors for expression within cells, recombinant Dicer products and PCR products.
  • siRNA duplexes within the aforementioned pools of siRNAs may correspond to overlapping sequences within a particular mRNA, or non-overlapping sequences of the mRNA. However, preferably they correspond to non-overlapping sequences. Further, each siRNA may be selected randomly, or one or more of the siRNA may be selected according to the criteria discussed above for maximizing the effectiveness of siRNA.
  • siRNAs that contain substituted and/or labeled nucleotides that may, for example, be labeled by radioactivity, fluorescence or mass.
  • the most common substitutions are at the T position of the ribose sugar, where moieties such as H (hydrogen) F, NH 3 , OCH 3 and other O- alkyl, alkenyl, alkynyl, and orthoesters, may be substituted, or in the phosphorous backbone, where sulfur, amines or hydrocarbons may be substituted for the bridging of non- bridging atomsjn the phosphodiester bond.
  • H (hydrogen) F NH 3 , OCH 3 and other O- alkyl, alkenyl, alkynyl, and orthoesters
  • sulfur, amines or hydrocarbons may be substituted for the bridging of non- bridging atomsjn the phosphodiester bond.
  • the cell type into which the siRNA is introduced may affect the ability of the siRNA to enter the cell; however, it does not appear to affect the ability of the siRNA to function once it enters the cell.
  • Methods for introducing double-stranded RNA into various cell types are well known to persons skilled in the art.
  • the presence of proteins such as RdRP, the RNA-dependent RNA polymerase may catalytically enhance the activity of the siRNA.
  • RdRP propagates the RNAi effect in C. elegans and other non-mammalian organisms.
  • the siRNA may be inherited.
  • Two other proteins that are well studied and known to be a part of the machinery are members of the Argonaute family and Dicer, as well as their homologues.
  • the RISC complex might be associated with the ribosome so the more efficiently translated mRNAs will be more susceptible to silencing than others.
  • siRNA localization Another very important factor in the efficacy of siRNA is mRNA localization. In general, only cytoplasmic mRNAs are considered to be accessible to RNAi to any appreciable degree. However, appropriately designed siRNAs, for example, siRNAs modified with internucleotide linkages or 2'-O-methyl groups, maybe able to cause silencing by acting in the nucleus. Examples of these types of modifications are described in commonly assigned U.S. Patent Application Serial Nos. 10/431,027 and 10/613,077.
  • the effectiveness of the two may be greater than one would predict based on the effectiveness of two individual siRNAs.
  • This additive or synergistic effect is particularly noticeable as one increases to at least three siRNAs, and even more noticeable as one moves to at least four siRNAs.
  • the pooling of the non ⁇ functional and semi-functional siRNAs, particularly more than five siRNAs can lead to a silencing mixture that is as effective if not more effective than any one particular functional siRNA.
  • each siRNA will be present in a concentration of between 0.001 and 200 ⁇ M, more preferably between 0.01 and 200 nM, and most preferably between 0.1 and 10 nM.
  • kits of the present invention will also preferably comprise a buffer to keep the siRNA duplex stable.
  • the buffer may be comprised of 100 mM KCl, 30 mM HEPES- pH 7.5, and 1 mM MgC ⁇ .
  • kits might contain complementary strands that contain any one of a number of chemical modifications (e.g., a 2'-0-ACE) that protect the agents from degradation by nucleases. In this instance, the user may (or may not) remove the modifying protective group (e.g., deprotect) before annealing the two complementary strands together.
  • kits may be organized such that pools of siRNA duplexes are provided on an array or microarray of wells or drops for a particular gene set or for unrelated genes.
  • the array may, for example, be in 96 wells, 384 wells or 1284 wells arrayed in a plastic plate or on a glass slide using techniques now known or that come to be known to persons skilled in the art.
  • controls such as functional anti-lamin AJC, cyclophilin and two siRNA duplexes that are not specific to the gene of interest.
  • siRNA pools Prior to usage, they may be retained in lyophilized form at minus twenty degrees (-2O 0 C) until they are ready for use. Prior to usage, they should be resuspended; however, even once resuspended, for example, in the aforementioned buffer, they should be kept at minus twenty degrees, (-2O 0 C) until used.
  • the aforementioned buffer, prior to use, may be stored at approximately 4 0 C or room temperature. Effective temperatures at which to conduct transfections are well known to persons skilled in the art and include for example, room temperature.
  • kits maybe applied either in vivo or in vitro.
  • the siRNA of the pools or kits is applied to a cell through transfection, employing standard transfection protocols.
  • These methods are well known to persons skilled in the art and include the use of lipid-based carriers, electroporation, cationic carriers, and microinjection.
  • one could apply the present invention by synthesizing equivalent DNA sequences (either as two separate, complementary strands, or as hairpin molecules) instead of siRNA sequences and introducing them into cells through vectors. Once in the cells, the cloned DNA could be transcribed, thereby forcing the cells to generate the siRNA.
  • vectors suitable for use with the present application include but are not limited to the standard transient expression vectors, adenoviruses, retroviruses, lentivirus-based vectors, as well as other traditional expression vectors. Any vector that has an adequate siRNA expression and procession module may be used. Furthermore, certain chemical modifications to siRNAs, including but not limited to conjugations to other molecules, may be used to facilitate delivery. For certain applications it may be preferable to deliver molecules without transfection by simply formulating in a physiological acceptable solution.
  • another embodiment includes the use of multiple siRNA targeting multiple genes. Multiple genes may be targeted through the use of high- or hyper- functional siRNA. High- or hyper- functional siRNA that exhibit increased potency, require lower concentrations to induce desired phenotypic (and thus therapeutic) effects. This circumvents RISC saturation. It therefore reasons that if lower concentrations of a single siRNA are needed for knockout or knockdown expression of one gene, then the remaining (uncomplexed) RISC will be free and available to interact with siRNA directed against two, three, four, or more, genes. Thus in this embodiment, the authors describe the use of highly functional or hyper-functional siRNA to knock out three separate genes.
  • siRNA of this type could be used to knockout or knockdown the expression of six or more genes.
  • hyperfunctional siRNA describes a subset of the siRNA population that induces RNAi in cells at low- or sub-nanomolar concentrations for extended periods of time. These traits, heightened potency and extended longevity of the RNAi phenotype, are highly attractive from a therapeutic standpoint. Agents having higher potency require lesser amounts of the molecule to achieve the desired physiological response, thus reducing the probability of side effects due to "off- target" interference. In addition to the potential therapeutic benefits associated with hyperfunctional siRNA, hf-siRNA are also desirable from an economic perspective. Hyperfunctional siRNA may cost less on a per-treatment basis, thus reducing overall expenditures to both the manufacturer and the consumer.
  • Identification of hyperfunctional siRNA involves multiple steps that are designed to examine an individual siRNA agent's concentration- and/or longevity- profiles.
  • a population of siRNA directed against a single gene are first analyzed using the previously described algorithm (Formula VIII). Individual siRNA are then introduced into a test cell line and assessed for the ability to degrade the target mRNA. It is important to note that when performing this step it is not necessary to test all of the siRNA. Instead, it is sufficient to test only those siRNA having the highest SMARTscoresTM (i.e., SMARTscoreTM > -10). Subsequently, the gene silencing data is plotted against the SMARTscoresTM (see Figure 9).
  • siRNAs that (1) induce a high degree of gene silencing (i.e., they induce greater than 80% gene knockdown) and (2) have superior SMARTscoresTM (i.e., a SMARTscoreTM of > -10, suggesting a desirable average internal stability profile) are selected for further investigations designed to better understand the molecule's potency and longevity.
  • an siRNA is introduced into one (or more) cell types in increasingly diminishing concentrations (e.g., 3.0 -> 0.3 nM).
  • siRNA that exhibit hyperfunctional potency i.e., those that induce 80% silencing or greater at, e.g., picomolar concentrations
  • siRNA having high (>-10) SMARTscoresTM and greater than 80% silencing are examined.
  • siRNA are introduced into a test cell line and the levels of RNAi are measured over an extended period of time (e.g., 24-168 hrs).
  • siRNAs that exhibit strong RNA interference patterns i.e., >80 % interference
  • periods of time greater than, e.g., 120 hours are thus identified.
  • siRNAs While the example(s) given above describe one means by which hyperfunctional siRNA can be isolated, neither the assays themselves nor the selection parameters used are rigid and can vary with each family of siRNA. Families of siRNA include siRNAs directed against a single gene, or directed against a related family of genes.
  • siRNA that, at picomolar concentrations, induces 99 + % silencing for a period of 10 days.
  • a second gene may yield an siRNA that at high nanomolar concentrations (e.g., 10OnM) induces only 75% silencing for a period of 2 days.
  • Both molecules represent the very optimum siRNA for their respective gene targets and therefore are designated "hyperfunctional.” Yet due to a variety of factors including but not limited to target concentration, siRNA stability, cell type, off-target interference, and others, equivalent levels of potency and longevity are not achievable.
  • the parameters described in the before mentioned assays can vary. While the initial screen selected siRNA that had SMARTscoresTM above -10 and a gene silencing capability of greater than 80%, selections that have stronger (or weaker) parameters can be implemented. Similarly, in the subsequent studies designed to identify molecules with high potency and longevity, the desired cutoff criteria (i.e. , the lowest concentration that induces a desirable level of interference, or the longest period of time that interference can be observed) can vary. The experimentation subsequent to application of the rational criteria of this application is significantly reduced where one is trying to obtain a suitable hyperfunctional siRNA for, for example, therapeutic use. When, for example, the additional experimentation of the type described herein is applied by one skilled in the art with this disclosure in hand, a hyperfunctional siRNA is readily identified.
  • the siRNA may be introduced into a cell by any method that is now known or that comes to be known and that from reading this disclosure, persons skilled in the art would determine would be useful in connection with the present invention in enabling siRNA to cross the cellular membrane.
  • These methods include, but are not limited to, any manner of transfection, such as, for example, transfection employing DEAE-Dextran, calcium phosphate, cationic lipids/liposomes, micelles, manipulation of pressure, microinjection, electroporation, imrnunoporation, use of vectors such as viruses, plasmids, cosmids, bacteriophages, cell fusions, and coupling of the polynucleotides to specific conjugates or ligands such as antibodies, antigens, or receptors, passive introduction, adding moieties to the siRNA that facilitate its uptake, and the like.
  • siRNA nomenclature All siRNA duplexes are referred to by sense strand.
  • the first nucleotide of the 5 '-end of the sense strand is position 1, which corresponds to position 19 of the antisense strand for a 19-mer.
  • silencing was determined by measuring specific transcript mRNA levels or enzymatic activity associated with specific transcript levels, 24 hours post-transfection, with siRNA concentrations held constant at 100 nM. For all experiments, unless otherwise specified, transfection efficiency was ensured to be over 95%, and no detectable cellular toxicity was observed.
  • F50 signifies at least 50% knockdown
  • F80 means at least 80%, and so forth.
  • all sub-F50 siRNAs were considered non-functional.
  • 96-well plates are coated with 50 ⁇ l of 50 mg/ml poly- L-lysine (Sigma) for 1 hr, and then washed 3X with distilled water before being dried for 20 min.
  • HEK293 cells or HEK293Lucs or any other cell type of interest are released from their solid support by trypsinization, diluted to 3.5 X 10 5 cells/ml, followed by the addition of 100 ⁇ L of cells/well. Plates are then incubated overnight at 37° C, 5% CO 2 . Transfection procedures can vary widely depending on the cell type and transfection reagents.
  • a transfection mixture consisting of 2 mL Opti-MEM I (Gibco-BRL), 80 ⁇ l Lipofectamine 2000 (Invitrogen), 15 ⁇ L SUPERNasin at 20 U/ ⁇ l (Ambion), and 1.5 ⁇ l of reporter gene plasmid at 1 ⁇ g/ ⁇ l is prepared in 5-ml polystyrene round bottom tubes.
  • One hundred ⁇ l of transfection reagent is then combined with 100 ⁇ l of siRNAs in polystyrene deep-well titer plates (Beckman) and incubated for 20 to 30 min at room temperature.
  • Opti-MEM Five hundred and fifty microliters of Opti-MEM is then added to each well to bring the final siRNA concentration to 100 nM. Plates are then sealed with parafilm and mixed. Media is removed from HEK293 cells and replaced with 95 ⁇ l of transfection mixture. Cells are incubated overnight at 37° C, 5% CO 2 .
  • Quantification of gene knockdown A variety of quantification procedures can be used to measure the level of silencing induced by siRNA or siRNA pools.
  • QuantiGene branched-DNA (bDNA) kits (Bayer) (Wang, et al, Regulation of insulin preRNA splicing by glucose. Proc. Natl. Acad. Sci. USA 1997, 94:4360.) are used according to manufacturer instructions.
  • bDNA QuantiGene branched-DNA kits
  • media is removed from HEK293 cells 24 hrs post-transfection, and 50 ⁇ l of Steady-GLO reagent (Promega) is added. After 5 minutes, plates are analyzed on a plate reader.
  • Example I Sequences Used to Develop the Algorithm. Anti-Firefly and anti-Cyclophilin siRNAs panels ( Figure 5a, b) sorted according to using Formula VIII predicted values. All siRNAs scoring more than 0 (formula VIII) and more then 20 (formula IX) are fully functional. AU ninety sequences for each gene (and DBI) appear below in Table III.
  • Cyclo 80 SEQ. ID OI lO GCGCUUCCCCGAUGAGAAC
  • DB 4 SEQ. ID 0124 GGCAAGGCCAAGUGGGAUG DB 5 SEQ.ID0125 GCAAGGCCAAGUGGGAUGC
  • Example II Validation of the Algorithm using DBI, Luciferase, PLK, EGFR, and SEAP.
  • the algorithm (Formula VIII) identified siRNAs for five genes, human DBI, firefly luciferase (fLuc), renilla luciferase (rLuc), human PLK, and human secreted alkaline phosphatase (SEAP).
  • fLuc firefly luciferase
  • rLuc renilla luciferase
  • SEAP human secreted alkaline phosphatase
  • Four individual siRNAs were selected on the basis of their SMARTscoresTM derived by analysis of their sequence using Formula VIII (all of the siRNAs would be selected with Formula IX as well) and analyzed for their ability to silence their targets' expression. In addition to the scoring, a BLAST search was conducted for each siRNA.
  • Figure 10 shows that the siRNAs selected by the algorithm disclosed herein were significantly more potent than randomly selected siRNAs.
  • the algorithm increased the chances of identifying an F50 siRNA from 48% to 91%, and an F80 siRNA from 13% to 57%.
  • pools of SMART siRNA silence the selected target better than randomly selected pools (see Figure 10F).
  • Example III Validation of the Algorithm Using Genes Involved in Clathrin- Dependent Endocytosis.
  • clathrin-mediated endocytosis pathway Components of clathrin-mediated endocytosis pathway are key to modulating intracellular signaling and play important roles in disease. Chromosomal rearrangements that result in fusion transcripts between the Mixed-Lineage Leukemia gene (MLL) and CALM (clathrin assembly lymphoid myeloid leukemia gene) are believed to play a role in leukemogenesis. Similarly, disruptions in Rab7 and Rab9, as well as HIPl (Huntingtin-interacting protein), genes that are believed to be involved in endocytosis, are potentially responsible for ailments resulting in lipid storage, and neuronal diseases, respectively. For these reasons, siRNA directed against clathrin and other genes involved in the clathrin-mediated endocytotic pathway are potentially important research and therapeutic tools.
  • siRNAs directed against genes involved in the clathrin-mediated endocytosis pathways were selected using Formula VIII.
  • the targeted genes were clathrin heavy chain (CHC, accession # NM_004859), clathrin light chain A (CLCa, NM_001833), clathrin light chain B (CLCb, NM_001834), CALM (U45976), ⁇ 2 subunit of AP-2 ( ⁇ 2, NM_001282), Epsl5 (NM_001981), Epsl5R (NMJD21235), dynamin II (DYNII, NM_004945), Rab5a (BC001267), Rab5b (NM_002868), Rab5c (AF141304), and EEA.l (XM_018197).
  • CHC clathrin heavy chain
  • CLCa clathrin light chain A
  • CLCb clathrin light chain B
  • CALM U45976
  • siRNAs duplexes with the highest scores were selected and a BLAST search was conducted for each of them using the Human EST database. In order to minimize the potential for off-target silencing effects, only those sequences with more than three mismatches against un-related sequences were used. All duplexes were synthesized at Dharmacon, Inc. as 21-mers with 3'-UU overhangs using a modified method of 2'-ACE chemistry, Scaringe, Advanced 5'-silyl-2'- orthoester approach to RNA oligonucleotide synthesis, Methods Enzymol 2000, 317:3, and the antisense strand was chemically phosphorylated to insure maximized activity.
  • HeLa cells were grown in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum, antibiotics and glutamine.
  • siRNA duplexes were resuspended in IX siRNA Universal buffer (Dharmacon, Inc.) to 20 ⁇ M prior to transfection.
  • HeLa cells in 12-well plates were transfected twice with 4 ⁇ l of 20 ⁇ M siRNA duplex in 3 ⁇ l Lipofectamine 2000 reagent (Invitrogen, Carlsbad, California, USA) at 24-hour intervals. For the transfections in which 2 or 3 siRNA duplexes were included, the amount of each duplex was decreased, so that the total amount was the same as in transfections with single siRNAs.
  • Cells were plated into normal culture medium 12 hours prior to experiments, and protein levels were measured 2 or 4 days after the first transfection.
  • Equal amounts of lysates were resolved by electrophoresis, blotted, and stained with the antibody specific to targeted protein, as well as antibodies specific to unrelated proteins, PPl phosphatase and TsglOl (not shown).
  • the cells were lysed in Triton X-100/glycerol solubilization buffer as described previously. Tebar, Bohlander, & Sorkin, Clathrin Assembly Lymphoid Myeloid Leukemia (CALM) Protein: Localization in Endocytic-coated Pits, Interactions with Clathrin, and the Impact of Overexpression on Clathrin-mediated Traffic, MoI. Biol. Cell Aug 1999, 10:2687.
  • CALM Lymphoid Myeloid Leukemia
  • the antibodies to assess the levels of each protein by Western blot were obtained from the following sources: monoclonal antibody to clathrin heavy chain (TD.1) was obtained from American Type Culture Collection (Rockville, MD, USA); polyclonal antibody to dynamin II was obtained from Affinity Bioreagents, Inc. (Golden, CO, USA); monoclonal antibodies to EEA.1 and Rab5a were purchased from BD Transduction Laboratories (Los Angeles, CA, USA); the monoclonal antibody to TsglOl was purchased from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA); the monoclonal antibody to GFP was from ZYMED Laboratories Inc.
  • Figure 11 demonstrates the in vivo functionality of 48 individual siRNAs, selected using Formula VIII (most of them will meet the criteria incorporated by Formula IX as well) targeting 12 genes.
  • Various cell lines were transfected with siRNA duplexes (Dupl-4) or pools of siRNA duplexes (Pool), and the cells were lysed 3 days after transfection with the exception of CALM (2 days) and ⁇ 2 (4 days).
  • CALM has two splice variants, 66 and 72 kD.
  • Eps 15R a doublet of ⁇ 130 kD
  • Epsl5R immunoprecipitates shown by arrows. The cells were lysed 3 days after transfection.
  • Equal amounts of lysates were resolved by electrophoresis and blotted with the antibody specific to a targeted protein (GFP antibody for YFP fusion proteins) and the antibody specific to unrelated proteins PPl phosphatase or ⁇ -actinin, and TSGlOl.
  • the amount of protein in each specific band was normalized to the amount of non-specific proteins in each lane of the gel. Nearly all of them appear to be functional, which establishes that Formula VIII and IX can be used to predict siRNAs' functionality in general in a genome wide manner.
  • YFP-Rab5b or YFP-Rab5c a DNA fragment encoding the full-length human Rab5b or Rab5c was obtained by PCR using Pfu polymerase (Stratagene) with a Sad restriction site introduced into the 5' end and a Kpnl site into the 3' end and cloned into pEYFP-Cl vector (CLONTECH, Palo Alto, CA, USA).
  • GFP-CALM and YFP- Rab5a were described previously Tebar, Bohlander, & Sorkin, Clathrin Assembly Lymphoid Myeloid Leukemia (CALM) Protein: Localization in Endocytic-coated Pits, Interactions with Clathrin, and the Impact of Overexpression on Clathrin-mediated Traffic, MoI. Biol. Cell Aug 1999, 10:2687.
  • Example IV Validation of the Algorithm Using Eg5, GADPH, ATEl, MEK2, MEKl, QB, LaminA/C, c-myc, human cyclophilin, and mouse cyclophilin.
  • Figure 12 illustrates four siRNAs targeting 10 different genes (Table V for sequence and accession number information) that were selected according to the Formula VIII and assayed as individuals and pools in HEK293 cells.
  • the level of siRNA induced silencing was measured using the B-DNA assay.
  • Bcl-2 is a ⁇ 25kD, 205-239 amino acid, anti-apoptotic protein that contains considerable homology with other members of the BCL family including BCLX, MCLl, BAX, BAD, and BIK.
  • the protein exists in at least two forms (Bcl2a, which has a hydrophobic tail for membrane anchorage, and Bcl2b, which lacks the hydrophobic tail) and is predominantly localized to the mitochondrial membrane. While Bcl2 expression is widely distributed, particular interest has focused on the expression of this molecule in B and T cells.
  • Bcl2 expression is down-regulated in normal germinal center B cells yet in a high percentage of follicular lymphomas, Bcl2 expression has been observed to be elevated.
  • Bcl-2 translocation makes this gene an attractive target for RNAi.
  • Identification of siRNA directed against the bcl2 transcript (or Bcl2-IgH fusions) would further our understanding Bcl2 gene function and possibly provide a future therapeutic agent to battle diseases that result from altered expression or function of this gene.
  • Bcl-2 siRNAs having the top ten SMARTscoresTM were selected and tested in a functional assay to determine silencing efficiency. To accomplish this, each of the ten duplexes were synthesized using 2'-0-ACE chemistry and transfected at 10OnM concentrations into cells. Twenty-four hours later assays were performed on cell extracts to assess the degree of target silencing. Controls used in these experiments included mock transfected cells, and cells that were transfected with a non-specific siRNA duplex.
  • siRNA 1 GGGAGAUAGUGAUGAAGUA SEQ. ID NO. 301
  • siRNA 2 GAAGUACAUCCAUUAUAAG SEQ. ID NO. 302
  • siRNA 3 GUACGACAACCGGGAGAUA SEQ. ID NO. 303
  • siRNA 4 AGAUAGUGAUGAAGUACAU SEQ. ID NO. 304
  • siRNA 5 UGAAGACUCUGCUCAGUUU SEQ. ID NO. 305
  • siRNA 6 GCAUGCGGCCUCUGUUUGA SEQ. ID NO. 306
  • siRNA 7 UGCGGCCUCUGUUUGAUUU SEQ. ID NO. 307
  • siRNA 8 GAGAUAGUGAUGAAGUACA SEQ. ID NO. 308
  • siRNA 9 GGAGAUAGUGAUGAAGUAC SEQ. ID NO. 309
  • siRNA 10 GAAGACUCUGCUCAGUUUG SEQ. ID NO. 310
  • Bcl2 siRNA Sense Strand, 5' ⁇ 3'
  • Example VI Sequences Selected by the Algorithm. Sequences of the siRNAs selected using Formulas (Algorithms) VIII and IX with their corresponding ranking, which have been evaluated for the silencing activity in vivo in the present study (Formula VIII and DC, respectively) are shown in Table V. It should be noted that the "t" residues in Table V, and elsewhere, when referring to siRNA, should be replaced by "u” residues. TABLE V
  • EPS15R NM_021235 SEQ. ID NO. 0321 GAAGTTACCTTGAGCAATC 48 33
  • ARF6 AF93885 SEQ. ID NO. 0330 GATGAGGGACGCCATAATC 7 -38.4
  • PLK NM_005030 SEQ. ID NO. 0354 ATGAAGATCTGGAGGTGAA 0 -4.3
  • PLK NM_005030 SEQ. ID NO. 0355 TTTGAGACTTCTTGCCTAA -5 -27.7
  • GAPDH NM_002046 SEQ. ID NO. 0357 CAACGGATTTGGTCGTATT 27 -2.8
  • MAP2K1 NM_002755 SEQ. ID NO. 0365 GCACATGGATGGAGGTTCT 26 .16
  • MAP2K2 NM_030662 SEQ. ID NO. 0369 CAAAGACGATGACTTCGAA 37 26.4
  • MAP2K2 NM_030662 SEQ. ID NO. 0370 GATCAGCATTTGCATGGAA 24 -0.7
  • MAP2K2 NM_030662 SEQ. ID NO. 0371 TCCAGGAGTTTGTCAATAA 17 -4.5
  • MAP2K2 NM_030662 SEQ. ID NO. 0372 GGAAGCTGATCCACCTTGA 16 59.2 TABLE V
  • CyclophilinA_ NM_021130 SEQ. ID NO. 0377 AGACAAGGTCCCAAAGACA -16 58.1
  • CyclophilinA_ NM_021130 SEQ. ID NO. 0378 GGAATGGCAAGACCAGCAA -6 36
  • CyclophilinA_ NM_021130 SEQ. ID NO. 0379 AGAATTATTCCAGGGTTTA -3 ' 16.1
  • CyclophilinA_ NM_021130 SEQ. ID NO. 0380 GCAGACAAGGTCCCAAAGA 8 8.9
  • CyclophilinB M60857 SEQ. ID NO. 0385 GAAAGAGCATCTACGGTGA 41 83.9
  • CyclophilinB M60857 SEQ. ID NO. 0386 GAAAGGATTTGGCTACAAA 53 59.1
  • CyclophilinB M60857 SEQ. ID NO. 0387 ACAGCAAATTCCATCGTGT -20 28.8
  • CyclophilinB M60857 SEQ. ID NO. 0388 GGAAAGACTGTTCCAAAAA 2 27
  • DBB NM_020548 SEQ. ID NO. 0391 AAGATGCCATGAAAGCTTA 17 22
  • I-LUC2 SEQ. ID NO. 0394 GCCAAGAAGTTTCCTAATA 50 13.7 rLUC3 SEQ. ID NO. 0395 CAGCATATCTTGAACCATT 41 -2.2 rLUC4 SEQ. ID NO. 0396 GAACAAAGGAAACGGATGA 39 29.2
  • SeAP2 NM_031313 SEQ. ID NO. 0398 GCTTCGAGCAGACATGATA 4 -11.2
  • each gene or family of genes in each organism plays an important role in maintaining physiological homeostasis and the algorithm can be used to develop functional, highly functional, or hyperfunctional siRNA to each gene.
  • the entire online ncbi refseq, locuslink, and/or unigene database for the human genome is first downloaded to local servers. Concommitantly, the most current version of the BLAST algorithm/program is also downloaded to enable analysis of all siRNA identified by the algorithm.
  • sequences Prior to applying the algorithm, sequences are filtered to eliminate all non-coding sequences ⁇ e.g., 3' and 5' UTRs) and sequences that contain single nucleotide polymorphisms (SNPs).
  • SNPs single nucleotide polymorphisms
  • siRNA selection process only those sequences that are associated with all isoforms (e.g., splice variants) of a given gene are reserved and considered for targeting. Subsequently, a list of all potential siRNAs (including a 19 basepair "core" sequence with two basepair 3' overhangs) is generated for each gene sequence.
  • This group is then filtered to eliminate sequences that contain any one of a number of undesirable traits including, but not limited to: 1) sequences that contain more than two GC basepairs in the last 5 nucleotides of the 3' end of the sense strand, and 2) sequences that contained internal repeats that could potentially form hairpin structures.
  • the output of these procedures are then submitted for scoring by the algorithm.
  • the pre- filtered database was processed with Formula VIII or Formula X and the top 5-100 siRNAs having scores of 75 (adjusted) or greater were selected. If desired, the sequences of these siRNA can be BLAST' ed against the Unigene database containing all sequences in the genome of choice (e.g.
  • the human genome to eliminate any duplexes that show undesirable degrees of homology to sequences other than the intended target.
  • the sequences of the (roughly) top 100 sequences for each gene are provided on the enclosed CDs in electronic form.
  • the Formula X sequences were first generated using the procedures described above and subsequently compared to Formula VIII generated sequences.
  • Formula VIII sequences that were also identified by Formula X were then removed (subtracted) from this database (Table XIH) to eliminate duplications.
  • Table XII which is located in a file entitled table- xii.txt, created 26 April 2004, with a file size of 110,486 kb, provides a list of the 5- 100 sequences for each target, identified by Formula VIII as having the highest relative SMARTscoresTM for the target analyzed.
  • Table XIII which is located in a file entitled table-xiii.txt, created 26 April 2004, with a file size of 23,146 kb, provides a list of the 5-100 sequences for each target identified by Formula X.
  • each table provides information concerning: the gene name, an NCBI accession number, an adjusted SMARTscore, and a sequence ID number. Any of the provided sequences can be used for gene silencing either alone or in combination with other sequences.
  • the information contained on the disks is part of this patent application and is incorporated into the specification by reference.
  • Table XII siRNA Selected by Formula VIII
  • Table XII is included on the compact disk labeled COPY 1 - TABLES PART DISK 1/1 , TABLES XII and XIII (provided in triplicate, which copies are identical), in a file entitled table-xii.txt, date of creation 26 April 2004, with a size of 110,486 kb.
  • Table XIII is included on the compact disk labeled COPY 1 - TABLES PART DISK 1/1, TABLES XII and XIII (provided in triplicate, which copies are identical), in file entitled table-xiii.txt, date of creation 26 April 2004, with a size of 23,146 kb.
  • siRNAs listed in the accompanying compact disk may potentially act as therapeutic agents.
  • a number of prophetic examples follow and should be understood in view of the siRNA that are identified on the accompanying CD.
  • the appropriate message sequence for each gene is analyzed using one of the before mentioned formulas (preferably formula VIII) to identify potential siRNA targets. Subsequently these targets are BLAST'ed to eliminate homology with potential off-targets.
  • BcIlO has been implicated in the development of MALT lymphoma (mucosa associated lymphoid tissue lymphoma) and thus, functional, highly functional, or hyperfunctional siRNA directed against that gene (e.g., SEQ. ID NO. 0427: GGAAACCUCUCAUUGCUAA; SEQ. ID NO. 0428: GAAAGAACCUUGCCGAUCA; SEQ. ID NO. 0429: GGAAAUACAUCAGAGCUUA, or SEQ. ID NO. 0430: GAAAGUAUGUGUCUUAAGU) may contribute to treatment of this disorder.
  • SEQ. ID NO. 0427 GGAAACCUCUCAUUGCUAA
  • SEQ. ID NO. 0428 GAAAGAACCUUGCCGAUCA
  • SEQ. ID NO. 0429 GGAAAUACAUCAGAGCUUA
  • SEQ. ID NO. 0430: GAAAGUAUGUGUCUUAAGU may contribute to treatment of this disorder.
  • siRNA SEQ. ID NO. 0433 UGAAACGGCUGCCUGAUUU; SEQ. ID NO. 0434 GAAGUUACCUCUUACAUUU; SEQ. ID NO. 0435 GUACGAAACUGUAUGAUUA; SEQ. ID NO. 0436 GGACGAGGCUAUCAUUAUG
  • siRNA SEQ. ID NO. 0433 UGAAACGGCUGCCUGAUUU; SEQ. ID NO. 0434 GAAGUUACCUCUUACAUUU; SEQ. ID NO. 0435 GUACGAAACUGUAUGAUUA; SEQ. ID NO. 0436 GGACGAGGCUAUCAUUAUG
  • VHL von Hippel-Lindau
  • RCC clear cell renal cell carcinoma
  • VEGF vascular endothelial growth factor
  • siRNAs directed against either HIF-I alpha SEQ. ID NO. 0437 GAAGGAACCUGAUGCUUUA; SEQ.IDNO.0438GCAUAUAUCUAGAAGGUAU;SEQ.IDNO.0439 GAACAAAUACAUGGGAUUA;SEQ.IDNO.0440 GGACACAGAUUUAGACUUG)orVEGF(SEQ.IDNO.0441 GAACGUACUUGCAGAUGUG;SEQ.IDNO.0442 GAGAAAGCAUUUGUUUGUA;SEQ.IDNO.0443 GGAGAAAGCAUUUGUUUGU;SEQ.IDNO.0444
  • CGAGGCAGCUUGAGUUAAA may be useful in the treatment of renal cell carcinoma.
  • PDGF-A and PDGF-B platelet derived growth factor A and B
  • PDGF-A and PDGF-B have been observed to be increased 22- and 6-fold, respectively, in renal tissues taken from patients with diabetic nephropathy as compared with controls.
  • SEQ. ID NO. 0454 UUUAUGAGAUGCUGAGUGA may be useful in the treatment of this form of kidney disorder:
  • glucose transporters e.g., GLUT12
  • cancer cells e.g., GLUT12
  • GLUT12 glucose transporters
  • siRNA-based therapies that target the molecules such as
  • GLUTl also known as SLC2A1: siRNA
  • GLUT12(also knownasSLCA12:siRNA SEQ.IDNO.0459:GAGACACUCUGAAAUGAUA; SEQ.IDNO.0460:GAAAUGAUGUGGAUAAGAG; SEQ.IDNO.0461:GAUCAAAUCCUCCCUGAAA;
  • SEQ. ID NO. 0462 UGAAUGAGCUGAUGAUUGU
  • siRNA sequences listed above are presented in a 5'- ⁇ 3' sense strand direction.
  • siRNA directed against the targets listed above as well as those directed against other targets and listed in the accompanying compact disk may be useful as therapeutic agents.
  • siRNA duplexes were synthesized using Dharmacon proprietary ACE® chemistry against one of the standard reporter genes: firefly luciferase. The duplexes were designed to start two base pairs apart and to cover approximately 180 base pairs of the luciferase gene (see sequences in Table III). Subsequently, the siRNA duplexes were co-transfected with a luciferase expression reporter plasmid into HEK293 cells using standard transfection protocols and luciferase activity was assayed at 24 and 48 hours.
  • FIG. 15 represents a typical screen of ninety siRNA duplexes (SEQ. ID NO. 0032- 0120) positioned two base pairs apart.
  • the functionality of the siRNA duplex is determined more by a particular sequence of the oligonucleotide than by the relative oligonucleotide position within a gene or excessively sensitive part of the mRNA, which is important for traditional anti-sense technology.
  • siRNA duplexes were pooled together in groups of five at a time, a significant functional cooperative action was observed.
  • pools of semi-active oligonucleotides were 5 to 25 times more functional than the most potent oligonucleotide in the pool. Therefore, pooling several siRNA duplexes together does not interfere with the functionality of the most potent siRNAs within a pool, and pooling provides an unexpected significant increase in overall functionality
  • Example XI Human cyclophilin B Table III above lists the siRNA sequences for the human cyclophilin B prot ⁇ n. siRNA may be selected by applying these sequences to any of Formula I to VII above.
  • kits for silencing a gene Preferably, one could pool 2, 3, 4, 5 or more of these sequences to create a kit for silencing a gene. Preferably, within the kit there would be at least one sequence that has a relatively high predicted functionality when any of Formulas I - VII is applied.
  • siRNA may be used as both research or diagnostic tools and therapeutic agents, either individually or in pools.
  • Genes involved in signal transduction, the immune response, apoptosis, DNA repair, cell cycle control, and a variety of other physiological functions have clinical relevance and therapeutic agents that can modulate expression of these genes may alleviate some or all of the associated symptoms, hi some instances, these genes can be described as a member of a family or class of genes and siRNA (randomly, conventionally, or rationally designed) can be directed against one or multiple members of the family to induce a desired result.
  • siRNA having heightened levels of potency can be identified by testing each of the before mentioned duplexes at increasingly limiting concentrations.
  • siRNA having increased levels of longevity can be identified by introducing each duplex into cells and testing functionality at 24, 48, 72, 96, 120, 144, 168, and 192 hours after transfection.
  • Agents that induce >95% silencing at sub-nanomolar concentrations and/or induce functional levels of silencing for >96 hours are considered hyperfunctional.
  • Tables XII and XIII provides the siRNA sequence (sense strand), the gene name, the NCBI accession number, the adjusted algorithm score, and the sequence ID number. All sequences have an adjusted score 5 of 75 or above.
  • Formula X derived sequences were compared with Formula VIII sequences. Sequences that were in common with both were eliminated from Table XIII. Pool picks are typically identified as gene specific siRNA that have the hightest adjusted scores.
  • Transporters, pumps, and channels represent one class of genes that are attractive targets for siRNAs.
  • One major class of transporter molecules are the ATP- binding cassette (ABC) transporters.
  • ABC ATP- binding cassette
  • MDRl which encodes the P-glycoprotein, NP_000918)
  • MRP 1--7 MDR-related proteins
  • BCRP breast cancer resistance protein
  • NBF nucleotide binding folds
  • TM transmembrane domains
  • the genes encoding this class of transporter are organized as either full transporters (i.e., containing two TM and two NBF domains) or as half transporters that assemble as either homodimers or heterodimers to create functional transporters. As a whole,
  • ABC-transporters have been implicated in several human diseases. For instance, molecular efflux pumps of this type play a major role in the development of 35 drug resistance exhibited by a variety of cancers and pathogenic microorganisms. In the case of human cancers, increased expression of the MDRl gene and related pumps have been observed to generate drug resistance to a broad collection of commonly used chemotherapeutics including doxorubicin, daunorubicin, vinblastine, vincristine, colchicines. In addition to the contribution these transporters make to the development of multi-drug resistance, there are currently 13 human genetic diseases associated with defects in 14 different transporters.
  • cystic fibrosis The most common of these conditions include cystic fibrosis, Stargardt disease, age-related macular degeneration, adrenoleukodystrophy, Tangier disease, Dubin- Johnson syndrome and progressive familial intrahepatic cholestasis. For this reason, siRNAs directed against members of this, and related, families are potentially valuable research and therapeutic tools.
  • K+ potassium
  • This list includes shaker (Sh), which encodes a voltage activated K + channel, slowpoke (SIo), a Ca 2+ activated K + channel, and ether-a-go-go (Eag).
  • the Eag family is further divided into three subfamilies: Eag, Elk (eag-like K channels), and Erg (Eag related genes).
  • the Erg subfamily contains three separate family members (Ergl-3) that are distantly related to the sh family of voltage activated K channels.
  • erg polypetides contain the classic six membrane spanning architecture of K + channels (S1-S6) but differ in that each includes a segment associated with the C-terminal cytoplasmic region that is homologous to cyclic nucleotide binding domains (cNBD).
  • cNBD cyclic nucleotide binding domains
  • erg mutants are temperature-sensitive paralytics, a phenotype caused by spontaneous repetitive firing (hyperactivity) in neurons and enhanced transmitter release at the neuromuscular junction.
  • HERG human ergl
  • LQT long-QT-syndrome
  • CLCA family that mediate a Ca 2+ -activated Cl ⁇ conductance in a variety of tissues.
  • mCLCAl; mCLCA2; mCLCA3 three mouse
  • hCLCAl; hCLCA2; hCLCA3; hCLCA4 human
  • CLCA family members have been isolated and patch-clamp studies with transfected human embryonic kidney (HEK-293) cells have shown that bCLCAl, mCLCAl, and hCLCAl mediate a Ca 2+ -activated CF conductance that can be inhibited by the anion channel blocker DIDS and the reducing agent dithiothreitol (DTT).
  • DIDS anion channel blocker
  • DTT dithiothreitol
  • the protein size, structure, and processing seem to be similar among different CLCA family members and has been studied in greatest detail for Lu-ECAM-I .
  • the Lu-ECAM-I open reading frame encodes a precursor glycoprotein of 130 kDa that is processed to a 90-kDa amino-terminal cleavage product and a group of 30- to 40-kDa glycoproteins that are glycosylation variants of a single polypeptide derived from its carboxy terminus. Both subunits are associated with the outer cell surface, but only the 90-kDa subunit is thought to be anchored to the cell membrane via four transmembrane domains.
  • bovine Lu-ECAM-I is expressed primarily in vascular endothelia
  • bCLCAl is exclusively detected in the trachea
  • hCLCAl is selectively expressed in a subset of human intestinal epithelial cells.
  • the emerging picture is that of a multigene family with members that are highly tissue specific, similar to the ClC family of voltage-gated CF channels.
  • the human channel, hCLCA2 is particular interesting from a medical and pharmacological standpoint.
  • CLC A2 is expressed on the luminal surface of lung vascular endothelia and serves as an adhesion molecule for lung metastatic cancer cells, thus mediating vascular arrest and lung colonization. Expression of this molecule in normal mammary epithelium is consistently lost in human breast cancer and in nearly all tumorigenic breast cancer cell lines. Moreover, re-expression of hCLCA2 in human breast cancer cells abrogates tumorigenicity in nude mice, implying that hCLCA2 acts as a tumour suppressor in breast cancer. For these reasons, siRNA directed against CLCA family members and related channels may prove to be valuable in research and therapeutic venues.
  • Synaptic transmission involves the release of a neurotransmitter into the synaptic cleft, interaction of that transmitter with a postsynaptic receptor, and subsequent removal of the transmitter from the cleft. In most synapses the signal is terminated by a rapid reaccumulation of the neurotransmitter into presynaptic terminals. This process is catalyzed by specific neurotransmitter transporters that are often energized by the electrochemical gradient of sodium across the plasma membrane of the presynaptic cells.
  • GABA Aminobutyric acid
  • GABA transporters GABA transporters
  • GABA1-GAT4 GABA transporters
  • Comparative sequence analysis has revealed that GABA transporters are related to several other proteins involved in neurotransmitter uptake including gamma-aminobutyric acid transporters, monoamine transporters, amino acid transporters, certain "orphan" transporters, and the recently discovered bacterial transporters.
  • Each of these proteins has a similar 12 transmembrane helices topology and relies upon the Na+/Cl- gradient for transport function. Transport rates are dependent on substrate concentrations, with half-maximal effective concentrations for transport frequently occurring in the submicromolar to low micromolar range. In addition, transporter function is bidirectional, and non- vesicular efflux of transmitter may contribute to ambient extracellular transmitter levels.
  • GABA transporters, and neurotransmitter transporters in general are not passive players in regulating neuronal signaling; rather, transporter function can be altered by a variety of initiating factors and signal transduction cascades.
  • this functional regulation occurs in two ways, either by changing the rate of transmitter flux through the transporter or by changing the number of functional transporters on the plasma membrane.
  • a recurring theme in transporter regulation is the rapid redistribution of the transporter protein between intracellular locations and the cell surface, hi general, this functional modulation occurs in part through activation of second messengers such as kinases, phosphatases, arachidonic acid, and pH.
  • second messengers such as kinases, phosphatases, arachidonic acid, and pH.
  • GABA transporters play a pathophysiological role in a number of human diseases including temporal lobe epilepsy and are the targets of pharmacological interventions.
  • Studies in seizure sensitive animals show some (but not all) of the GAT transporters have altered levels of expression at times prior to and post seizure, suggesting this class of transporter may affect epileptogenesis, and that alterations following- seizure may be compensatory responses to modulate seizure activity.
  • siRNAs directed against members of this family of genes may prove to be valuable research and therapeutic tools.
  • the human body is continuously exposed to a great variety of xenobiotics, via food, drugs, occupation, and environment.
  • Excretory organs such as kidney, liver, and intestine defend the body against the potentially harmful effects of these compounds by transforming them into less active metabolites that are subsequently secreted from the system.
  • Carrier-mediated transport of xenobiotics and their metabolites exist for the active secretion of organic anions and cations. Both systems are characterized by a high clearance capacity and tremendous diversity of substances accepted, properties that result from the existance of multiple transporters with overlapping substrate specificities.
  • the class of organic anion transporters plays a critical role in the elimination of a large number of drugs (e.g., antibiotics, chemotherapeutics, diuretics, nonsteroidal anti-inflammatory drugs, radiocontrast agents, cytostatics); drug metabolites (especially conjugation products with glutathione, glucuronide, glycine, sulfate, acetate); and toxicants and their metabolites (e.g., mycotoxins, herbicides, plasticizers, glutathione .S-conjugates of polyhaloalkanes,polyhaloalkenes, hydroquinones, aminophenols), many of which are specifically harmful to the kidney.
  • drugs e.g., antibiotics, chemotherapeutics, diuretics, nonsteroidal anti-inflammatory drugs, radiocontrast agents, cytostatics
  • drug metabolites especially conjugation products with glutathione, glucuronide, glycine, sulfate, acetate
  • the organic anion-transporting polypeptide 1 (Oatpl) is a Na + - and ATP- independent transporter originally cloned from rat liver.
  • the tissue distribution and transport properties of the Oatpl gene product are complex.
  • Oatpl is localized to the basolateral membrane of hepatocytes, and is found on the apical membrane of S3 proximal tubules.
  • transiently transfected cells e.g., HeLa cells
  • Oatp family members are highly conserved, hydrophobic, and have 12 transmembrane domains. Decreases in expression of Oatp family members have been associated with cholestatic liver diseases and human hepatoblastomas, making this family of proteins of key interest to researchers and the medical community. For these reasons, siRNAs directed against OAT family members (including but not limited to SLC21 A2, 3, 6, 8, 9, 11, 12, 14, 15, and related transporters) are potentially useful as research and therapeutic tools.
  • Nucleoside transporters play key roles in physiology and pharmacology.
  • nucleoside transporters also control the extracellular concentration of adenosine in the vicinity of its cell surface receptors and regulate processes such as neurotransmission and cardiovascular activity.
  • Adenosine itself is used clinically to treat cardiac arrhythmias, and nucleoside transport inhibitors such as dipyridamole, dilazep, and draflazine function as coronary vasodilators.
  • CNTs are expressed in a tissue- specific fashion; ENTs are present inmost, possibly all, cell types and are responsible for the movement of hydrophilic nucleosides and nucleoside analogs down their concentration gradients.
  • structure/function studies of ENT family members have predicted these molecules to contain eleven transmembrane helical segments with an amino terminus that is intracellular and a carboxyl terminus that is extracellular.
  • the proteins have a large glycosylated loop between TMs 1 and 2 and a large cytoplasmic loop between TMs 6 and 7. Recent investigations have implicated the TM 3-6 region as playing a central role in solute recognition.
  • the medical importance of the ENT family of proteins is broad. In humans adenosine exerts a range of cardioprotective effects and inhibitors of ENTs are seen as being valuable in alleviating a variety of cardio/cardio vascular ailments. In addition, responses to nucleoside analog drugs has been observed to vary considerably amongst, e.g., cancer patients.
  • ENT transporters While some forms of drug resistance have been shown to be tied to the up-regulation of ABC-transporters (e.g., MDRl), resistance may also be the result of reduced drug uptake (i.e., reduced ENT expression). Thus, a clearer understanding of ENT transporters may aid in optimizing drug treatments for patients suffering a wide range of malignancies. For these reasons, siRNAs directed against this class of molecules (including SLC28A1-3, SLC29A1-4, and related molecules) may be useful as therapeutic and research tools.
  • Sulfate Transporters All cells require inorganic sulfate for normal function. Sulfate is the fourth most abundant anion in human plasma and is the major source of sulfur in many organisms. Sulfation of extracellular matrix proteins is critical for maintaining normal cartilage metabolism and sulfate is an important constituent of myelin membranes found in the brain
  • sulfate is a hydrophilic anion that cannot passively cross the lipid bilayer of cell membranes, all cells require a mechanism for sulfate influx and efflux to ensure an optimal supply.
  • sulfate transporters have been identified in tissues from many origins. These include the renal sulfate transporters (NaSi-I and Sat-1), the ubiquitously expressed diastrophic dysplasia sulfate transporter (DTDST), the intestinal sulfate transporter (DRA), and the erythrocyte anion exchanger (AEl). Most, if not all, of these molecules contain the classic 12 transmembrane spanning domain architecture commonly found amongst members of the anion transporter superfamily.
  • DTDST diastrophic dysplasia
  • CLD congenital chloride diarrhea
  • PDS Pendred syndrome
  • Impaired function of the DTDST gene product leads to undersulfation of proteoglycans and a complex family of recessively inherited osteochondrodysplasias (achondrogenesis type IB, atelosteogenesis type II, and diastrophic dysplasia) with clinical features including but not limited to, dwarfism, spinal deformation, and specific joint abnormalities.
  • achondrogenesis type IB achondrogenesis type II
  • diastrophic dysplasia with clinical features including but not limited to, dwarfism, spinal deformation, and specific joint abnormalities.
  • siRNAs directed against this class of genes may be potentially helpful in both therapeutic and research venues.
  • Intracellular pH regulatory mechanisms are critical for the maintenance of countless cellular processes. For instance, in muscle cells, contractile processes and metabolic reactions are influenced by pH. During periods of increased energy demands and ischemia, muscle cells produce large amounts of lactic acid that, without quick and efficient disposal, would lead to acidification of the sarcoplasm.
  • Intracellular pH regulatory processes that have been characterized functionally include but are not limited to the Na + /H + exchange, the Na(HCO 3 ) overlook cotransport, and the Na + -dependent and -independent Cl ⁇ ase exchangers.
  • bicarbonate and CO 2 comprise the major pH buffer of biological fluids, sodium biocarbonate cotransporters (NBCs) are critical. Studies have shown that these molecules exist in numerous tissues including the kidney, brain, liver, cornea, heart, and lung, suggesting that NBCs play an important role in mediating HCO 3 " transport in both epithelial as well as nonepithelial cells.
  • AE4 When expressed in COS-7 cells and Xenopus oocytes AE4 exhibits sodium-independent and DIDS-insensitive anion exchanger activity.
  • Exchangers have been shown to be responsible for a variety of human diseases. For instance, mutations in three genes of the anion transporter family (SLC) are believed to cause known hereditary diseases, including chondrodysplasia (SLC26A2, DTD), diarrhea (A3, down-regulated in adenoma/chloride-losing diarrhea protein: DRA/CLD), and goiter/deafness syndrome (A4, pendrin).
  • SLC26A2 chondrodysplasia
  • DTD diarrhea
  • DRA/CLD diarrhea
  • goiter/deafness syndrome A4, pendrin
  • mutations in Na+/HCO3 co- transporters have also been associated with various human maladies. For these reasons, siRNAs directed against these sorts of genes ⁇ e.g., SLC4A4-10, and related genes) may
  • Glycine receptors display significant sequence homology to several other receptors including the nicotinic acetylcholine receptor, the aminobutyric acid receptor type A (GABAAR), and the serotonin receptor type 3 (5-HT 3 R) subunits. As members of the superfamily of ligand-gated ion channels, these polypeptides share common topological features.
  • the glycine receptor is composed of two types of glycosylated integral membrane proteins ( ⁇ l- ⁇ 4 and ⁇ ) arranged in a pentameric suprastructure.
  • the alpha subunit encodes a large extracellular, N-terminal domain that carries the structural determinants essential for agonist and antagonist binding, followed by four transmembrane spanning regions (TMl -TM4), with TM2 playing the critical role of forming the inner wall of the chloride channel.
  • TMl -TM4 transmembrane spanning regions
  • the density, location, and subunit composition of glycine neurotransmitter receptors changes over the course of development. It has been observed that the amount of GIyR gene translation (assessed by the injection of developing rat cerebral cortex rnRNA into Xenopus oocytes) decreases with age, whereas that of GABARs increases. In addition, the type and location of mRNAs coding for GIyR changes over the course of development.
  • alpha 1 and alpha 2 subunits were scarce in the alpha 1 mRNA, but the germinal zone (matrix layer) at El 1-14 expressed higher levels of the message.
  • the alpha 1 signals became manifested throughout the gray matter of the spinal cord.
  • the spinal tissues at PO exhibited the highest levels of alpha 2 mRNA, which decreased with the postnatal development.
  • GIyR subunit genes result in hereditary motor disorders characterized by exaggerated startle responses and increased muscle tone.
  • Pathological alleles of the Glral gene are associated with the murine phenotypes oscillator (spd 01 ) and spasmodic (spd).
  • spd 01 murine phenotypes oscillator
  • spd spasmodic
  • a mutant allele of Glrb has been found to underly the molecular pathology of the spastic mouse (spa).
  • GLRAl mutant alleles Resembling the situation in the mouse, a variety of GLRAl mutant alleles have been shown to be associated with the human neurological disorder hyperekplexia or startle disease.
  • siRNA directed against glycine receptors GLRA 1-3, GLRB, and related molecules
  • glutamate receptors glutamate receptors
  • GABA receptors GABA receptors
  • ATP receptors ATP receptors
  • neurotransmitter receptor molecules may be valuable
  • kallikreins serine endopeptidases that split peptide substrates preferentially on the C-terminal side of internal arginyl and lysyl residues.
  • Kallikreins are generally divided into two distinct groups, plasma kallikreins and tissue kallikreins. Tissue kallikreins represent a large group of enzymes that have substantial similarities at both the gene and protein level. The genes encoding this group are frequently found on a single chromosome, are organized in clusters, and are expressed in a broad range of tissues ⁇ e.g., pancreas, ovaries, breast).
  • the plasma form of the enzyme is encoded by a single gene (e.g., KLK3) that has been localized to chromosome 4q34-35 in humans.
  • the gene encoding plasma kallikrein is expressed solely in the liver, contains 15 exons, and encodes a glycoprotein that is translated as a preprotein called prekallikrein.
  • Kallikreins are believed to play an important role in a host of physiological events.
  • the immediate consequence of plasma prekallikrein activation is the cleavage of high molecular weight kininogen (HK) and the subsequent liberation of bradykinin, a nine amino acid vasoactive peptide that is an important mediator of inflammatory responses.
  • plasma kallikrein promotes single-chain urokinase activation and subsequent plasminogen activation, events that are critical to blood coaggulation and wound healing.
  • siRNAs directed against this class of genes may prove valuable in both research and therapeutic settings.
  • ADAM Proteins The process of fertilization takes place in a series of discrete steps whereby the sperm interacts with, i) the cumulus cells and the hyaluronic acid extracellular matrix (ECM) in which they are embedded, ii) the egg's own ECM, called the zona pellucida (ZP), and iii) the egg plasma membrane.
  • ECM extracellular matrix
  • ZP zona pellucida
  • the egg plasma membrane iii
  • the "acrosome reaction” the exocytosis of the acrosome vesicle on the head of the sperm, is induced, allowing the sperm to penetrate the ZP and gain access to the perivitelline space.
  • This process exposes new portions of the sperm membrane, including the inner acrosomal membrane and the equatorial segment, regions of the sperm head that can participate in initial gamete membrane binding.
  • the interactions of the gamete plasma membranes appear to involve multiple ligands and receptors and are frequently compared to leukocyte-endothelial interactions. These interactions lead to a series of signal transduction events in the egg, known as collectively as egg activation and include the initiation of oscillations in intracellular calcium concentration, the exit from meiosis, the entry into the first embryonic mitosis, and the formation of a block to polyspermy via the release of ZP- modifying enzymes from the egg's cortical granules. Ultimately, sperm and egg not only adhere to each other but also go on to undergo membrane fusion, making one cell (the zygote) from two.
  • ADAM Disintegrin And Metalloprotease
  • GEF epidermal growth factor
  • One of the best-studied members of the ADAM family is fertilin, a heterodimeric protein comprised of at least two subunits, fertilin alpha and fertilin beta.
  • the fertilin beta gene (AD AM2) has been disrupted with a targeting gene construct corresponding to the exon encoding the fertilin beta disintegrin domain.
  • Sperm from males homozygous for disruptions in this region exhibit defects in multiple facets of sperm function including reduced levels of sperm transit from the uterus to the oviduct, reduced sperm-ZP binding, and reduced sperm-egg binding, all of which contribute to male infertility.
  • ADAM family members ADAM 24-27
  • the deduced amino acid sequences show that all four contain the complete domain organization common to ADAM family members and Northern Blot analysis has shown all four to be specific to the testes.
  • siRNAs directed against this class of genes e.g., ADAM2 and related proteins
  • ADAM2 and related proteins may be useful as research tools and therapeutics directed toward fertility and birth control.
  • Aminopeptidases are proteases that play critical roles in processes such as protein maturation, protein digestion in its terminal stage, regulation of hormone levels, selective or homeostatic protein turnover, and plasmid stabilization. These enzymes generally have broad substrate specificity, occur in several forms and play a major role in physiological homeostasis. For instance, the effects of bradykinin, angiotensin converting enzyme (ACE), and other vasoactive molecules are muted by one of several peptidases that cleave the molecule at an internal position and eliminate its ability to bind its cognate receptor (e.g., for bradykinin, the B2 -receptor).
  • ACE angiotensin converting enzyme

Abstract

Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rational design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes. Methods, compositions, and kits generated through rational design of siRNAs are disclosed.

Description

METHODS AND COMPOSITIONS FOR SELECTING siRNA OF IMPROVED FUNCTIONALITY
REFERENCETOTABLESSUBMITTEDINELECTRONICFORM
In accordance with PCT Administrative Instructions Part 8, Applicant submits a compact disc of tables related to sequences and hereby incorporates by reference the material submitted herewith, on the compact disk labeled COPY 1 - TABLES PART DISK 1/1 , TABLES XII and XIII (provided in triplicate, which copies are identical), in files entitled table-xii.txt, date of creation 26 April 2004, with a size of 110,486 kb, and table-xiii.txt, date of creation 26 April 2004, with a size of 23,146 kb; and in accordance with PCT Administrative Instructions Section 801(a)(i) on the compact disk labeled CRF (with three further copies, which copies are identical) in a file entitled 13608PCT.txt, date of creation 26 April 2004, with a size of 556,776 kb.
FIELD OF INVENTION
The present invention relates to RNA interference ("RNAi").
BACKGROUND OF THE INVENTION
Relatively recently, researchers observed that double stranded RNA ("dsRNA") could be used to inhibit protein expression. This ability to silence a gene has broad potential for treating human diseases, and many researchers and commercial entities are currently investing considerable resources in developing therapies based on this technology.
Double stranded RNA induced gene silencing can occur on at least three different levels: (i) transcription inactivation, which refers to RNA guided DNA or histone methylation; (ii) siRNA induced rnRNA degradation; and (iii) mRNA induced transcriptional attenuation.
It is generally considered that the major mechanism of RNA induced silencing (RNA interference, or RNAi) in mammalian cells is mRNA degradation. Initial attempts to use RNAi in mammalian cells focused on the use of long strands of dsRNA. However, these attempts to induce RNAi met with limited success, due in part to the induction of the interferon response, which results in a general, as opposed to a target-specific, inhibition of protein synthesis. Thus, long dsRNA is not a viable option for RNAi in mammalian systems.
More recently it has been shown that when short (18-30 bp) RNA duplexes are introduced into mammalian cells in culture, sequence-specific inhibition of target mRNA can be realized without inducing an interferon response. Certain of these short dsRNAs, referred to as small inhibitory RNAs ("siRNAs"), can act catalytically at sub-molar concentrations to cleave greater than 95% of the target mRNA in the cell. A description of the mechanisms for siRNA activity, as well as some of its applications are described in Provost et al, Ribonuclease Activity and RNA Binding of Recombinant Human Dicer, E.M.B.O. J., 2002 Nov. 1; 21(21): 5864 -5874; Tabara et al, The dsRNA Binding Protein RDE-4 Interacts with RDE-I, DCR-I and a DexH- boxHelicase to Direct RNAi in C. elegans, Cell 2002, June 28;109(7):861-71; Ketting et al., Dicer Functions in RNA Interference and in Synthesis of Small RNA Involved in Developmental Timing in C. elegans; Martinez et al, Single-Stranded Antisense siRNAs Guide Target RNA Cleavage in RNAi, Cell 2002, Sept. 6; 110(5):563; Hutvagner & Zamore, A microRNA in a multiple-turnover RNAi enzyme complex, Science 2002, 297:2056.
From a mechanistic perspective, introduction of long double stranded RNA into plants and invertebrate cells is broken down into siRNA by a Type III endonuclease known as Dicer. Sharp, RNA interference — 2001, Genes Dev. 2001, 15:485. Dicer, a ribonuclease-III-like enzyme, processes the dsRNA into 19-23 base pair short interfering RNAs with characteristic two base 3' overhangs. Bernstein, Caudy, Hammond, & Harmon, Role for a bidentate ribonuclease in the initiation step of RNA interference, Nature 2001, 409:363. The siRNAs are then incorporated into an RNA-induced silencing complex (RISC) where one or more helicases unwind the siRNA duplex, enabling the complementary antisense strand to guide target recognition. Nykanen, Haley, & Zamore, ATP requirements and small interfering RNA structure in the RNA interference pathway, Cell 2001, 107:309. Upon binding to the appropriate target mRNA, one or more endonucleases within the RISC cleaves the target to induce silencing. Elbashir, Lendeckel, & Tuschl, RNA interference is mediated by 21- and 22 -nucleotide RNAs1 Genes Dev 2001, 15:188, Figure 1.
The interference effect can be long lasting and may be detectable after many cell divisions. Moreover, RNAi exhibits sequence specificity, Kisielow, M. et al. (2002) Isoform-specific knockdown and expression of adaptor protein ShcA using small interfering RNA, J. of Biochemistry 363: 1-5. Thus, the RNAi machinery can specifically knock down one type of transcript, while not affecting closely related mRNA. These properties make siRNA a potentially valuable tool for inhibiting gene expression and studying gene function and drug target validation. Moreover, siRNAs are potentially useful as therapeutic agents against: (1) diseases that are caused by over-expression or misexpression of genes; and (2) diseases brought about by expression of genes that contain mutations.
Successful siRNA-dependent gene silencing depends on a number of factors.
One of the most contentious issues in RNAi is the question of the necessity of siRNA design, i.e., considering the sequence of the siRNA used. Early work in C. elegans and plants circumvented the issue of design by introducing long dsRNA (see, for instance, Fire, A. et al. (1998) Nature 391:806-811). In this primitive organism, long dsRNA molecules are cleaved into siRNA by Dicer, thus generating a diverse population of duplexes that can potentially cover the entire transcript. While some fraction of these molecules are non-functional (i.e., induce little or no silencing) one or more have the potential to be highly functional, thereby silencing the gene of interest and alleviating the need for siRNA design. Unfortunately, due to the interferon response, this same approach is unavailable for mammalian systems. While this effect can be circumvented by bypassing the Dicer cleavage step and directly introducing siRNA, this tactic carries with it the risk that the chosen siRNA sequence may be non-functional or semi-functional.
A number of researches have expressed the view that siRNA design is not a crucial element of RNAi. On the other hand, others in the field have begun to explore the possibility that RNAi can be made more efficient by paying attention to the design of the siRNA. Unfortunately, none of the reported methods have provided a satisfactory scheme for reliably selecting siRNA with acceptable levels of functionality. Accordingly, there is a need to develop rational criteria by which to select siRNA with an acceptable level of functionality, and to identify siRNA that have this improved level of functionality, as well as to identify siRNAs that are hyperfunctional.
SUMMARY OF THE INVENTION
The present invention is directed to increasing the efficiency of RNAi, particularly in mammalian systems. Accordingly, the present invention provides kits, siRNAs and methods for increasing siRNA efficacy.
According to a first embodiment, the present invention provides a kit for gene silencing, wherein said kit is comprised of a pool of at least two siRNA duplexes, each of which is comprised of a sequence that is complementary to a portion of the sequence of one or more target messenger RNA, and each of which is selected using non-target specific criteria.
According to a second embodiment, the present invention provides a method for selecting an siRNA, said method comprising applying selection criteria to a set of , potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; and determining the relative functionality of the at least two siRNAs.
In one embodiment, the present invention also provides a method wherein said selection criteria are embodied in a formula comprising:
Formula VIII: (-14)*G13-13*A1-12*U7-ll*U2-10*A11-10*U4-10*C3-10*C5-10*C6-
9*Aio-9*U9-9*Ci8-8*Gio-7*Ui-7*Ui6-7*C17-7*Ci9 +7*U17+8*A2+8*A4 +8*A5+8*C4 +9*G8 +10*A7+l 0*U18+l 1 *A19+
11*C9+15*G1+ 18*A3+19*U10-Tm-3* (GCtotai) - 6*(GC15_19)- 30*X; or
Formula X (-8)*Al+(-l)*A2+(12)*A3+(7)*A4+(18)*A5+(12)*A6+ (19)*A7+(6)*A8+(-4)*A9+(-5)*A10+(-2)*Al l+(- 5)*A12+(17)*A13+(-3)*A14+(4)*A15+(2)*A16+(8)*A17+ (l l)*A18+(30)*A19+(-13)nJl+(-10)nJ2+(2)nJ3+(-2)*U4+(- 5)*U5+(5)*U6+(-2)*U7+(-10)*U8+(-5)*U9+(l 5)*U10+(- l)!f:Ul l+(0)*U12+(10)*U13+(-9)*U14+(-13)*U15+(- 10)*U16+(3)*U17+(9)*U18+(9)*U19+(7)*Cl+(3)*C2+(- 21)*C3+(5)*C4+(-9)*C5+(-20)*C6+(-18)*C7+(- 5)*C8+(5)*C9+(l)*C10+(2)*Cl l+(-5)*C12+(-3)*C13+(-6)*C14+(- 2)*C15+(-5)*C16+(-3)*C17+(-12)*C18+(-
18)*C19+(14)*Gl+(8)*G2+(7)*G3+(-10)*G4+(- 4)*G5+(2)*G6+(l)*G7+(9)*G8+(5)*G9+(- 1 l)*G10+(l)*Gl l+(9)*G12+(-
24)*G13+(18)*G14+(ll)*G15+(13)*G16+(-7)5!:G17+(-9)*G18+(- 22)*G19 + 6*(number of A+U in position 15-19) - 3*(number of G+C in whole siRNA), wherein position numbering begins at the 5 '-most position of a sense strand, and A1 = 1 if A is the base at position 1 of the sense strand, otherwise its value is 0; A2 = 1 if A is the base at position 2 of the sense strand, otherwise its value is 0; A3 = 1 if A is the base at position 3 of the sense strand, otherwise its value is 0; A4 = 1 if A is the base at position 4 of the sense strand, otherwise its value is 0; A5 = 1 if A is the base at position 5 of the sense strand, otherwise its value is 0; A6 = 1 if A is the base at position 6 of the sense strand, otherwise its value is 0; A7= 1 if A is the base at position 7 of the sense strand, otherwise its value is 0; A1O= 1 if A is the base at position 10 of the sense strand, otherwise its value is 0; A11 = 1 if A is the base at position 11 of the sense strand, otherwise its value is 0; A13 = 1 if A is the base at position 13 of the sense strand, otherwise its value is 0; A1Q = 1 if A is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
C3 = 1 if C is the base at position 3 of the sense strand, otherwise its value is 0; C4 = 1 if C is the base at position 4 of the sense strand, otherwise its value is 0; C5 = 1 if C is the base at position 5 of the sense strand, otherwise its value is 0; C6 = 1 if C is the base at position 6 of the sense strand, otherwise its value is 0; C7 = 1 if C is the base at position 7 of the sense strand, otherwise its value is 0; C9 = 1 if C is the base at position 9 of the sense strand, otherwise its value is 0; C17 = 1 if C is the base at position 17 of the sense strand, otherwise its value is 0; C18 = 1 if C is the base at position 18 of the sense strand, otherwise its value is 0; Ci9 = 1 if C is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
G1 = 1 if G is the base at position 1 on the sense strand, otherwise its value is 0;
G2 = 1 if G is the base at position 2 of the sense strand, otherwise its value is 0; G8 = 1 if G is the base at position 8 on the sense strand, otherwise its value is 0;
G1O = 1 if G is the base at position 10 on the sense strand, otherwise its value is 0;
G13 = 1 if G is the base at position 13 on the sense strand, otherwise its value is 0;
G\g = 1 if G is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
U1 = 1 if U is the base at position 1 on the sense strand, otherwise its value is 0;
U2 = 1 if U is the base at position 2 on the sense strand, otherwise its value is 0;
U3 = 1 if U is the base at position 3 on the sense strand, otherwise its value is 0;
U4 = 1 if U is the base at position 4 on the sense strand, otherwise its value is 0; U7 = 1 if U is the base at position 7 on the sense strand, otherwise its value is 0;
U9 = 1 if U is the base at position 9 on the sense strand, otherwise its value is 0;
U10 = 1 if U is the base at position 10 on the sense strand, otherwise its value is 0;
U15 = 1 if U is the base at position 15 on the sense strand, otherwise its value is 0;
U16 = 1 if U is the base at position 16 on the sense strand, otherwise its value is 0; U17 = 1 if U is the base at position 17 on the sense strand, otherwise its value is 0;
U1S = 1 if U is the base at position 18 on the sense strand, otherwise its value is 0.
GQ5-49 = the number of G and C bases within positions 15 - 19 of the sense strand, or within positions 15 -18 if the sense strand is only 18 base pairs in length; GCtotai - the number of G and C bases in the sense strand;
Tm = 100 if the siRNA oligo has the internal repeat longer then 4 base pairs, otherwise its value is 0; and
X = the number of times that the same nucleotide repeats four or more times in a row. According to a third embodiment, the invention provides a method for developing an algorithm for selecting siRNA, said method comprising: (a) selecting a set of siRNA; (b) measuring gene silencing ability of each siRNA from said set; (c) determining relative functionality of each siRNA; (d) determining improved functionality by the presence or absence of at least one variable selected from the group consisting of the presence or absence of a particular nucleotide at a particular position, the total number of As and Us in positions 15-19, the number of times that the same nucleotide repeats within a given sequence, and the total number of Gs and Cs; and (e) developing an algorithm using the information of step (d).
According to a fourth embodiment, the present invention provides a kit, wherein said kit is comprised of at least two siRNAs, wherein said at least two siRNAs comprise a first optimized siRNA and a second optimized siRNA, wherein said first optimized siRNA and said second optimized siRNA are optimized according a formula comprising Formula X.
According to .a fifth embodiment, the present invention provides a method for identifying a hyperfunctional siRNA, comprising applying selection criteria to a set of potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; determining the relative functionality of the at least two siRNAs and assigning each of the at least two siRNAs a functionality score; and selecting siRNAs from the at least two siRNAs that have a functionality score that reflects greater than 80 percent silencing at a concentration in the picomolar range, wherein said greater than 80 percent silencing endures for greater than 120 hours.
According to a sixth embodiment, the present invention provides a hyperfunctional siRNA that is capable of silencing Bcl2.
According to a seventh embodiment, the present invention provides a method for developing an siRNA algorithm for selecting functional and hyperfunctional siRNAs for a given sequence. The method comprises: (a) selecting a set of siRNAs;
(b) measuring the gene silencing ability of each siRNA from said set;
(c) determining the relative functionality of each siRNA;
(d) determining the amount of improved functionality by the presence or absence of at least one variable selected from the group consisting of the total GC content, melting temperature of the siRNA, GC content at positions 15 -19, the presence or absence of a particular nucleotide at a particular position, relative thermodynamic stability at particular positions in a duplex, and the number of times that the same nucleotide repeats within a given sequence; and
(e) developing an algorithm using the information of step (d).
According to this embodiment, preferably the set of siRNAs comprises at least 90 siRNAs from at least one gene, more preferably at least 180 siRNAs from at least two different genes, and most preferably at least 270 and 360 siRNAs from at least three and four different genes, respectively. Additionally, in step (d) the determination is made with preferably at least two, more preferably at least three, even more preferably at least four, and most preferably all of the variables. The resulting algorithm is not target sequence specific.
In another embodiment, the present invention provides rationally designed siRNAs identified using the formulas above.
In yet another embodiment, the present invention is directed to hyperfunctional siRNA.
The ability to use the above algorithms, which are not sequence or species specific, allows for the cost-effective selection of optimized siRNAs for specific target sequences. Accordingly, there will be both greater efficiency and reliability in the use of siRNA technologies .
For a better understanding of the present invention together with other and further advantages and embodiments, reference is made to the following description taken in conjunction with the examples, the scope of which is set forth in the appended claims.
BRIEF DESCRIPTION OF THE FIGURES Figure 1 shows a model for siRNA-RISC interactions. RISC has the ability to interact with either end of the siRNA or miRNA molecule. Following binding, the duplex is unwound, and the relevant target is identified, cleaved, and released.
Figure 2 is a representation of the functionality of two hundred and seventy siRNA duplexes that were generated to target human cyclophilin, human diazepam-binding inhibitor (DB), and firefly luciferase.
Figure 3a is a representation of the silencing effect of 30 siRNAs in three different cells lines, HEK293, DU 145, and HeIa. Figure 3b shows the frequency of different functional groups (>95% silencing (black), >80% silencing (gray), >50% silencing (dark gray), and <50% silencing (white)) based on GC content. In cases where a given bar is absent from a particular GC percentage, no siRNA were identified for that particular group. Figure 3c shows the frequency of different functional groups based on melting temperature (Tm).
Figure 4 is a representation of a statistical analysis that revealed correlations between silencing and five sequence-related properties of siRNA: (A) an A at position 19 of the sense strand, (B) an A at position 3 of the sense strand, (C) a U at position 10 of the sense strand, (D) a base other than G at position 13 of the sense strand, and (E) a base other than C at position 19 of the sense strand. All variables were correlated with siRNA silencing of firefly luciferase and human cyclophilin. siRNAs satisfying the criterion are grouped on the left (Selected) while those that do not, are grouped on the right (Eliminated). Y-axis is "% Silencing of Control." Each position on the X- axis represents a unique siRNA.
Figures 5 A and 5 B are representations of firefly luciferase and cyclophilin siRNA panels sorted according to functionality and predicted values using Formula VIII. The siRNA found within the circle represent those that have Formula VIII values (SMARTscores™) above zero. siRNA outside the indicated area have calculated Formula VIII values that are below zero. Y-axis is "Expression (% Control)." Each position on the X-axis represents a unique siRNA.
Figure 6 A is a representation of the average internal stability profile (AISP) derived from 270 siRNAs taken from three separate genes (cyclophilin B, DBI and firefly luciferase). Graphs represent AISP values of highly functional, functional, and non¬ functional siRNA. Figure 6B is a comparison between the AISP of naturally derived GFP siRNA (filled squares) and the AISP of siRNA from cyclophilin B, DBI, and luciferase having >90% silencing properties (no fill) for the antisense strand. "DG" is the symbol for ΔG, free energy.
Figure 7 is a histogram showing the differences in duplex functionality upon introduction of basepair mismatches. The X-axis shows the mismatch introduced in the siRNA and the position it is introduced (e.g., 8C >A reveals that position 8 (which normally has a C) has been changed to an A). The Y-axis is "% Silencing (Normalized to Control)."
Figure 8a is histogram that shows the effects of 5 'sense and antisense strand modification with 2'-O-methylation on functionality. Figure 8b is an expression profile showing a comparison of sense strand off-target effects for IGF1R-3 and 2'-O- methyl IGF1R-3. Sense strand off-targets (lower box) are not induced when the 5' end of the sense strand is modified with 2'-O-methyl groups (top box).
Figure 9 shows a graph of SMARTscores™ versus RNAi silencing values for more than 360 siRNA directed against 30 different genes. siRNA to the right of the vertical bar represent those siRNA that have desirable SMARTscores™.
Figures 1OA - E compare the RNAi of five different genes (SEAP5 DBI, PLK5 Firefly Luciferase, and Renila Luciferase) by varying numbers of randomly selected siRNA and four rationally designed (SMART-selected) siRNA chosen using the algorithm described in Formula VIII. In addition, RNAi induced by a pool of the four SMART-selected siRNA is reported at two different concentrations (100 and 40OnM). 1OF is a comparison between a pool of randomly selected EGFR siRNA (Pool 1) and a pool of SMART selected EGFR siRNA (Pool 2). Pool 1, Sl- S4 and Pool 2 Sl- S4 represent the individual members that made up each respective pool. Note that numbers for random siRNAs represent the position of the 5' end of the sense strand of the duplex. The Y-axis represents the % expression of the control(s). The X-axis is the percent expression of the control.
Figure 11 shows the Western blot results from cells treated with siRNA directed against twelve different genes involved in the clathrin-dependent endocytosis pathway (CHC, DynII, CALM, CLCa, CLCb, Epsl5, Epsl5R, Rab5a, Rab5b, Rab5c, β2 subunit of AP-2 and EEA.l). siRNA were selected using Formula VIII. "Pool" represents a mixture of duplexes 1-4. Total concentration of each siRNA in the pool is 25 nM. Total concentration = 4 x 25 = 100 nM.
Figure 12 is a representation of the gene silencing capabilities of rationally-selected siRNA directed against ten different genes (human and mouse cyclophilin, C-myc, human lamin AJC, QB (ubiquinol-cytochrome c reductase core protein I), MEKl and MEK2, ATEl (arginyl-tRNA protein transferase), GAPDH, and Eg5). The Y-axis is the percent expression of the control. Numbers 1, 2, 3 and 4 represent individual rationally selected siRNA. "Pool" represents a mixture of the four individual siRNA.
Figure 13 is the sequence of the top ten Bcl2 siRNAs as determined by Formula VIII. Sequences are listed 5' to 3'.
Figure 14 is the knockdown by the top ten Bcl2 siRNAs at 10OnM concentrations. The Y-axis represents the amount of expression relative to the non-specific (ns) and transfection mixture control.
Figure 15 represents a functional walk where siRNA beginning on every other base pair of a region of the luciferase gene are tested for the ability to silence the luciferase gene. The Y-axis represents the percent expression relative to a control. The X-axis represents the position of each individual siRNA. Figure 16 is a histogram demonstrating the inhibition of target gene expression by pools of 2 and 3 siRNAs duplexes taken from the walk described in Figure 15. The Y-axis represents the percent expression relative to control. The X-axis represents the position of the first siRNA in paired pools, or trios of siRNA. For instance, the first paired pool contains siRNA 1 and 3. The second paired pool contains siRNA 3 and 5. Pool 3 (of paired pools) contains siRNA 5 and 7, and so on.
Figure 17 is a histogram demonstrating the inhibition of target gene expression by pools of 4 and 5 siRNA duplexes. The Y-axis represents the percent expression relative to a control. The X-axis represents the position of the first siRNA in each pool.
Figure 18 is a histogram demonstrating the inhibition of target gene expression by siRNAs that are ten and twenty basepairs apart. The Y-axis represents the percent expression relative to a control. The X-axis represents the position of the first siRNA in each pool.
Figure 19 shows that pools of siRNAs (dark gray bar) work as well (or better) than the best siRNA in the pool (light gray bar). The Y-axis represents the percent expression relative to a control. The-X axis represents the position of the first siRNA in each pool.
Figure 20 shows that the combination of several semifunctional siRNAs (dark gray) result in a significant improvement of gene expression inhibition over individual (semi-functional; light gray) siRNA. The Y-axis represents the percent expression relative to a control.
Figure 21 shows both pools (Library, Lib) and individual siRNAs in inhibition of gene expression of Beta-Galactosidase, Renilla Luciferase and SEAP (alkaline phosphatase). Numbers on the X-axis indicate the position of the 5'-most nucleotide of the sense strand of the duplex. The Y-axis represents the percent expression of each gene relative to a control. Libraries contain 19 nucleotide long siRNAs (not including overhangs) that begin at the following nucleotides: SEAP: Lib 1 : 206, 766, 812,923, Lib 2: 1117, 1280, 1300, 1487, Lib 3: 206, 766, 812, 923, 1117, 1280, 1300,1487, Lib 4: 206, 812, 1117, 1300, Lib 5: 766, 923, 1280, 1487, Lib 6: 206, 1487; Bgal: Lib 1: 979, 1339, 2029, 2590, Lib 2: 1087,1783,2399,3257, Lib 3: 979, 1783, 2590, 3257, Lib 4: 979, 1087, 1339, 1783, 2029, 2399,2590,3257, Lib 5: 979, 1087, 1339, 1783, Lib 6: 2029,2399,2590,3257; Renilla: Lib 1: 174,300,432,568, Lib 2: 592, 633, 729,867, Lib 3: 174, 300, 432, 568, 592, 633,729,867, Lib 4: 174, 432, 592, 729, Lib 5: 300,568,633,867, Lib 6: 592,568.
Figure 22 shows the results of an EGFR and TfiiR internalization assay when single gene knockdowns are performed. The Y-axis represents percent internalization relative to control.
Figure 23 shows the results of an EGFR and TfnR internalization assay when multiple genes are knocked down {e.g., Rab5a, b, c). The Y-axis represents the percent internalization relative to control.
Figure 24 shows the simultaneous knockdown of four different genes. siRNAs directed against G6PD, GAPDH, PLK5 and UQCwere simultaneously introduced into cells. Twenty-four hours later, cultures were harvested and assayed for mRNA target levels for each of the four genes. A comparison is made between cells transfected with individual siRNAs vs. a pool of siRNAs directed against all four genes.
Figure 25 shows the functionality often siRNAs at 0.3nM concentrations.
DETAILED DESCRIPTION Definitions
Unless stated otherwise, the following terms and phrases have the meanings provided below:
siRNA The term "siRNA" refers to small inhibitory RNA duplexes that induce the
RNA interference (RNAi) pathway. These molecules can vary in length (generally 18-30 basepairs) and contain varying degrees of complementarity to their target mRNA in the antisense strand. Some, but not all, siRNA have unpaired overhanging bases on the 5' or 3' end of the sense strand and/or the antisense strand. The term "siRNA" includes duplexes of two separate strands, as well as single strands that can form hairpin structures comprising a duplex region.
siRNA may be divided into five (5) groups (non-functional, semi-functional, functional, highly functional, and hyper-functional) based on the level or degree of silencing that they induce in cultured cell lines. As used herein, these definitions are based on a set of conditions where the siRNA is transfected into said cell line at a concentration of 10OnM and the level of silencing is tested at a time of roughly 24 hours after transfection, and not exceeding 72 hours after transfection. hi this context, "non-functional siRNA" are defined as those siRNA that induce less than 50%
(<50%) target silencing. "Semi-functional siRNA" induce 50-79% target silencing. "Functional siRNA" are molecules that induce 80-95% gene silencing. "Highly- functional siRNA" are molecules that induce greater than 95% gene silencing. "Hyperfunctional siRNA" are a special class of molecules. For purposes of this document, hyperfunctional siRNA are defined as those molecules that: (1) induce greater than 95% silencing of a specific target when they are transfected at subnanomolar concentrations (i.e., less than one nanomolar); and/or (2) induce functional (or better) levels of silencing for greater than 96 hours. These relative functionalities (though not intended to be absolutes) may be used to compare siRNAs to a particular target for applications such as functional genomics, target identification and therapeutics.
mJRNA
The term "miRNA" refers to microRNA.
Gene silencing
The phrase "gene silencing" refers to a process by which the expression of a specific gene product is lessened or attenuated. Gene silencing can take place by a variety of pathways. Unless specified otherwise, as used herin, gene silencing refers to decreases in gene product expression that results from RNA interference (RNAi), a defined, though partially characterized pathway whereby small inhibitory RNA (siRNA) act in concert with host proteins (e.g., the RNA induced silencing complex, RISC) to degrade messenger RNA (mRNA) in a sequence-dependent fashion. The level of gene silencing can be measured by a variety of means, including, but not limited to, measurement of transcript levels by Northern Blot Analysis, B-DNA techniques, transcription-sensitive reporter constructs, expression profiling (e.g., DNA chips), and related technologies. Alternatively, the level of silencing can be measured by assessing the level of the protein encoded by a specific gene. This can be accomplished by performing a number of studies including Western Analysis, measuring the levels of expression of a reporter protein that has e.g., fluorescent properties (e.g., GFP) or enzymatic activity (e.g., alkaline phosphatases), or several other procedures.
Filters
The term "filter" refers to one or more procedures that are performed on sequences that are identified by the algorithm. In some instances, filtering includes in silico procedures where sequences identified by the algorithm can be screened to identify duplexes carrying desirable or undesirable motifs. Sequences carrying such motifs can be selected for, or selected against, to obtain a final set with the preferred properties. In other instances, filtering includes wet lab experiments. For instance, sequences identified by one or more versions of the algorithm can be screened using any one of a number of procedures to identify duplexes that have hyperfunctional traits (e.g., they exhibit a high degree of silencing at subnanomolar concentrations and/or exhibit high degrees of silencing longevity).
Transfection
The term "transfection" refers to a process by which agents are introduced into a cell. The list of agents that can be transfected is large and includes, but is not limited to, siRNA, sense and/or anti-sense sequences, DNA encoding one or more genes and organized into an expression plasmid, proteins, protein fragments, and more. There are multiple methods for transfecting agents into a cell including, but not limited to, electroporation, calcium phosphate-based transfections, DEAE-dextran- based transfections, lipid-based transfections, molecular conjugate-based transfections (e.g., polylysine-DNA conjugates), microinjection and others.
Target
The term "target" is used in a variety of different forms throughout this document and is defined by the context in which it is used. "Target rnRNA" refers to a messenger RNA to which a given siRNA can be directed against. "Target sequence" and "target site" refer to a sequence within the mRNA to which the sense strand of an siRNA shows varying degrees of homology and the antisense strand exhibits varying degrees of complementarity. The phrase "siRNA target" can refer to the gene, mRNA, or protein against which an siRNA is directed. Similarly, "target silencing" can refer to the state of a gene, or the corresponding mRNA or protein.
Off-target silencing and Off-target interference
The phrases "off-target silencing" and "off-target interference" are defined as degradation of mRNA other than the intended target mRNA due to overlapping and/or partial homology with secondary mRNA messages.
SMARTscore™
The term "SMARTscore™" refers to a number determined by applying any of the Formulas I - Formula X to a given siRNA sequence. The phrases "SMART- selected" or "rationally selected" or "rational selection" refer to siRNA that have been selected on the basis of their SMARTscores™.
Complementary The term "complementary" refers to the ability of polynucleotides to form base pairs with one another. Base pairs are typically formed by hydrogen bonds between nucleotide units in antiparallel polynucleotide strands. Complementary polynucleotide strands can base pair in the Watson-Crick manner {e.g., A to T, A to U, C to G), or in any other manner that allows for the formation of duplexes. As persons skilled in the art are aware, when using RNA as opposed to DNA, uracil rather than thymine is the base that is considered to be complementary to adenosine. However, when a U is denoted in the context of the present invention, the ability to substitute a T is implied, unless otherwise stated.
Perfect complementarity or 100% complementarity refers to the situation in which each nucleotide unit of one polynucleotide strand can hydrogen bond with a nucleotide unit of a second polynucleotide strand. Less than perfect complementarity refers to the situation in which some, but not all, nucleotide units of two strands can " hydrogen bond with each other. For example, for two 20-mers, if only two base pairs on each strand can hydrogen bond with each other, the polynucleotide strands exhibit 10% complementarity. In the same example, if 18 base pairs on each strand can hydrogen bond with each other, the polynucleotide strands exhibit 90% complementarity. "Substantial complementarity" refers to polynucleotide strands exhibiting 79% or greater complementarity, excluding regions of the polynucleotide strands, such as overhangs, that are selected so as to be noncomplementary. ("Substantial similarity" refers to polynucleotide strands exhibiting 79% or greater similarity, excluding regions of the polynucleotide strands, such as overhangs, that are selected so as not to be similar.) Thus, for example, two polynucleotides of 29 nucleotide units each, wherein each comprises a di-dT at the 3' terminus such that the duplex region spans 27 bases, and wherein 26 of the 27 bases of the duplex region on each strand are complementary, are substantially complementary since they are 96.3% complementary when excluding the di-dT overhangs.
Deoxynucleotide
The term "deoxynucleotide" refers to a nucleotide or polynucleotide lacking a hydroxyl group (OH group) at the 2' and/or 3' position of a sugar moiety. Instead, it has a hydrogen bonded to the 2' and/or 3' carbon. Within an RNA molecule that comprises one or more deoxynucleotides, "deoxynucleotide" refers to the lack of an OH group at the T position of the sugar moiety, having instead a hydrogen bonded directly to the 2' carbon.
Deoxyribonucleotide
The terms "deoxvribonucleotide" and "DNA" refer to a nucleotide or polynucleotide comprising at least one sugar moiety that has an H5 rather than an OH, at its 2' and/or 3 'position.
Substantially Similar
The phrase "substantially similar" refers to a similarity of at least 90% with respect to the identity of the bases of the sequence.
Duplex Region
The phrase "duplex region" refers to the region in two complementary or substantially complementary polynucleotides that form base pairs with one another, either by Watson-Crick base pairing or any other manner that allows for a stabilized duplex between polynucleotide strands that are complementary or substantially complementary. For example, a polynucleotide strand having 21 nucleotide units can base pair with another polynucleotide of 21 nucleotide units, yet only 19 bases on each strand are complementary or substantially complementary, such that the "duplex region" has 19 base pairs. The remaining bases may, for example, exist as 5' and 3' overhangs. Further, within the duplex region, 100% complementarity is not required; substantial complementarity is allowable within a duplex region. Substantial complementarity refers to 79% or greater complementarity. For example, a mismatch in a duplex region consisting of 19 base pairs results in 94.7% complementarity, rendering the duplex region substantially complementary.
Nucleotide
The term "nucleotide" refers to a ribonucleotide or a deoxyribonucleotide or modified form thereof, as well as an analog thereof. Nucleotides include species that comprise purines, e.g., adenine, hypoxanthine, guanine, and their derivatives and analogs, as well as pyrimidines, e.g., cytosine, uracil, thymine, and their derivatives and analogs.
Nucleotide analogs include nucleotides having modifications in the chemical structure of the base, sugar and/or phosphate, including, but not limited to, 5-position pyrimidine modifications, 8-position purine modifications, modifications at cytosine exocyclic amines, and substitution of 5-bromo-uracil; and 2'-position sugar modifications, including but not limited to, sugar-modified ribonucleotides in which the 2'-OH is replaced by a group such as an H, OR, R, halo, SH, SR, NH2, NHR, NR2, or CN, wherein R is an alkyl moiety. Nucleotide analogs are also meant to include nucleotides with bases such as inosine, queuosine, xanthine, sugars such as 2'-methyl ribose, non-natural phosphodiester linkages such as methylphosphonates, phosphorothioates and peptides.
Modified bases refer to nucleotide bases such as, for example, adenine, guanine, cytosine, thymine, uracil, xanthine, inosine, and queuosine that have been modified by the replacement or addition of one or more atoms or groups. Some examples of types of modifications that can comprise nucleotides that are modified with respect to the base moieties include but are not limited to, alkylated, halogenated, thiolated, aminated, amidated, or acetylated bases, individually or in combination. More specific examples include, for example, 5-propynyluridine, 5-propynylcytidine, 6-methyladenine, 6-metliylguanine, N,N,-dimethyladenine, 2 -propyl adenine, 2- propylguanine, 2-aminoadenine, 1-methylinosine, 3-methyluridine, 5-methylcytidine, 5-methyluridine and other nucleotides having a modification at the 5 position, 5-(2- amino)propyl uridine, 5-halocytidine, 5-halouridine, 4-acetylcytidine, 1- methyladenosine, 2-methyladenosine, 3-methylcytidine, 6-methyluridine, 2- methylguanosine, 7-methylguanosine, 2,2-dimethylguanosine, 5- methylaminoethyluridine, 5-methyloxyuridine, deazanucleotides such as 7-deaza- adenosine, 6-azouridine, 6-azocytidine, 6-azothymidine, 5-methyl-2-tbiouridine, other thio bases such as 2-tliiouridine and 4-thiouridine and 2-thiocytidine, dihydrouridine, pseudouridine, queuosine, archaeosine, naphthyl and substituted naphthyl groups, any O- and N-alkylated purines and pyrimidines such as N6-methyladenosine, 5- methylcarbonylmethyluridine, uridine 5-oxyacetic acid, ρyridine-4-one, pyridine-2- one, phenyl and modified phenyl groups such as aminophenol or 2,4,6-trimethoxy benzene, modified cytosines that act as G-clamp nucleotides, 8-substituted adenines and guanines, 5-substituted uracils and thymines, azapyrimidines, carboxyhydroxyalkyl nucleotides, carboxyalkylaminoalkyl nucleotides, and alkylcarbonylalkylated nucleotides. Modified nucleotides also include those nucleotides that are modified with respect to the sugar moiety, as well as nucleotides having sugars or analogs thereof that are not ribosyl. For example, the sugar moieties may be, or be based on, mannoses, arabinoses, glucopyranoses, galactopyranoses, 4'- thioribose, and other sugars, heterocycles, or carbocycles.
The term nucleotide is also meant to include what are known in the art as universal bases. By way of example, universal bases include but are not limited to 3- nitropyrrole, 5-nitroindole, or nebularine. The term "nucleotide" is also meant to include the N3' to P5' phosphoramidate, resulting from the substitution of a ribosyl 3' oxygen with an amine group.
Further, the term nucleotide also includes those species that have a detectable label, such as for example a radioactive or fluorescent moiety, or mass label attached to the nucleotide. Polynucleotide
The term "polynucleotide" refers to polymers of nucleotides, and includes but is not limited to DNA, RNA, DNA/RNA hybrids including polynucleotide chains of regularly and/or irregularly alternating deoxyribosyl moieties and ribosyl moieties
(i.e., wherein alternate nucleotide units have an -OH, then and -H, then an -OH, then an -H, and so on at the T position of a sugar moiety), and modifications of these kinds of polynucleotides, wherein the attachment of various entities or moieties to the nucleotide units at any position are included.
Polyribonucleotide
The term "polyribonucleotide" refers to a polynucleotide comprising two or more modified or unmodified ribonucleotides and/or their analogs. The term
"polyribonucleotide" is used interchangeably with the term "oligoribonucleotide."
Ribonucleotide and ribonucleic acid
The term "ribonucleotide" and the phrase "ribonucleic acid" (RNA), refer to a modified or unmodified nucleotide or polynucleotide comprising at least one ribonucleotide unit. A ribonucleotide unit comprises an hydroxyl group attached to the 2' position of a ribosyl moiety that has a nitrogenous base attached in N- glycosidic linkage at the 1' position of a ribosyl moiety, and a moiety that either allows for linkage to another nucleotide or precludes linkage.
DETAILED DESCRIPTION OF THE INVENTION
The present invention is directed to improving the efficiency of gene silencing by siRNA. Through the inclusion of multiple siRNA sequences that are targeted to a particular gene and/or selecting an siRNA sequence based on certain defined criteria, improved efficiency may be achieved.
The present invention will now be described in connection with preferred embodiments. These embodiments are presented in order to aid in an understanding of the present invention and are not intended, and should not be construed, to limit the invention in any way. All alternatives, modifications and equivalents that may become apparent to those of ordinary skill upon reading this disclosure are included within the spirit and scope of the present invention.
Furthermore, this disclosure is not a primer on RNA interference. Basic concepts known to persons skilled in the art have not been set forth in detail.
The present invention is directed to increasing the efficiency of RNAi, particularly in mammalian systems. Accordingly, the present invention provides kits, siRNAs and methods for increasing siRNA efficacy.
According to a first embodiment, the present invention provides a kit for gene silencing, wherein said kit is comprised of apool of at least two siRNA duplexes, each of which is comprised of a sequence that is complementary to a portion of the sequence of one or more target messenger RNA, and each of which is selected using non-target specific criteria. Each of the at least two siRNA duplexes of the kit complementary to a portion of the sequence of one or more target mRNAs is preferably selected using Formula X.
According to a second embodiment, the present invention provides a method for selecting an siRNA, said method comprising applying selection criteria to a set of potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; and determining the relative functionality of the at least two siRNAs.
In one embodiment, the present invention also provides a method wherein said selection criteria are embodied in a formula comprising:
Formula VIII: (-14)*G13-13*A1-12*U7-l l*U2-10:i:A11-10:1:U4-10:1:C3-10*C5-10*C6- 9*Alo-9nj 9-9*C18-8*Gio-7nj 1-7*Ui6-7*C17-7*C19 +7*U17+8*A2+8*A4+8*A5+8*C4+9*G8+10*A7+10*U18+l l*A19+ 11*C9+15*G1+ 18*A3+19*U10-Tm-3* (GCtotai) - 6*(GC15_i9)- 30*X; or
Formula X (-8)*Al+(-l)*A2+(12)*A3+(7)*A4+(18)*A5+(12)*A6+
(19)*A7+(6)*A8+(-4)*A9+(-5)*A10+(-2)*All+(- 5)* A12+(l 7)* Al 3+(-3)* Al 4+(4)* Al 5+(2)* Al 6+(8)* Al 7+ (ll)*A18+(30)*A19+(-13)*Ul+(-10)*U2+(2)*U3+(-2)*U4+(- 5)*U5+(5)*U6+(-2)*U7+(-10)*U8+(-5)*U9+(15)*U10+(- 1)*U1 l+(0)*U12+(10)*U13+(-9)*U14+(-13)*U15+(-
10)*U16+(3)*U17+(9)*U18+(9)*U19+(7)*Cl+(3)*C2+(- 21)*C3+(5)*C4+(-9)*C5+(-20)*C6+(-18)*C7+(- 5)*C8+(5)*C9+(l)*C10+(2):i:Cl l+(-5)*C12+(-3)*C13+(-6);f:C14+(- 2)*C15+(-5)*C16+(-3)*C17+(-12)*C18+(- 18)*C19+(14)*Gl+(8)*G2+(7)*G3+(-10)*G4+(-
4)*G5+(2)*G6+(l)*G7+(9)*G8+(5)*G9+(- 11)*G1O+(1)*G1 l+(9)*G12+(-
24)*G13+(18)*G14+(l l)*G15+(13)*G16+(-7)*G17+(-9)*G18+(- 22)*G19 + 6*(number of A+U in position 15-19) - 3*(number of G+C in whole siRNA), wherein position numbering begins at the 5 '-most position of a sense strand, and A1 = 1 if A is the base at position 1 of the sense strand, otherwise its value is 0; A2= 1 if A is the base at position 2 of the sense strand, otherwise its value is 0; A3 = 1 if A is the base at position 3 of the sense strand, otherwise its value is 0; A4 = 1 if A is the base at position 4 of the sense strand, otherwise its value is 0; A5 = 1 if A is the base at position 5 of the sense strand, otherwise its value is 0; A6= 1 if A is the base at position 6 of the sense strand, otherwise its value is 0; A7 = 1 if A is the base at position 7 of the sense strand, otherwise its value is 0; A10= 1 if A is the base at position 10 of the sense strand, otherwise its value is 0; A11 = 1 if A is the base at position 11 of the sense strand, otherwise its value is 0; A13 = 1 if A is the base at position 13 of the sense strand, otherwise its value is 0; Ai9 = 1 if A is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0; C3 = 1 if C is the base at position 3 of the sense strand, otherwise its value is 0; C4 = 1 if C is the base at position 4 of the sense strand, otherwise its value is 0; C5 = 1 if C is the base at position 5 of the sense strand, otherwise its value is 0; C6 = 1 if C is the base at position 6 of the sense strand, otherwise its value is 0; C7 = 1 if C is the base at position 7 of the sense strand, otherwise its value is 0; C9 = 1 if C is the base at position 9 of the sen^e strand, otherwise its value is 0; C17 = 1 if C is the base at position 17 of the sense strand, otherwise its value is 0; C18 = 1 if C is the base at position 18 of the sense strand, otherwise its value is 0; C19 = 1 if C is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
G1 = 1 if G is the base at position 1 on the sense strand, otherwise its value is 0; G2 = 1 if G is the base at position 2 of the sense strand, otherwise its value is 0; G8 = 1 if G is the base at position 8 on the sense strand, otherwise its value is 0; G10 = 1 if G is the base at position 10 on the sense strand, otherwise its value is 0; G13 = 1 if G is the base at position 13 on the sense strand, otherwise its value is 0; G19 = 1 if G is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
U1 = 1 if U is the base at position 1 on the sense strand, otherwise its value is 0;
U2 = 1 if U is the base at position 2 on the sense strand, otherwise its value is 0;
U3 = 1 if U is the base at position 3 on the sense strand, otherwise its value is 0;
U4 = 1 if U is the base at position 4 on the sense strand, otherwise its value is 0;
U7 = 1 if U is the base at position 7 on the sense strand, otherwise its value is 0; U9 = 1 if U is the base at position 9 on the sense strand, otherwise its value is 0;
U1O = 1 if U is the base at position 10 on the sense strand, otherwise its value is 0;
U15 = 1 if U is the base at position 15 on the sense strand, otherwise its value is 0;
U16 = 1 if U is the base at position 16 on the sense strand, otherwise its value is 0;
U17 = 1 if U is the base at position 17 on the sense strand, otherwise its value is 0; U18 = 1 if U is the base at position 18 on the sense strand, otherwise its value is 0.
GC15 _!9 = the number of G and C bases within positions 15 - 19 of the sense strand, or within positions 15 -18 if the sense strand is only 18 base pairs in length; GQotai = the number of G and C bases in the sense strand; Tm = 100 if the siRNA oligo has the internal repeat longer then 4 base pairs, otherwise its value is 0; and
X = the number of times that the same nucleotide repeats four or more times in a row.
Any of the methods of selecting siRNA in accordance with the invention can further comprise comparing the internal stability profiles of the siRNAs to be selected, and selecting those siRNAs with the most favorable internal stability profiles. Any of the methods of selecting siRNA can further comprise selecting either for or against sequences that contain motifs that induce cellular stress. Such motifs include, for example, toxicity motifs. Any of the methods of selecting siRNA can further comprise either selecting for or selecting against sequences that comprise stability motifs.
In another embodiment, the present invention provides a method of gene silencing, comprising introducing into a cell at least one siRNA selected according to any of the methods of the present invention. The siRNA can be introduced by allowing passive uptake of siRNA, or through the use of a vector.
According to a third embodiment, the invention provides a method for developing an algorithm for selecting siRNA, said method comprising: (a) selecting a set of siRNA; (b) measuring gene silencing ability of each siRNA from said set; (c) determining relative functionality of each siRNA; (d) determining improved functionality by the presence or absence of at least one variable selected from the group consisting of the presence or absence of a particular nucleotide at a particular position, the total number of As and Us in positions 15-19, the number of times that the same nucleotide repeats within a given sequence, and the total number of Gs and Cs; and (e) developing an algorithm using the information of step (d).
In another embodiment, the invention provides a method for selecting an siRNA with improved functionality, comprising using the above-mentioned algorithm to identify an siRNA of improved functionality. According to a fourth embodiment, the present invention provides a kit, wherein said kit is comprised of at least two siRNAs, wherein said at least two siRNAs comprise a first optimized siRNA and a second optimized siRNA, wherein said first optimized siRNA and said second optimized siRNA are optimized according a formula comprising Formula X.
According to a fifth embodiment, the present invention provides a method for identifying a hyperfunctional siRNA, comprising applying selection criteria to a set of potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; determining the relative functionality of the at least two siRNAs and assigning each of the at least two siRNAs a functionality score; and selecting siRNAs from the at least two siRNAs that have a functionality score that reflects greater than 80 percent silencing at a concentration in the picomolar range, wherein said greater than 80 percent silencing endures for greater than 120 hours.
In other embodiments, the invention provides kits and/or methods wherein the siRNA are comprised of two separate polynucleotide strands; wherein the siRNA are comprised of a single contiguous molecule such as, for example, a unimolecular siRNA (comprising, for example, either a nucleotide or non-nucleotide loop); wherein the siRNA are expressed from one or more vectors; and wherein two or more genes are silenced by a single administration of siRNA.
According to a sixth embodiment, the present invention provides a hyperfunctional siRNA that is capable of silencing BcI 2.
According to a seventh embodiment, the present invention provides a method for developing an siRNA algorithm for selecting functional and hyperfunctional siRNAs for a given sequence. The method comprises:
(a) selecting a set of siRNAs;
(b) measuring the gene silencing ability of each siRNA from said set;
(c) determining the relative functionality of each siRNA; (d) determining the amount of improved functionality by the presence or absence of at least one variable selected from the group consisting of the total GC content, melting temperature of the siRNA, GC content at positions 15 -19, the presence or absence of a particular nucleotide at a particular position, relative thermodynamic stability at particular positions in a duplex, and the number of times that the same nucleotide repeats within a given sequence; and
(e) developing an algorithm using the information of step (d).
According to this embodiment, preferably the set of siRNAs comprises at least 90 siRNAs from at least one gene, more preferably at least 180 siRNAs from at least two different genes,.and most preferably at least 270 and 360 siRNAs from at least three and four different genes, respectively. Additionally, in step (d) the determination is made with preferably at least two, more preferably at least three, even more preferably at least four, and most preferably all of the variables. The resulting algorithm is not target sequence specific.
In another embodiment, the present invention provides rationally designed siRNAs identified using the formulas above.
In yet another embodiment, the present invention is directed to hyperfunctional siRNA.
The ability to use the above algorithms, which are not sequence or species specific, allows for the cost-effective selection of optimized siRNAs for specific target sequences. Accordingly, there will be both greater efficiency and reliability in the use of siRNA technologies.
The methods disclosed herein can be used in conjunction with comparing internal stability profiles of selected siRNAs, and designing an siRNA with a desireable internal stability profile; and/or in conjunction with a selection either for or against sequences that contain motifs that induce cellular stress, for example, cellular toxicity. Any of the methods disclosed herein can be used to silence one or more genes by introducing an siRNA selected, or designed, in accordance with any of the methods disclosed herein. The siRNA(s) can be introduced into the cell by any method known in the art, including passive uptake or through the use of one or more vectors.
Any of the methods and kits disclosed herein can employ either unimolecular siRNAs, siRNAs comprised of two separate polynucleotide strands, or combinations thereof. Any of the methods disclosed herein can be used in gene silencing, where two or more genes are silenced by a single administration of siRNA(s). The siRNA(s) can be directed against two or more target genes, and administered in a single dose or single transfection, as the case may be.
Optimizing siRNA According to one embodiment, the present invention provides a method for improving the effectiveness of gene silencing for use to silence a particular gene through the selection of an optimal siRNA. An siRNA selected according to this method may be used individually, or in conjunction with the first embodiment, i.e., with one or more other siRNAs, each of which may or may not be selected by this criteria in order to maximize their efficiency.
The degree to which it is possible to select an siRNA for a given mRNA that maximizes these criteria will depend on the sequence of the mRNA itself. However, the selection criteria will be independent of the target sequence. According to this method, an siRNA is selected for a given gene by using a rational design. That said, rational design can be described in a variety of ways. Rational design is, in simplest terms, the application of a proven set of criteria that enhance the probability of identifying a functional or hyperfunctional siRNA. hi one method, rationally designed siRNA can be identified by maximizing one or more of the following criteria:
1. A low GC content, preferably between about 30 -52%.
2. At least 2, preferably at least 3 A or U bases at positions 15- 19 of the siRNA on the sense strand. 3. An A base at position 19 of the sense strand.
4. An A base at position 3 of the sense strand.
5. A U base at position 10 of the sense strand.
6. An A base at position 14 of the sense strand. 7. A base other than C at position 19 of the sense strand.
8. A base other than G at position 13 of the sense strand.
9. A Tm, which refers to the character of the internal repeat that results in inter- or intramolecular structures for one strand of the duplex, that is preferably not stable at greater than 50°C, more preferably not stable at . greater than 370C, even more preferably not stable at greater than 3O0C and most preferably not stable at greater than 20°C.
10. A base other than U at position 5 of the sense strand.
11. A base other than A at position 11 of the sense strand.
12. A base other than an A at position 1 of the sense strand. 13. A base other than an A at position 2 of the sense strand.
14. An A base at position 4 of the sense strand.
15. An A base at position 5 of the sense strand.
16. An A base at position 6 of the sense strand.
17. An A base at position 7 of the sense strand. 18. An A base at position 8 of the sense strand.
19. A base other than an A at position 9 of the sense strand.
20. A base other than an A at position 10 of the sense strand.
21. A base other than an A at position 11 of the sense strand.
22. A base other than an A at position 12 of the sense strand. 23. An A base at position 13 of the sense strand.
24. A base other than an A at position 14 of the sense strand.
25. An A base at position 15 of the sense strand
26. An A base at position 16 of the sense strand.
27. An A base at position 17 of the sense strand. 28. An A base at position 18 of the sense strand.
29. A base other than a U at position 1 of the sense strand.
30. A base other than a U at position 2 of the sense strand.
31. A U base at position 3 of the sense strand.
32. A base other than a U at position 4 of the sense strand. 33. A base other than a U at position 5 of the sense strand.
34. A U base at position 6 of the sense strand.
35. A base other than a U at position 7 of the sense strand.
36. A base other than a U at position 8 of the sense strand. 37. A base other than a U at position 9 of the sense strand.
38. A base other than a U at position 11 of the sense strand.
39. A U base at position 13 of the sense strand.
40. A base other than a U at position 14 of the sense strand.
41. A base other than a U at position 15 of the sense strand. 42. A base other than a U at position 16 of the sense strand.
43. A U base at position 17 of the sense strand.
44. A U base at position 18 of the sense strand.
45. A U base at position 19 of the sense strand.
46. A C base at position 1 of the sense strand. 47. A C base at position 2 of the sense strand.
48. A base other than a C at position 3 of the sense strand.
49. A C base at position 4 of the sense strand.
50. A base other than a C at position 5 of the sense strand.
51. A base other than a C at position 6 of the sense strand. 52. A base other than a C at position 7 of the sense strand.
53. A base other than a C at position 8 of the sense strand.
54. A C base at position 9 of the sense strand.
55. A C base at position 10 of the sense strand.
56. A C base at position 11 of the sense strand. 57. A base other than a C at position 12 of the sense strand.
58. A base other than a C at position 13 of the sense strand.
59. A base other than a C at position 14 of the sense strand.
60. A base other than a C at position 15 of the sense strand.
61. A base other than a C at position 16 of the sense strand. 62. A base other than a C at position 17 of the sense strand.
63. A base other than a C at position 18 of the sense strand.
64. A G base at position 1 of the sense strand.
65. A G base at position 2 of the sense strand.
66. A G base at position 3 of the sense strand. 67. A base other than a G at position 4 of the sense strand.
68. A base other than a G at position 5 of the sense strand.
69. A G base at position 6 of the sense strand.
70. A G base at position 7 of the sense strand. 71. A G base at position 8 of the sense strand.
72. A G base at position 9 of the sense strand.
73. A base other than a G at position 10 of the sense strand.
74. A G base at position 11 of the sense strand.
75. A G base at position 12 of the sense strand. 76. A G base at position 14 of the sense strand.
77. A G base at position 15 of the sense strand.
78. A G base at position 16 of the sense strand.
79. A base other than a G at position 17 of the sense strand.
80. A base other than a G at position 18 of the sense strand. 81. A base other than a G at position 19 of the sense strand.
The importance of various criteria can vary greatly. For instance, a C base at position 10 of the sense strand makes a minor contribution to duplex functionality. In contrast, the absence of a C at position 3 of the sense strand is very important. Accordingly, preferably an siRNA will satisfy as many of the aforementioned criteria as possible.
With respect to the criteria, GC content, as well as a high number of AU in positions 15-19 of the sense strand, maybe important for easement of the unwinding of double stranded siRNA duplex. Duplex unwinding has been shown to be crucial for siRNA functionality in vivo.
With respect to criterion 9, the internal structure is measured in terms of the melting temperature of the single strand of siRNA, which is the temperature at which 50% of the molecules will become denatured. With respect to criteria 2 - 8 and 10 - 11, the positions refer to sequence positions on the sense strand, which is the strand that is identical to the mRNA. In one preferred embodiment, at least criteria 1 and 8 are satisfied. In another preferred embodiment, at least criteria 7 and 8 are satisfied. In still another preferred embodiment, at least criteria 1, 8 and 9 are satisfied.
It should be noted that all of the aforementioned criteria regarding sequence position specifics are with respect to the 5' end of the sense strand. Reference is made to the sense strand, because most databases contain information that describes the information of the mRNA. Because according to the present invention a chain can be from 18 to 30 bases in length, and the aforementioned criteria assumes a chain 19 base pairs in length, it is important to keep the aforementioned criteria applicable to the correct bases.
When there are only 18 bases, the base pair that is not present is the base pair that is located at the 3' of the sense strand. When there are twenty to thirty bases present, then additional bases are added at the 5' end of the sense chain and occupy positions "1 to ~11. Accordingly, with respect to SEQ. ID NO. 0001 NNANANNNNUCNAANNNNA and SEQ. ID NO. 0028 GUCNNANANNNNUCNAANNNNA, both would have A at position 3, A at position 5, U at position 10, C at position 11, A and position 13, A and position 14 and A at position 19. However, SEQ. ID NO. 0028 would also have C at position -1 , U at position —2 and G at position -3.
For a 19 base pair siRNA, an optimal sequence of one of the strands may be represented below, where N is any base, A, C, G, or U:
SEQ.IDNO.0001. NNANANNNNUCNAANNNNA
SEQ.IDNO.0001. NNANANNNNUGNAANNNNA
SEQ.IDNO.0002. NNANANNNNUUNAANNNNA
SEQ.IDNO.0003. NNANANNNNUCNCANNNNA SEQ.IDNO.0004.NNANANNNNUGNCANNNNA
SEQ.IDNO.0005.NNANANNNNUUNCANNNNA
SEQ.IDNO.0006.NNANANNNNUCNUANNNNA
SEQ.IDNO.0007.NNANANNNNUGNUANNNNA
SEQ.IDNO.0008.NNANANNNNUUNUANNNNA SEQ.IDNO.0010.NNANCNNNNUCNAANNNNA
SEQ.IDNO.0011.NNANCNNNNUGNAANNNNA
SEQ.IDNO.0012.NNANCNNNNUUNAANNNNA
SEQ.IDNO.0013.NNANCNNNNUCNCANNNNA SEQ.IDNO.0014.NNANCNNNNUGNCANNNNA
SEQ.IDNO.0015.NNANCNNNNUUNCANNNNA
SEQ.IDNO.0016.NANCNNNNUCNUANNNNA
SEQ.IDNO.0017.NNANCNNNNUGNUANNNNA
SEQ.IDNO.0018.NNANCNNNMJUNUANNNNA SEQ.IDNO.0019.NNANGNNNNUCNAANNNNA
SEQ.IDNO.0020.NNANGNNNNUGNAANNNNA
SEQ.IDNO.0021.NNANGNNNNUUNAANNNNA
SEQ.IDNO.0022.NNANGNNNNUCNCANNNNA
SEQ.IDNO.0023.NNANGNNNNUGNCANNNNA SEQ.IDNO.0024.NNANGNNNNUUNCANNNNA
SEQ.IDNO.0025.NNANGNNNNUCNUANNNNA
SEQ.IDNO.0026.NNANGNNNNUGNUANNNNA
SEQ.IDNO.0027.NNANGNNNNNUNUANNNNA
In one embodiment, the sequence used as an siRNA is selected by choosing the siRNA that score highest according to one of the following seven algorithms that are represented by Formulas I - VII:
Formula I Relative functionality of siRNA = -(GC/3) +(AU15-19) -(Tm2o°c)*3 -(G13)*3 -(C19) +(A19)*2 +(A3) +(U10)+(A14) -(U5) -(A11)
Formula II
Relative functionality of siRNA = -(GC/3) -(AU15-19)*3 -(G13)*3 -(C19) +(A19)*2 +(A3)
Formula III
Relative functionality of siRNA = -(GC/3) +(AU15-19) -(Tm2o°c)*3 Formula IV
Relative functionality of siRNA =
-GC/2-K AU15-19)/2-(Tm20°c)*2 -(G13)*3 -(C19) +(A19)*2 +(A3) +(UW)+(A14) -(U5) - (A11)
Formula V
Relative functionality of siRNA - -(G13)*3 -(C19) +(A19)*2 +(A3) + (U1O)+(AU) -
(Us) -(A11)
Formula VI
Relative functionality of siRNA = -(G13)*3 -(C19) +(A19)*2 +(A3)
Formula VII
Relative functionality of siRNA = -(GC/2) +(AU15-19)/2 -( Tm20°c)*l -(G13)*3 -(C19) +(A19)*3 +(A3)*3 +(Uio)/2+(A14)/2 -(U5)/2 -(An)/2
In Formulas I - VII: wherein A19 = 1 if A is the base at position 19 on the sense strand, otherwise its value is O, AU15-19 = 0 - 5 depending on the number of A or U bases on the sense strand at positions 15 —19;
G13 = 1 if G is the base at position 13 on the sense strand, otherwise its value is
0;
C19 = 1 if C is the base at position 19 of the sense strand, otherwise its value is 0;
GC = the number of G and C bases in the entire sense strand;
Tm 20°c = 1 if the Tm is greater than 20°C;
A3 = 1 if A is the base at position 3 on the sense strand, otherwise its value is
0; U10 = 1 if U is the base at position 10 on the sense strand, otherwise its value is O;
A !4 = 1 if A is the base at position 14 on the sense strand, otherwise its value is O; U5 = 1 if U is the base at position 5 on the sense strand, otherwise its value is 0; and
A11 = 1 if A is the base at position 11 of the sense strand, otherwise its value is 0.
Formulas I -VII provide relative information regarding functionality. When the values for two sequences are compared for a given formula, the relative functionality is ascertained; a higher positive number indicates a greater functionality. For example, in many applications a value of 5 or greater is beneficial.
Additionally, in many applications, more than one of these formulas would provide useful information as to the relative functionality of potential siRNA sequences. However, it is beneficial to have more than one type of formula, because not every formula will be able to help to differentiate among potential siRNA sequences. For example, in particularly high GC mRNAs, formulas that take that parameter into account would not be useful and application of formulas that lack GC elements (e.g., formulas V and VI) might provide greater insights into duplex functionality. Similarly, formula II might by used in situations where hairpin structures are not observed in duplexes, and formula IV might be applicable for sequences that have higher AU content. Thus, one may consider a particular sequence in light of more than one or even all of these algorithms to obtain the best differentiation among sequences. In some instances, application of a given algorithim may identify an unususally large number of potential siRNA sequences, and in those cases, it may be appropriate to re-analyze that sequence with a second algorithm that is, for instance, more stringent. Alternatively, it is conceivable that analysis of a sequence with a given formula yields no acceptable siRNA sequences (i.e., low SMARTscores™). In this instance, it may be appropriate to re-analyze that sequences with a second algorithm that is, for instance, less stringent. In still other instances, analysis of a single sequence with two separate formulas may give rise to conflicting results (i.e., one formula generates a set of siRNA with high SMARTscores™ while the other formula identifies a set of siRNA with low SMARTscores™). hi these instances, it may be necessary to determine which weighted factor(s) (e.g., GC content) are contributing to the discrepancy and assessing the sequence to decide whether these factors should or should not be included. Alternatively, the sequence could be analyzed by a third, fourth, or fifth algorithm to identify a set of rationally designed siRNA.
The above-referenced criteria are particularly advantageous when used in combination with pooling techniques as depicted in Table I:
Figure imgf000037_0001
The term "current" used in Table I refers to TuschFs conventional siRNA parameters (Elbashir, S.M. et al. (2002) "Analysis of gene function in somatic mammalian cells using small interfering RNAs" Methods 26: 199-213). "New" refers to the design parameters described in Formulas I- VII. "GC" refers to criteria that select siRNA solely on the basis of GC content.
As Table I indicates, when more functional siRNA duplexes are chosen, siRNAs that produce <70% silencing drops from 23% to 8% and the number of siRNA duplexes that produce >80% silencing rises from 50% to 88.5%. Further, of the siRNA duplexes with >80% silencing, a larger portion of these siRNAs actually silence >95% of the target expression (the new criteria increases the portion from 33% to 50%). Using this new criteria in pooled siRNAs, shows that, with pooling, the amount of silencing >95% increases from 79.5% to 93.8% and essentially eliminates any siRNA pool from silencing less than 70%.
Table II similarly shows the particularly beneficial results of pooling in combination with the aforementioned criteria. However, Table II, which takes into account each of the aforementioned variables, demonstrates even a greater degree of improvement in functionality.
Figure imgf000038_0001
The terms "functional," "Average," and "Non-functional" used in Table II, refer to siRNA that exhibit >80%, >50%, and <50% functionality, respectively. Criteria 1 and 4 refer to specific criteria described above.
The above-described algorithms may be used with or without a computer program that allows for the inputting of the sequence of the mRNA and automatically outputs the optimal siRNA. The computer program may, for example, be accessible from a local terminal or personal computer, over an internal network or over the Internet.
In addition to the formulas above, more detailed algorithms may be used for selecting siRNA. Preferably, at least one RNA duplex of 18-30 base pairs is selected such that it is optimized according a formula selected from:
Formula VIII: (-14)*G13-13:lϊA1-12*U7-ll*U2-10*A11-10!i:U4-10*C3-10:!;C5-10:i:C6-
9*Ai0-9πj 9-9*C18-8*G10-7HJ1-7*U16-7*C17-7*C19 +7*U17+8*A2+8*A4 +8*A5+8*C4 +9*G8 +10*A7+10*U18+l 1 *A19+ l l*C9+15*Gi+ 18*A3+19*U10-Tm-3* (GCtotai) - 6*(GC15 --19)- 30*X; and
Formula IX: (14.1) *A3+(14.9) *A6+(17.6) *A13+(24.7) *A19+(14.2) *U10+(10.5) * C9+(23.9)*G1+(16.3)*G2+(-12.3)*Aπ+(-19.3)*Uj+(-12.1)*U2+ (-l l)*U3+(-15.2)*Ui5+(-11.3)*U16 + (-11.8)*C3+(-17.4):i:C6+(- 10.5)*C7+ (-13.7)*G13+(-25.9)*G19-Tin-3* (GCtotal) - 6*(GC15_19)- 30*X; and
Formula X
(-8)*Al+(-l)*A2+(12)*A3+(7)*A4+(18)*A5+(12)*A6+
(19)*A7+(6)*A8+(-4)*A9+(-5)*A10+(-2)*All+(-
5)*A12+(17)*A13+(-3)*A14+(4)*A15+(2)*A16+(8)*A17+
(ll)*A18+(30)*A19+(-13)*UH-(-10)*U2+(2)*U3+(-2):|:U4+(-
5)*U5+(5)*U6+(-2)*U7+(- 10)*U8+(-5)*U9+(l 5)*U10+(- l)*Ul l+(0)*U12+(10)*U13+(-9)*U14+(-13)*U15+(-
10)*U16+(3)*U17+(9)*U18+(9)*U19+(7):i:Cl+(3)*C2+(-
21)*C3+(5)*C4+(-9)*C5+(-20)*C6+(-18)*C7+(-
5)*C8+(5)*C94<l)*C10+(2)*α i+(-5)*C12+(-3)*C13+(-6)*C14+(-
2)*C15+(-5)*C16+(-3)*C17+(-12)*C18+(-
18)*C19+(14)*Gl+(8)*G2+(7)*G3+(-10)*G4+(-
4)*G5+(2)*G6+(l)*G7+(9)*G8+(5)*G9+(-
1 l)*G10+(l)*Gl l+(9)*G12+(-
24)*G13+(18)*G14+(ll)*G15+(13)*G16+(-7)*G17+(-9)*G18+(-
22)*G19 + 6*(number of A+U in position 15-19) - 3*(number of G+C in whole siRNA).
wherein
A1 = 1 if A is the base at position 1 of the sense strand, otherwise its value is 0;
A2 = 1 if A is the base at position 2 of the sense strand, otherwise its value is 0; A3 = 1 if A is the base at position 3 of the sense strand, otherwise its value is 0;
A4 = 1 if A is the base at position 4 of the sense strand, otherwise its value is 0;
A5 = 1 if A is the base at position 5 of the sense strand, otherwise its value is 0;
A6 = 1 if A is the base at position 6 of the sense strand, otherwise its value is 0;
A7 = 1 if A is the base at position 7 of the sense strand, otherwise its value is 0; A1O = 1 if A is the base at position 10 of the sense strand, otherwise its value is 0;
A11 = 1 if A is the base at position 11 of the sense strand, otherwise its value is 0;
A13 = 1 if A is the base at position 13 of the sense strand, otherwise its value is 0;
Ai9 = 1 if A is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0; C3 = 1 if C is the base at position 3 of the sense strand, otherwise its value is 0; C4 = 1 if C is the base at position 4 of the sense strand, otherwise its value is 0; C5 = 1 if C is the base at position 5 of the sense strand, otherwise its value is 0; C6 = 1 if C is the base at position 6 of the sense strand, otherwise its value is 0; C7 = 1 if C is the base at position 7 of the sense strand, otherwise its value is 0; C9 = 1 if C is the base at position 9 of the sense strand, otherwise its value is 0; C17 = 1 if C is the base at position 17 of the sense strand, otherwise its value is 0; C18 = 1 if C is the base at position 18 of the sense strand, otherwise its value is 0; C19 = 1 if C is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
G1 = 1 if G is the base at position 1 on the sense strand, otherwise its value is 0;
G2 = 1 if G is the base at position 2 of the sense strand, otherwise its value is 0; G8 = 1 if G is the base at position 8 on the sense strand, otherwise its value is 0;
G1O= 1 if G is the base at position 10 on the sense strand, otherwise its value is 0;
G13 = 1 if G is the base at position 13 on the sense strand, otherwise its value is 0;
G19 = 1 if G is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
U1 = 1 if U is the base at position 1 on the sense strand, otherwise its value is 0;
U2 = 1 if U is the base at position 2 on the sense strand, otherwise its value is 0;
U3 = 1 if U is the base at position 3 on the sense strand, otherwise its value is 0;
U4 = 1 if U is the base at position 4 on the sense strand, otherwise its value is 0; U7 = 1 if U is the base at position 7 on the sense strand, otherwise its value is 0;
U9 = 1 if U is the base at position 9 on the sense strand, otherwise its value is 0;
U10 = 1 if U is the base at position 10 on the sense strand, otherwise its value is 0;
U15 = 1 if U is the base at position 15 on the sense strand, otherwise its value is 0;
U16 = 1 if U is the base at position 16 on the sense strand, otherwise its value is 0; U17 = 1 if U is the base at position 17 on the sense strand, otherwise its value is 0;
U18 = 1 if U is the base at position 18 on the sense strand, otherwise its value is 0;
GC15_19 = the number of G and C bases within positions 15 - 19 of the sense strand, or within positions 15 -18 if the sense strand is only 18 base pairs in length; GCtotai = the number of G and C bases in the sense strand;
Tm = 100 if the siRNA oligo has the internal repeat longer then 4 base pairs, otherwise its value is 0; and
X = the number of times that the same nucleotide repeats four or more times in a row.
The above formulas VIII, IX, and X, as well as formulas I - VII, provide methods for selecting siRNA in order to increase the efficiency of gene silencing. A subset of variables of any of the formulas may be used, though when fewer variables are used, the optimization hierarchy becomes less reliable.
With respect to the variables of the above-referenced formulas, a single letter of A or C or G or U followed by a subscript refers to a binary condition. The binary condition is that either the particular base is present at that particular position (wherein the value is "1") or the base is not present (wherein the value is "0").
Because position 19 is optional, i.e., there might be only 18 base pairs, when there are only 18 base pairs, any base with a subscript of 19 in the formulas above would have a zero value for that parameter. Before or after each variable is a number followed by *, which indicates that the value of the variable is to be multiplied or weighed by that number.
The numbers preceding the variables A, or G, or C, or U in Formulas VIII, IX, and X (or after the variables in Formula I - VII) were determined by comparing the difference in the frequency of individual bases at different positions in functional siRNA and total siRNA. Specifically, the frequency in which a given base was observed at a particular position in functional groups was compared with the frequency that that same base was observed in the total, randomly selected siRNA set. If the absolute value of the difference between the functional and total values was found to be greater than 6%, that parameter was included in the equation. Thus, for instance, if the frequency of finding a "G" at position 13 (G13) is found to be 6% in a given functional group, and the frequency of Gi3 in the total population of siRNAs is 20%, the difference between the two values is 6%-20% = -14%. As the absolute value is greater than six (6), this factor (-14) is included in the equation. Thus, in Formula VIII, in cases where the siRNA under study has a G in position 13, the accrued value is (-14) * (1) = -14. In contrast, when a base other than G is found at position 13, the accrued value is (-14) * (0) = 0.
When developing a means to optimize siRNAs, the inventors observed that a bias toward low internal thermodynamic stability of the duplex at the 5'-antisense (AS) end is characteristic of naturally occurring miRNA precursors. The inventors extended this observation to siRNAs for which functionality had been assessed in tissue culture.
With respect to the parameter GC15-19, a value of 0 - 5 will be ascribed depending on the number of G or C bases at positions 15 to 19. If there are only 18 base pairs, the value is between 0 and 4.
With respect to the criterion GCtotai content, a number from 0 - 30 will be ascribed, which correlates to the total number of G and C nucleotides on the sense strand, excluding overhangs. Without wishing to be bound by any one theory, it is postulated that the significance of the GC content (as well as AU content at positions 15-19, which is a parameter for formulas III - VII) relates to the easement of the unwinding of a double-stranded siRNA duplex. Duplex unwinding is believed to be crucial for siRNA functionality in vivo and overall low internal stability, especially low internal stability of the first unwound base pair is believed to be important to maintain sufficient processivity of RISC complex-induced duplex unwinding. If the duplex has 19 base pairs, those at positions 15-19 on the sense strand will unwind first if the molecule exhibits a sufficiently low internal stability at that position. As persons skilled in the art are aware, RISC is a complex of approximately twelve proteins; Dicer is one, but not the only, helicase within this complex. Accordingly, although the GC parameters are believed to relate to activity with Dicer, they are also important for activity with other RISC proteins.
The value of the parameter Tm is 0 when there are no internal repeats longer than (or equal to) four base pairs present in the siRNA duplex; otherwise the value is 1. Thus for example, if the sequence ACGUACGU, or any other four nucleotide (or more) palindrome exists within the structure, the value will be one (1). Alternatively if the structure ACGGACG, or any other 3 nucleotide (or less) palindrome exists, the value will be zero (0).
The variable "X" refers to the number of times that the same nucleotide occurs contiguously in a stretch of four or more units. If there are, for example, four contiguous As in one part of the sequence and elsewhere in the sequence four contiguous Cs, X = 2. Further, if there are two separate contiguous stretches of four of the same nucleotides or eight or more of the same nucleotides in a row, then X = 2. However, X does not increase for five, six or seven contiguous nucleotides.
Again, when applying Formula VIII, Formula IX, or Formula X, to a given mRNA, (the "target RNA" or "target molecule"), one may use a computer program to evaluate the criteria for every sequence of 18 - 30 base pairs or only sequences of a fixed length, e.g., 19 base pairs. Preferably the computer program is designed such that it provides a report ranking of all of the potential siRNAs 18-30 base pairs, ranked according to which sequences generate the highest value. A higher value refers to a more efficient siRNA for a particular target gene. The computer program that may be used may be developed in any computer language that is known to be useful for scoring nucleotide sequences, or it may be developed with the assistance of commercially available product such as Microsoft's product.net. Additionally, rather than run every sequence through one and/or another formula, one may compare a subset of the sequences, which may be desirable if for example only a subset are available. For instance, it may be desirable to first perform a BLAST (Basic Local Alignment Search Tool) search and to identify sequences that have no homology to other targets. Alternatively, it may be desirable to scan the sequence and to identify regions of moderate GC context, then perform relevant calculations using one of the above-described formulas on these regions. These calculations can be done manually or with the aid of a computer.
As with Formulas I - VII, either Formula VIII, Formula IX, or Formula X may be used for a given mRNA target sequence. However, it is possible that according to one or the other formula more than one siRNA will have the same value. Accordingly, it is beneficial to have a second formula by which to differentiate sequences. Formulas IX and X were derived in a similar fashion as Formula VIII, yet used a larger data set and thus yields sequences with higher statistical correlations to highly functional duplexes. The sequence that has the highest value ascribed to it may be referred to as a "first optimized duplex." The sequence that has the second highest value ascribed to it may be referred to as a "second optimized duplex." Similarly, the sequences that have the third and fourth highest values ascribed to them may be referred to as a third optimized duplex and a fourth optimized duplex, respectively. When more than one sequence has the same value, each of them may, for example, be referred to as first optimized duplex sequences or co-first optimized duplexes. Formula X is similar to Formula IX, yet uses a greater numbers of variables and for that reason, identifies sequences on the basis of slightly different criteria.
It should also be noted that the output of a particular algorithm will depend on several of variables including: (1) the size of the data base(s) being analyzed by the algorithm, and (2) the number and stringency of the parameters being applied to screen each sequence. Thus, for example, in US Patent Application Serial No. 10/714,333, entitled "Functional and Hyperfunctional siRNA," filed November 14, 2003, Formula VIII was applied to the known human genome (ncbi refseq database) through Entrez (efetch). As a result of these procedures, roughly 1.6 million siRNA sequences were identified. Application of Formula VIII to the same database in
March of 2004 yielded roughly 2.2 million sequences, a difference of approximately 600,000 sequences resulting from the growth of the database over the course of the months that span this period of time. Application of other formulas (e.g., Formula X) that change the emphasis of, include, or eliminate different variables can yield unequal numbers of siRNAs. Alternatively, in cases where application of one formula to one or more genes fails to yield sufficient numbers of siRNAs with scores that would be indicative of strong silencing, said genes can be reassessed with a second algorithm that is, for instance, less stringent.
siRNA sequences identified using Formula VIII and Formula X (minus sequences generated by Formula VIII) are contained within the enclosed compact disks. The data included on the enclosed compact disks is described more fully below. The sequences identified by Formula VIII and Formula X that are disclosed in the compacts disks may be used in gene silencing applications. It should be noted that for Formulas VIII, IX, and X all of the aforementioned criteria are identified as positions on the sense strand when oriented in the 5' to 3' direction as they are identified in connection with Formulas I — VII unless otherwise specified.
Formulas I - X, may be used to select or to evaluate one, or more than one, siRNA in order to optimize silencing. Preferably, at least two optimized siRNAs that have been selected according to at least one of these formulas are used to silence a gene, more preferably at least three and most preferably at least four. The siRNAs may be used individually or together in a pool or kit. Further, they may be applied to a cell simultaneously or separately. Preferably, the at least two siRNAs are applied simultaneously. Pools are particularly beneficial for many research applications. However, for therapeutics, it may be more desirable to employ a single hyperfunctional siRNA as described elsewhere in this application.
When planning to conduct gene silencing, and it is necessary to choose between two or more siRNAs, one should do so by comparing the relative values when the siRNA are subjected to one of the formulas above. In general a higher scored siRNA should be used.
Useful applications include, but are not limited to, target validation, gene functional analysis, research and drug discovery, gene therapy and therapeutics. Methods for using siRNA in these applications are well known to persons of skill in the art.
Because the ability of siRNA to function is dependent on the sequence of the RNA and not the species into which it is introduced, the present invention is applicable across a broad range of species, including but not limited to all mammalian species, such as humans, dogs, horses, cats, cows, mice, hamsters, chimpanzees and gorillas, as well as other species and organisms such as bacteria, viruses, insects, plants and C. elegans. The present invention is also applicable for use for silencing a broad range of genes, including but not limited to the roughly 45,000 genes of a human genome, and has particular relevance in cases where those genes are associated with diseases such as diabetes, Alzheimer's, cancer, as well as all genes in the genomes of the aforementioned organisms.
The siRNA selected according to the aforementioned criteria or one of the aforementioned algorithms are also, for example, useful in the simultaneous screening and functional analysis of multiple genes and gene families using high throughput strategies, as well as in direct gene suppression or silencing.
Development of the Algorithms
To identify siRNA sequence features that promote functionality and to quantify the importance of certain currently accepted conventional factors — such as G/C content and target site accessibility — the inventors synthesized an siRNA panel consisting of 270 siRNAs targeting three genes, Human Cyclophilin, Firefly Luciferase, and Human DBI. In all three cases, siRNAs were directed against specific regions of each gene. For Human Cyclophilin and Firefly Luciferase, ninety siRNAs were directed against a 199 bp segment of each respective mRNA. For DBI, 90 siRNAs were directed against a smaller, 109 base pair region of the mRNA. The sequences to which the siRNAs were directed are provided below.
It should be noted that in certain sequences, "t" is present. This is because many databases contain information in this manner. However, the t denotes a uracil residue in mRNA and siRNA. Any algorithm will, unless otherwise specified, process a t in a sequence as a u.
Human cvclophilin: 193—390, M60857
SEQ. ID NO. 29: gttccaaaaacagtggataattttgtggccttagctacaggagagaaaggatttggctacaaaaacagcaaattccatcgtgt aatcaaggacttcatgatccagggcggagacttcaccaggggagatggcacaggaggaaagagcatctacggtgagcg cttccccgatgagaacttcaaactgaagcactacgggcctggctggg
Firefly luciferase: 1434 — 1631. U47298 foGL3. Promega) SEQ. ID NO. 30: tgaacttcccgccgccgttgttgttttggagcacggaaagacgatgacggaaaaagagatcgtggattacgtcgccagtca agtaacaaccgcgaaaaagttgcgcggaggagttgtgtttgtggacgaagtaccgaaaggtcttaccggaaaactcgacg caagaaaaatcagagagatcctcataaaggccaagaagg
DBL NM 020548 ( 202-310) (every position)
SEQ. ID NO. 0031: acgggcaaggccaagtgggatgcctggaatgagctgaaagggacttccaaggaagatgccatgaaagcttacatcaaca aagtagaagagctaaagaaaaaatacggg
A list of the siRNAs appears in Table III (see Examples Section, Example II)
The set of duplexes was analyzed to identify correlations between siRNA functionality and other biophysical or thermodynamic properties. When the siRNA panel was analyzed in functional and non-functional subgroups, certain nucleotides were much more abundant at certain positions in functional or non-functional groups. More specifically, the frequency of each nucleotide at each position in highly functional siRNA duplexes was compared with that of nonfunctional duplexes in order to assess the preference for or against any given nucleotide at every position. These analyses were used to determine important criteria to be included in the siRNA algorithms (Formulas VIII, IX, and X).
The data set was also analyzed for distinguishing biophysical properties of siRNAs in the functional group, such as optimal percent of GC content, propensity for internal structures and regional thermodynamic stability. Of the presented criteria, several are involved in duplex recognition, RISC activation/duplex unwinding, and target cleavage catalysis.
The original data set that was the source of the statistically derived criteria is shown in Figure 2. Additionally, this figure shows that random selection yields siRNA duplexes with unpredictable and widely varying silencing potencies as measured in tissue culture using HEK293 cells. In the figure, duplexes are plotted such that each x-axis tick-mark represents an individual siRNA, with each subsequent siRNA differing in target position by two nucleotides for Human Cyclophilin B and Firefly Luciferase, and by one nucleotide for Human DBI. Furthermore, the y-axis denotes the level of target expression remaining after transfection of the duplex into cells and subsequent silencing of the target.
siRNA identified and optimized in this document work equally well in a wide range of cell types. Figure 3a shows the evaluation of thirty siRNAs targeting the DBI gene in three cell lines derived from different tissues. Each DBI siRNA displays very similar functionality in HEK293 (ATCC, CRL-1573, human embryonic kidney), HeLa (ATCC, CCL-2, cervical epithelial adenocarcinoma) and DU 145 (HTB-81, prostate) cells as deterimined by the B-DNA assay. Thus, siRNA functionality is determined by the primary sequence of the siRNA and not by the intracellular environment. Additionally, it should be noted that although the present invention provides for a determination of the functionality of siRNA for a given target, the same siRNA may silence more than one gene. For example, the complementary sequence of the silencing siRNA may be present in more than one gene. Accordingly, in these circumstances, it may be desirable not to use the siRNA with highest SMARTscore™. In such circumstances, it may be desirable to use the siRNA with the next highest SMARTscore™.
To determine the relevance of G/C content in siRNA function, the G/C content of each duplex in the panel was calculated and the functional classes of siRNAs (<F50, > F50, > F80, > F95 where F refers to the percent gene silencing) were sorted accordingly. The majority of the highly-functional siRNAs (>F95) fell within the G/C content range of 36% — 52% (Figure 3B). Twice as many non-functional (< F50) duplexes fell within the high G/C content groups (>57% GC content) compared to the 36% — 52% group. The group with extremely low GC content (26% or less) contained a higher proportion of non-functional siRNAs and no highly- functional siRNAs. The G/C content range of 30% — 52% was therefore selected as Criterion I for siRNA functionality, consistent with the observation that a G/C range 30% — 70% promotes efficient RNAi targeting. Application of this criterion alone provided only a marginal increase in the probability of selecting functional siRNAs from the panel: selection of F50 and F95 siRNAs was improved by 3.6% and 2.2%, respectively. The siRNA panel presented here permitted a more systematic analysis and quantification of the importance of this criterion than that used previously. A relative measure of local internal stability is the A/U base pair (bp) content; therefore, the frequency of A/U bp was determined for each of the five terminal positions of the duplex (5' sense (S)/5' antisense (AS)) of all siRNAs in the panel. Duplexes were then categorized by the number of A/U bp in positions 1 — 5 and 15 — 19 of the sense strand. The thermodynamic flexibility of the duplex 5'-end (positions 1 — 5; S) did not appear to correlate appreciably with silencing potency, while that of the 3'-end (positions 15 — 19; S) correlated with efficient silencing. No duplexes lacking A/U bp in positions 15 — 19 were functional. The presence of one A/U bp in this region conferred some degree of functionality, but the presence of three or more A/Us was preferable and therefore defined as Criterion II. When applied to the test panel, only a marginal increase in the probability of functional siRNA selection was achieved: a 1.8% and 2.3% increase for F50 and F95 duplexes, respectively (Table IV).
The complementary strands of siRNAs that contain internal repeats or palindromes may form internal fold-back structures. These hairpin-like structures exist in equilibrium with the duplexed form effectively reducing the concentration of functional duplexes. The propensity to form internal hairpins and their relative stability can be estimated by predicted melting temperatures. High Tm reflects a tendency to form hairpin structures. Lower Tm values indicate a lesser tendency to form hairpins. When the functional classes of siRNAs were sorted by Tm (Figure 3c), the following trends were identified: duplexes lacking stable internal repeats were the most potent silencers (no F95 duplex with predicted hairpin structure Tw > 60 0C). In contrast, about 60% of the duplexes in the groups having internal hairpins with calculated TTO values less than 20 0C were F80. Thus, the stability of internal repeats is inversely proportional to the silencing effect and defines Criterion III (predicted hairpin structure TOT < 20 0C).
Sequence-based determinants of siRNA functionality
When the siRNA panel was sorted into functional and non-functional groups, the frequency of a specific nucleotide at each position in a functional siRNA duplex was compared with that of a nonfunctional duplex in order to assess the preference for or against a certain nucleotide. Figure 4 shows the results of these queries and the subsequent resorting of the data set (from Figure T). The data is separated into two sets: those duplexes that meet the criteria, a specific nucleotide in a certain position - grouped on the left (Selected) and those that do not - grouped on the right (Eliminated). The duplexes are further sorted from most functional to least functional with the y-axis of Figure 4a-e representing the % expression i.e., the amount of silencing that is elicited by the duplex (Note: each position on the X-axis represents a different duplex). Statistical analysis revealed correlations between silencing and several sequence-related properties of siRNAs. Figure 4 and Table IV show quantitative analysis for the following five sequence-related properties of siRNA: (A) an A at position 19 of the sense strand; (B) an A at position 3 of the sense strand; (C) a U at position 10 of the sense strand; (D) a base other than G at position 13 of the sense strand; and (E) a base other than C at position 19 of the sense strand.
When the siRNAs in the panel were evaluated for the presence of an A at position 19 of the sense strand, the percentage of non-functional duplexes decreased from 20% to 11.8%, and the percentage of F95 duplexes increased from 21.7% to 29.4% (Table FV). Thus, the presence of an A in this position defined Criterion IV.
Another sequence-related property correlated with silencing was the presence of an A in position 3 of the sense strand (Figure 4b). Of the siRNAs with A3, 34.4% were F95, compared with 21.7% randomly selected siRNAs. The presence of a U base in position 10 of the sense strand exhibited an even greater impact (Figure 4c). Of the duplexes in this group, 41.7% were F95. These properties became criteria V and VI, respectively.
Two negative sequence-related criteria that were identified also appear on Figure 4. The absence of a G at position 13 of the sense strand, conferred a marginal increase in selecting functional duplexes (Figure 4d). Similarly, lack of a C at position 19 of the sense strand also correlated with functionality (Figure 4e). Thus, among functional duplexes, position 19 was most likely occupied by A, and rarely occupied by C. These rules were defined as criteria VII and VIII, respectively.
Application of each criterion individually provided marginal but statistically significant increases in the probability of selecting a potent siRNA. Although the results were informative, the inventors sought to maximize potency and therefore consider multiple criteria or parameters. Optimization is particularly important when developing therapeutics. Interestingly, the probability of selecting a functional siRNA based on each thermodynamic criteria was 2% — 4% higher than random, but 4% — 8% higher for the sequence-related determinates. Presumably, these sequence-related increases reflect the complexity of the RNAi mechanism and the multitude of protein- RNA interactions that are involved in RNAi-mediated silencing.
Table IV
Improvement
Criterion % Functional over Random
I. 30%— 52% G/C content < F50 16.4% -3.6%
> F50 83.6% 3.6%
> F80 60.4% 4.3%
> F95 23.9% 2.2%
Jl. At least 3 A/U bases at positions < F50 18.2% -1.8%
15 — 19 of the sense strand > F50 81.8% 1.8%
> F80 59.7% 3.6%
> F95 24.0% 2.3%
III. Absence of internal repeats, < F50 16.7% -3.3% as measured by Tm of > F50 83.3% 3.3% secondary structure < 2O0C > F80 61.1% 5.0%
> F95 24.6% 2.9%
IV. An A base at position 19 < F50 11.8% -8.2% of the sense strand > F50 88.2% 8.2%
> F80 75.0% 18.9%
> F95 29.4% 7.7%
V. An A base at position 3 < F50 17.2% -2.8% of the sense strand > F50 82.8% 2.8%
> F80 62.5% 6.4%
> F95 34.4% 12.7%
Vl. A U base at position 10 < F50 13.9% -6.1% of the sense strand > F50 86.1% 6.1%
> F80 69.4% 13.3%
> F95 41.7% 20%
VII. A base other than C at < F50 18.8% -1.2% position 19 of the sense strand > F50 81.2% 1.2%
> F80 59.7% 3.6%
> F95 24.2% 2.5%
VIII. A base other than G at < F50 15.2% -4.8% position 13 of the sense strand > F50 84.8% 4.8%
> F80 61.4% 5.3%
> F95 26.5% 4.8%
The siRNA selection algorithm
In an effort to improve selection further, all identified criteria, including but not limited to those listed in Table IV were combined into the algorithms embodied in Formula VIII, Formula IX, and Formula X. Each siRNA was then assigned a score (referred to as a SMARTscore™) according to the values derived from the formulas. Duplexes that scored higher than 0 or -20 (unadjusted), for Formulas VIII and IX, respectively, effectively selected a set of functional siRNAs and excluded all non¬ functional siRNAs. Conversely, all duplexes scoring lower than 0 and -20 (minus 20) according to formulas VIII and IX, respectively, contained some functional siRNAs but included all non-functional siRNAs. A graphical representation of this selection is shown in Figure 5. It should be noted that the scores derived from the algorithm can also be provided as "adjusted" scores. To convert Formula VIII unadjusted scores into adjusted scores it is necessary to use the following equation:
(160 + unadjusted score) / 2.25
When this takes place, an unadjusted score of "0" (zero) is converted to 75. Similarly, unadjusted scores for Formula X can be converted to adjusted scores. In this instance, the following equation is applied:
(228 + unadjusted score) / 3.56
When these manipulations take place, an unadjusted score of 38 is converted to an adjusted score of 75.
The methods for obtaining the seven criteria embodied in Table IV are illustrative of the results of the process used to develop the information for Formulas VIII, IX, and X. Thus similar techniques were used to establish the other variables and their multipliers. As described above, basic statistical methods were use to determine the relative values for these multipliers.
To determine the value for "Improvement over Random" the difference in the frequency of a given attribute (e.g., GC content, base preference) at a particular position is determined between individual functional groups (e.g., <F50) and the total siRNA population studied (e.g., 270 siRNA molecules selected randomly). Thus, for instance, in Criterion I (30%-52% GC content) members of the <F50 group were observed to have GC contents between 30-52% in 16.4% of the cases. In contrast, the total group of 270 siRNAs had GC contents in this range, 20% of the time. Thus for this particular attribute, there is a small negative correlation between 30%-52% GC content and this functional group (i.e., 16.4%-20% = -3.6%). Similarly, for Criterion VI, (a "U" at position 10 of the sense strand), the >F95 group contained a "U" at this position 41.7% of the time. In contrast, the total group of 270 siRNAs had a "U" at this position 21.7% of the time, thus the improvement over random is calculated to be 20% (or 41.7%-21.7%).
Identifying The Average Internal Stability Profile of Strong siRNA In order to identify an internal stability profile that is characteristic of strong siRNA, 270 different siRNAs derived from the cyclophilin B, the diazepam binding inhibitor (DBI), and the luciferase gene were individually transfected into HEK293 cells and tested for their ability to induce RNAi of the respective gene. Based on their performance in the in vivo assay, the sequences were then subdivided into three groups, (i) >95% silencing; (ii) 80-95% silencing; and (iii) less than 50% silencing. Sequences exhibiting 51-84% silencing were eliminated from further consideration to reduce the difficulties in identifying relevant thermodynamic patterns.
Following the division of siRNA into three groups, a statistical analysis was performed on each member of each group to determine the average internal stability profile (AISP) of the siRNA. To accomplish this the Oligo 5.0 Primer Analysis Software and other related statistical packages {e.g., Excel) were exploited to determine the internal stability of pentamers using the nearest neighbor method described by Freier et al., (1986) Improved fi'ee-energy parameters for predictions of RNA duplex stability, Proc Natl. Acad. Sci. U. S. A. 83(24): 9373-7. Values for each group at each position were then averaged, and the resulting data were graphed on a linear coordinate system with the Y-axis expressing the ΔG (free energy) values in kcal/mole and the X-axis identifying the position of the base relative to the 5' end.
The results of the analysis identified multiple key regions in siRNA molecules that were critical for successful gene silencing. At the 3 '-most end of the sense strand (5'antisense), highly functional siRNA (>95% gene silencing, see Figure 6a, >F95) have a low internal stability (AISP of position 19 = ~ -7.6kcal/mol). hi contrast low- efficiency siRNA (i.e., those exhibiting less than 50% silencing, <F50) display a distinctly different profile, having high ΔG values (~ -8.4kcal/mol) for the same position. Moving in a 5' (sense strand) direction, the internal stability of highly efficient siRNA rises (position 12 = ~ -8.3kcal/mole) and then drops again (position 7 = ~ -7.7kcal/mol) before leveling off at a value of approximately -8. lkcal/mol for the 5' terminus. siRNA with poor silencing capabilities show a distinctly different profile. While the AISP value at position 12 is nearly identical with that of strong siRNAs, the values at positions 7 and 8 rise considerably, peaking at a high of- -9.0 kcal/mol. In addition, at the 5' end of the molecule the AISP profile of strong and weak siRNA differ dramatically. Unlike the relatively strong values exhibited by siRNA in the >95% silencing group, siRNAs that exhibit poor silencing activity have weak AISP values (-7.6, -7.5, and -7.5 kcal/mol for positions 1, 2 and 3 respectively).
Overall the profiles of both strong and weak siRNAs form distinct sinusoidal shapes that are roughly 180° out-of-phase with each other. While these thermodynamic descriptions define the archetypal profile of a strong siRNA, it will likely be the case that neither the ΔG values given for key positions in the profile or the absolute position of the profile along the Y-axis (i.e., the ΔG -axis) are absolutes. Profiles that are shifted upward or downward (i.e., having on an average, higher or lower values at every position) but retain the relative shape and position of the profile along the X-axis can be foreseen as being equally effective as the model profile described here. Moreover, it is likely that siRNA that have strong or even stronger gene-specific silencing effects might have exaggerated ΔG values (either higher or lower) at key positions. Thus, for instance, it is possible that the 5 '-most position of the sense strand (position 19) could have ΔG values of 7.4 kcal/mol or lower and still be a strong siRNA if, for instance, a G-C -> G-TYU mismatch were substituted at position 19 and altered duplex stability. Similarly, position 12 and position 7 could have values above 8.3 kcal/mol and below 7.7 kcal/mole, respectively, without abating the silencing effectiveness of the molecule. Thus, for instance, at position 12, a stabilizing chemical modification (e.g., a chemical modification of the 2' position of the sugar backbone) could be added that increases the average internal stability at that position. Similarly, at position 7, mismatches similar to those described previously could be introduced that would lower the ΔG values at that position.
Lastly, it is important to note that while functional and non-functional siRNA were originally defined as those molecules having specific silencing properties, both broader or more limiting parameters can be used to define these molecules. As used herein, unless otherwise specified, "non-functional siRNA" are defined as those siRNA that induce less than 50% (<50%) target silencing, "semi-functional siRNA" induce 50-79% target silencing, "functional siRNA" are molecules that induce 80- 95% gene silencing, and "highly-functional siRNA" are molecules that induce great than 95% gene silencing. These definitions are not intended to be rigid and can vary depending upon the design and needs of the application. For instance, it is possible that a researcher attempting to map a gene to a chromosome using a functional assay, may identify an siRNA that reduces gene activity by only 30%. While this level of gene silencing may be "non-functional" for, e.g., therapeutic needs, it is sufficient for gene mapping purposes and is, under these uses and conditions, "functional." For these reasons, functional siRNA can be defined as those molecules having greater than 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% silencing capabilities at 10OnM transfection conditions. Similarly, depending upon the needs of the study and/or application, non-functional and semi-functional siRNA can be defined as having different parameters. For instance, semi-functional siRNA can be defined as being those molecules that induce 20%, 30%, 40%, 50%, 60%, or 70% silencing at 10OnM transfection conditions. Similarly, non-functional siRNA can be defined as being those molecules that silence gene expression by less than 70%, 60%, 50%, 40%, 30%, or less. Nonetheless, unless otherwise stated, the descriptions stated in the "Definitions" section of this text should be applied.
Functional attributes can be assigned to each of the key positions in the AISP of strong siRNA. The low 5' (sense strand) AISP values of strong siRNAs maybe necessary for determining which end of the molecule enters the RISC complex. In contrast, the high and low AISP values observed in the central regions of the molecule may be critical for siRNA-target niRNA interactions and product release, respectively.
If the AISP values described above accurately define the thermodynamic parameters of strong siRNA, it would be expected that similar patterns would be observed in strong siRNA isolated from nature. Natural siRNAs exist in a harsh, RNase-rich environment and it can be hypothesized that only those siRNA that exhibit heightened affinity for RISC (i.e., siRNA that exhibit an average internal stability profile similar to those observed in strong siRNA) would survive in an intracellular environment. This hypothesis was tested using GFP-specific siRNA isolated from N. benthamiana. Llave et al. (2002) Endogenous and Silencing- Associated Small RNAs in Plants, The Plant Cell 14, 1605-1619, introduced long double-stranded GFP-encoding RNA into plants and subsequently re-isolated GFP- specific siRNA from the tissues. The AISP of fifty-nine of these GFP-siRNA were determined, averaged, and subsequently plotted alongside the AISP profile obtained from the cyclophilin B/DBI/ luciferase siRNA having >90% silencing properties (Figure 6b). Comparison of the two groups show that profiles are nearly identical. This finding validates the information provided by the internal stability profiles and demonstrates that: (1) the profile identified by analysis of the cyclophilin B/DBI/ luciferase siRNAs are not gene specific; and (2) AISP values can be used to search for strong siRNAs in a variety of species.
Both chemical modifications and base-pair mismatches can be incorporated into siRNA to alter the duplex's AISP and functionality. For instance, introduction of mismatches at positions 1 or 2 of the sense strand destabilized the 5 'end of the sense strand and increases the functionality of the molecule (see Luc, Figure 7). Similarly, addition of 2'-O-methyl groups to positions 1 and 2 of the sense strand can also alter the AISP and (as a result) increase both the functionality of the molecule and eliminate off-target effects that results from sense strand homology with the unrelated targets (Figures 8a, 8b).
Rationale for Criteria in a Biological Context
The fate of siRNA in the RNAi pathway may be described in 5 major steps: (1) duplex recognition and pre-RISC complex formation; (2) ATP-dependent duplex unwinding/strand selection and RISC activation; (3) mRNA target identification; (4) mRNA cleavage, and (5) product release (Figure 1). Given the level of nucleic acid- protein interactions at (each step, siRNA functionality is likely influenced by specific biophysical and molecular properties that promote efficient interactions within the context of the multi-component complexes. Indeed, the systematic analysis of the siRNA test set identified multiple factors that correlate well with functionality. When combined into a single algorithm, they proved to be very effective in selecting active siRNAs. The fadtors described here may also be predictive of key functional associations important for each step in RNAi. For example, the potential formation of internal hairpin structures correlated negatively with siRNA functionality. Complementary strands with stable internal repeats are more likely to exist as stable hairpins thus decreasing the effective concentration of the functional duplex form. This suggests that the duplex is the preferred conformation for initial pre-RISC association. Indeed, although single complementary strands can induce gene silencing, the effective concentration required is at least two orders of magnitude higher than that of the duplex form.
siRNA-pre-RISC complex formation is followed by an ATP-dependent duplex unwinding step and "activation" of the RISC. The siRNA functionality was shown to correlate with overall low internal stability of the duplex and low internal stability of the 3' sense end (or differential internal stability of the 3' sense compare to the 5' sense strand), which may reflect strand selection and entry into the RISC. Overall duplex stability and low internal stability at the 3' end of the sense strand were also correlated with siRNA functionality. Interestingly, siRNAs with very high and very low overall stability profiles correlate strongly with non-functional duplexes. One interpretation is that high internal stability prevents efficient unwinding while very low stability reduces siRNA target affinity and subsequent mRNA cleavage by the RISC.
Several criteria describe base preferences at specific positions of the sense strand and are even more intriguing when considering their potential mechanistic roles in target recognition and mRNA cleavage. Base preferences for A at position 19 of the sense strand but not C, are particularly interesting because they reflect the same base preferences observed for naturally occurring miRNA precursors. That is, among the reported miRNA precursor sequences 75% contain a U at position 1 which corresponds to an A in position 19 of the sense strand of siRNAs, while G was under- represented in this same position for miRNA precursors. These observations support the hypothesis that both miRNA precursors and siRNA duplexes are processed by very similar if not identical protein machinery. The functional interpretation of the predominance of a U/A base pair is that it promotes flexibility at the 5'antisense ends of both siRNA duplexes and miRNA precursors and facilitates efficient unwinding and selective strand entrance into an activated RISC.
Among the criteria associated with base preferences that are likely to influence mRNA cleavage or possibly product release, the preference for U at position 10 of the sense strand exhibited the greatest impact, enhancing the probability of selecting an F80 sequence by 13.3%. Activated RISC preferentially cleaves target mRNA between nucleotides 10 and 11 relative to the 5' end of the complementary targeting strand. Therefore, it may be that U, the preferred base for most endoribonucleases, at this position supports more efficient cleavage. Alternatively, a U/A bp between the targeting siRNA strand and its cognate target mRNA may create an optimal conformation for the RISC-associated "'slicing" activity.
Post Algorithm Filters According to another embodiment, the output of any one of the formulas previously listed can be filtered to remove or select for siRNAs containing undesirable or desirable motifs or properties, respectively. In one example, sequences identified by any of the formulas can be filtered to remove any and all sequences that induce toxicity or cellular stress. Introduction of an siRNA containing a toxic motif into a cell can induce cellular stress and/or cell death (apoptosis) which in turn can mislead researchers into associating a particular (e.g., nonessential) gene with, e.g., an essential function. Alternatively, sequences generated by any of the before mentioned formulas can be filtered to identify and retain duplexes that contain toxic motifs. Such duplexes may be valuable from a variety of perspectives including, for instance, uses as therapeutic molecules. A variety of toxic motifs exist and can exert their influence on the cell through RNAi and non-RNAi pathways. Examples of toxic motifs are explained more fully in commonly assigned U.S. Provisional Patent Application Serial No. 60/538,874, entitled "Identification of Toxic Sequences," filed January 23, 2004. Briefly, toxic motifs include A/G UUU A/G/U, G/C AAA G/C, and GCCA, or a complement of any of the foregoing.
hi another instance, sequences identified by any of the before mentioned formulas can be filtered to identify duplexes that contain motifs (or general properties) that provide serum stability or induce serum instability. In one envisioned application of siRNA as therapeutic molecules, duplexes targeting disease-associated genes will be introduced into patients intravenously. As the half-life of single and double stranded RNA in serum is short, post-algorithm filters designed to select molecules that contain motifs that enhance duplex stability in the presence of serum and/or (conversely) eliminate duplexes that contain motifs that destabilize siRNA in the presence of serum, would be beneficial.
In another instance, sequences identified by any of the before mentioned formulas can be filtered to identify duplexes that are hyperfunctional. Hyperfunctional sequences are defined as those sequences that (1) induce greater than 95% silencing of a specific target when they are transfected at subnanomolar concentrations (i.e., less than one nanomolar); and/or (2) induce functional (or better) levels of silencing for greater than 96 hours. Filters that identify hyperfunctional molecules can vary widely. In one example, the top ten, twenty, thirty, or forty siRNA can be assessed for the ability to silence a given target at, e.g. , concentrations of InM and 0.5nM to identify hyperfunctional molecules.
Pooling
According to another embodiment, the present invention provides a pool of at least two siRNAs, preferably in the form of a kit or therapeutic reagent, wherein one strand of each of the siRNAs, the sense strand comprises a sequence that is substantially similar to a sequence within a target mRNA. The opposite strand, the antisense strand, will preferably comprise a sequence that is substantially complementary to that of the target mRNA. More preferably, one strand of each siRNA will comprise a sequence that is identical to a sequence that is contained in the target mRNA. Most preferably, each siRNA will be 19 base pairs in length, and one strand of each of the siRNAs will be 100% complementary to a portion of the target mRNA.
By increasing the number of siRNAs directed to a particular target using a pool or kit, one is able both to increase the likelihood that at least one siRNA with satisfactory functionality will be included, as well as to benefit from additive or synergistic effects. Further, when two or more siRNAs directed against a single gene do not have satisfactory levels of functionality alone, if combined, they may satisfactorily promote degradation of the target messenger RNA and successfully inhibit translation. By including multiple siRNAs in the system, not only is the probability of silencing increased, but the economics of operation are also improved when compared to adding different siRNAs sequentially. This effect is contrary to the conventional wisdom that the concurrent use of multiple siRNA will negatively impact gene silencing {e.g., Holen, T. et al. (2003) "Similar behavior of single strand and double strand siRNAs suggests they act through a common RNAi pathway." NAR 31: 2401-21407).
In fact, when two siRNAs were pooled together, 54% of the pools of two siRNAs induced more than 95% gene silencing. Thus, a 2.5-fold increase in the percentage of functionality was achieved by randomly combining two siRNAs. Further, over 84% of pools containing two siRNAs induced more than 80% gene silencing.
More preferably, the kit is comprised of at least three siRNAs, wherein one strand of each siRNA comprises a sequence that is substantially similar to a sequence of the target mRNA and the other strand comprises a sequence that is substantially complementary to the region of the target mRNA. As with the kit that comprises at least two siRNAs, more preferably one strand will comprise a sequence that is identical to a sequence that is contained in the mRNA and another strand that is 100% complementary to a sequence that is contained in the mRNA. During experiments, when three siRNAs were combined together, 60% of the pools induced more than 95% gene silencing and 92% of the pools induced more than 80% gene silencing.
Further, even more preferably, the kit is comprised of at least four siRNAs, wherein one strand of each siRNA comprises a sequence that is substantially similar to a region of the sequence of the target mRNA, and the other strand comprises a sequence that is substantially complementary to the region of the target mRNA. As with the kit or pool that comprises at least two siRNAs, more preferably one strand of each of the siRNA duplexes will comprise a sequence that is identical to a sequence that is contained in the mRNA, and another strand that is 100% complementary to a sequence that is contained in the mRNA. Additionally, kits and pools with at least five, at least six, and at least seven siRNAs may also be useful with the present invention. For example, pools of five siRNA induced 95% gene silencing with 77% probability and 80% silencing with 98.8% probability. Thus, pooling of siRNAs together can result in the creation of a target-specific silencing reagent with almost a 99% probability of being functional. The fact that such high levels of success are achievable using such pools of siRNA, enables one to dispense with costly and time-consuming target-specific validation procedures.
For this embodiment, as well as the other aforementioned embodiments, each of the siRNAs within a pool will preferably comprise 18-30 base pairs, more preferably 18-25 base pairs, and most preferably 19 base pairs. Within each siRNA, preferably at least 18 contiguous bases of the antisense strand will be 100% complementary to the target mRNA. More preferably, at least 19 contiguous bases of the antisense strand will be 100% complementary to the target mRNA. Additionally, there may be overhangs on either the sense strand or the antisense strand, and these overhangs may be at either the 5' end or the 3' end of either of the strands, for example there may be one or more overhangs of 1-6 bases. When overhangs are present, they are not included in the calculation of the number of base pairs. The two nucleotide 3' overhangs mimic natural siRNAs and are commonly used but are not essential. Preferably, the overhangs should consist of two nucleotides, most often dTdT or UU at the 3' end of the sense and antisense strand that are not complementary to the target sequence. The siRNAs may be produced by any method that is now known or that comes to be known for synthesizing double stranded RNA that one skilled in the art would appreciate would be useful in the present invention. Preferably, the siRNAs will be produced by Dharmacon's proprietary ACE® technology. However, other methods for synthesizing siRNAs are well known to persons skilled in the art and include, but are not limited to, any chemical synthesis of RNA oligonucleotides, ligation of shorter oligonucleotides, in vitro transcription of RNA oligonucleotides, the use of vectors for expression within cells, recombinant Dicer products and PCR products.
The siRNA duplexes within the aforementioned pools of siRNAs may correspond to overlapping sequences within a particular mRNA, or non-overlapping sequences of the mRNA. However, preferably they correspond to non-overlapping sequences. Further, each siRNA may be selected randomly, or one or more of the siRNA may be selected according to the criteria discussed above for maximizing the effectiveness of siRNA.
Included in the definition of siRNAs are siRNAs that contain substituted and/or labeled nucleotides that may, for example, be labeled by radioactivity, fluorescence or mass. The most common substitutions are at the T position of the ribose sugar, where moieties such as H (hydrogen) F, NH3, OCH3 and other O- alkyl, alkenyl, alkynyl, and orthoesters, may be substituted, or in the phosphorous backbone, where sulfur, amines or hydrocarbons may be substituted for the bridging of non- bridging atomsjn the phosphodiester bond. Examples of modified siRNAs are explained more fully in commonly assigned U.S. Patent Application Ser. No. 10/613,077, filed July 1, 2003.
Additionally, as noted above, the cell type into which the siRNA is introduced may affect the ability of the siRNA to enter the cell; however, it does not appear to affect the ability of the siRNA to function once it enters the cell. Methods for introducing double-stranded RNA into various cell types are well known to persons skilled in the art.
As persons skilled in the art are aware, in certain species, the presence of proteins such as RdRP, the RNA-dependent RNA polymerase, may catalytically enhance the activity of the siRNA. For example, RdRP propagates the RNAi effect in C. elegans and other non-mammalian organisms. In fact, in organisms that contain these proteins, the siRNA may be inherited. Two other proteins that are well studied and known to be a part of the machinery are members of the Argonaute family and Dicer, as well as their homologues. There is also initial evidence that the RISC complex might be associated with the ribosome so the more efficiently translated mRNAs will be more susceptible to silencing than others.
Another very important factor in the efficacy of siRNA is mRNA localization. In general, only cytoplasmic mRNAs are considered to be accessible to RNAi to any appreciable degree. However, appropriately designed siRNAs, for example, siRNAs modified with internucleotide linkages or 2'-O-methyl groups, maybe able to cause silencing by acting in the nucleus. Examples of these types of modifications are described in commonly assigned U.S. Patent Application Serial Nos. 10/431,027 and 10/613,077.
As described above, even when one selects at least two siRNAs at random, the effectiveness of the two may be greater than one would predict based on the effectiveness of two individual siRNAs. This additive or synergistic effect is particularly noticeable as one increases to at least three siRNAs, and even more noticeable as one moves to at least four siRNAs. Surprisingly, the pooling of the non¬ functional and semi-functional siRNAs, particularly more than five siRNAs, can lead to a silencing mixture that is as effective if not more effective than any one particular functional siRNA.
Within the kits of the present invention, preferably each siRNA will be present in a concentration of between 0.001 and 200 μM, more preferably between 0.01 and 200 nM, and most preferably between 0.1 and 10 nM.
In addition to preferably comprising at least four or five siRNAs, the kits of the present invention will also preferably comprise a buffer to keep the siRNA duplex stable. Persons skilled in the art are aware of buffers suitable for keeping siRNA stable. For example, the buffer may be comprised of 100 mM KCl, 30 mM HEPES- pH 7.5, and 1 mM MgC^. Alternatively, kits might contain complementary strands that contain any one of a number of chemical modifications (e.g., a 2'-0-ACE) that protect the agents from degradation by nucleases. In this instance, the user may (or may not) remove the modifying protective group (e.g., deprotect) before annealing the two complementary strands together.
By way of example, the kits may be organized such that pools of siRNA duplexes are provided on an array or microarray of wells or drops for a particular gene set or for unrelated genes. The array may, for example, be in 96 wells, 384 wells or 1284 wells arrayed in a plastic plate or on a glass slide using techniques now known or that come to be known to persons skilled in the art. Within an array, preferably there will be controls such as functional anti-lamin AJC, cyclophilin and two siRNA duplexes that are not specific to the gene of interest.
In order to ensure stability of the siRNA pools prior to usage, they may be retained in lyophilized form at minus twenty degrees (-2O0C) until they are ready for use. Prior to usage, they should be resuspended; however, even once resuspended, for example, in the aforementioned buffer, they should be kept at minus twenty degrees, (-2O0C) until used. The aforementioned buffer, prior to use, may be stored at approximately 40C or room temperature. Effective temperatures at which to conduct transfections are well known to persons skilled in the art and include for example, room temperature.
The kits maybe applied either in vivo or in vitro. Preferably, the siRNA of the pools or kits is applied to a cell through transfection, employing standard transfection protocols. These methods are well known to persons skilled in the art and include the use of lipid-based carriers, electroporation, cationic carriers, and microinjection. Further, one could apply the present invention by synthesizing equivalent DNA sequences (either as two separate, complementary strands, or as hairpin molecules) instead of siRNA sequences and introducing them into cells through vectors. Once in the cells, the cloned DNA could be transcribed, thereby forcing the cells to generate the siRNA. Examples of vectors suitable for use with the present application include but are not limited to the standard transient expression vectors, adenoviruses, retroviruses, lentivirus-based vectors, as well as other traditional expression vectors. Any vector that has an adequate siRNA expression and procession module may be used. Furthermore, certain chemical modifications to siRNAs, including but not limited to conjugations to other molecules, may be used to facilitate delivery. For certain applications it may be preferable to deliver molecules without transfection by simply formulating in a physiological acceptable solution.
This embodiment may be used in connection with any of the aforementioned embodiments. Accordingly, the sequences within any pool may be selected by rational design. Multigene Silencing
In addition to developing kits that contain multiple siRNA directed against a single gene, another embodiment includes the use of multiple siRNA targeting multiple genes. Multiple genes may be targeted through the use of high- or hyper- functional siRNA. High- or hyper- functional siRNA that exhibit increased potency, require lower concentrations to induce desired phenotypic (and thus therapeutic) effects. This circumvents RISC saturation. It therefore reasons that if lower concentrations of a single siRNA are needed for knockout or knockdown expression of one gene, then the remaining (uncomplexed) RISC will be free and available to interact with siRNA directed against two, three, four, or more, genes. Thus in this embodiment, the authors describe the use of highly functional or hyper-functional siRNA to knock out three separate genes. More preferably, such reagents could be combined to knockout four distinct genes. Even more preferably, highly functional or hyperfunctional siRNA could be used to knock out five distinct genes. Most preferably, siRNA of this type could be used to knockout or knockdown the expression of six or more genes.
Hyperfunctional siRNA
The term hyperfunctional siRNA (hf-siRNA) describes a subset of the siRNA population that induces RNAi in cells at low- or sub-nanomolar concentrations for extended periods of time. These traits, heightened potency and extended longevity of the RNAi phenotype, are highly attractive from a therapeutic standpoint. Agents having higher potency require lesser amounts of the molecule to achieve the desired physiological response, thus reducing the probability of side effects due to "off- target" interference. In addition to the potential therapeutic benefits associated with hyperfunctional siRNA, hf-siRNA are also desirable from an economic perspective. Hyperfunctional siRNA may cost less on a per-treatment basis, thus reducing overall expenditures to both the manufacturer and the consumer.
Identification of hyperfunctional siRNA involves multiple steps that are designed to examine an individual siRNA agent's concentration- and/or longevity- profiles. In one non-limiting example, a population of siRNA directed against a single gene are first analyzed using the previously described algorithm (Formula VIII). Individual siRNA are then introduced into a test cell line and assessed for the ability to degrade the target mRNA. It is important to note that when performing this step it is not necessary to test all of the siRNA. Instead, it is sufficient to test only those siRNA having the highest SMARTscores™ (i.e., SMARTscore™ > -10). Subsequently, the gene silencing data is plotted against the SMARTscores™ (see Figure 9). siRNA that (1) induce a high degree of gene silencing (i.e., they induce greater than 80% gene knockdown) and (2) have superior SMARTscores™ (i.e., a SMARTscore™ of > -10, suggesting a desirable average internal stability profile) are selected for further investigations designed to better understand the molecule's potency and longevity. In one, non-limiting study dedicated to understanding a molecule's potency, an siRNA is introduced into one (or more) cell types in increasingly diminishing concentrations (e.g., 3.0 -> 0.3 nM). Subsequently, the level of gene silencing induced by each concentration is examined and siRNA that exhibit hyperfunctional potency (i.e., those that induce 80% silencing or greater at, e.g., picomolar concentrations) are identified. In a second study, the longevity profiles of siRNA having high (>-10) SMARTscores™ and greater than 80% silencing are examined. In one non-limiting example of how this is achieved, siRNA are introduced into a test cell line and the levels of RNAi are measured over an extended period of time (e.g., 24-168 hrs). siRNAs that exhibit strong RNA interference patterns (i.e., >80 % interference) for periods of time greater than, e.g., 120 hours, are thus identified. Studies similar to those described above can be performed on any and all of the >106 siRNA included in this document to further define the most functional molecule for any given gene. Molecules possessing one or both properties (extended longevity and heightened potency) are labeled "hyperfunctional siRNA," and earmarked as candidates for future therapeutic studies.
While the example(s) given above describe one means by which hyperfunctional siRNA can be isolated, neither the assays themselves nor the selection parameters used are rigid and can vary with each family of siRNA. Families of siRNA include siRNAs directed against a single gene, or directed against a related family of genes.
The highest quality siRNA achievable for any given gene may vary considerably. Thus, for example, in the case of one gene (gene X), rigorous studies such as those described above may enable the identification of an siRNA that, at picomolar concentrations, induces 99+% silencing for a period of 10 days. Yet identical studies of a second gene (gene Y) may yield an siRNA that at high nanomolar concentrations (e.g., 10OnM) induces only 75% silencing for a period of 2 days. Both molecules represent the very optimum siRNA for their respective gene targets and therefore are designated "hyperfunctional." Yet due to a variety of factors including but not limited to target concentration, siRNA stability, cell type, off-target interference, and others, equivalent levels of potency and longevity are not achievable. Thus, for these reasons, the parameters described in the before mentioned assays can vary. While the initial screen selected siRNA that had SMARTscores™ above -10 and a gene silencing capability of greater than 80%, selections that have stronger (or weaker) parameters can be implemented. Similarly, in the subsequent studies designed to identify molecules with high potency and longevity, the desired cutoff criteria (i.e. , the lowest concentration that induces a desirable level of interference, or the longest period of time that interference can be observed) can vary. The experimentation subsequent to application of the rational criteria of this application is significantly reduced where one is trying to obtain a suitable hyperfunctional siRNA for, for example, therapeutic use. When, for example, the additional experimentation of the type described herein is applied by one skilled in the art with this disclosure in hand, a hyperfunctional siRNA is readily identified.
The siRNA may be introduced into a cell by any method that is now known or that comes to be known and that from reading this disclosure, persons skilled in the art would determine would be useful in connection with the present invention in enabling siRNA to cross the cellular membrane. These methods include, but are not limited to, any manner of transfection, such as, for example, transfection employing DEAE-Dextran, calcium phosphate, cationic lipids/liposomes, micelles, manipulation of pressure, microinjection, electroporation, imrnunoporation, use of vectors such as viruses, plasmids, cosmids, bacteriophages, cell fusions, and coupling of the polynucleotides to specific conjugates or ligands such as antibodies, antigens, or receptors, passive introduction, adding moieties to the siRNA that facilitate its uptake, and the like. Having described the invention with a degree of particularity, examples will now be provided. These examples are not intended to and should not be construed to limit the scope of the claims in any way.
EXAMPLES
General Techniques and Nomenclatures siRNA nomenclature. All siRNA duplexes are referred to by sense strand. The first nucleotide of the 5 '-end of the sense strand is position 1, which corresponds to position 19 of the antisense strand for a 19-mer. In most cases, to compare results from different experiments, silencing was determined by measuring specific transcript mRNA levels or enzymatic activity associated with specific transcript levels, 24 hours post-transfection, with siRNA concentrations held constant at 100 nM. For all experiments, unless otherwise specified, transfection efficiency was ensured to be over 95%, and no detectable cellular toxicity was observed. The following system of nomenclature was used to compare and report siRNA-silencing functionality: "F" followed by the degree of minimal knockdown. For example, F50 signifies at least 50% knockdown, F80 means at least 80%, and so forth. For this study, all sub-F50 siRNAs were considered non-functional.
Cell culture and transfection. 96-well plates are coated with 50 μl of 50 mg/ml poly- L-lysine (Sigma) for 1 hr, and then washed 3X with distilled water before being dried for 20 min. HEK293 cells or HEK293Lucs or any other cell type of interest are released from their solid support by trypsinization, diluted to 3.5 X 105 cells/ml, followed by the addition of 100 μL of cells/well. Plates are then incubated overnight at 37° C, 5% CO2. Transfection procedures can vary widely depending on the cell type and transfection reagents. In one non-limiting example, a transfection mixture consisting of 2 mL Opti-MEM I (Gibco-BRL), 80 μl Lipofectamine 2000 (Invitrogen), 15 μL SUPERNasin at 20 U/μl (Ambion), and 1.5 μl of reporter gene plasmid at 1 μg/ μl is prepared in 5-ml polystyrene round bottom tubes. One hundred μl of transfection reagent is then combined with 100 μl of siRNAs in polystyrene deep-well titer plates (Beckman) and incubated for 20 to 30 min at room temperature. Five hundred and fifty microliters of Opti-MEM is then added to each well to bring the final siRNA concentration to 100 nM. Plates are then sealed with parafilm and mixed. Media is removed from HEK293 cells and replaced with 95 μl of transfection mixture. Cells are incubated overnight at 37° C, 5% CO2.
Quantification of gene knockdown. A variety of quantification procedures can be used to measure the level of silencing induced by siRNA or siRNA pools. In one non-limiting example: to measure mRNA levels 24 hrs post-transfection, QuantiGene branched-DNA (bDNA) kits (Bayer) (Wang, et al, Regulation of insulin preRNA splicing by glucose. Proc. Natl. Acad. Sci. USA 1997, 94:4360.) are used according to manufacturer instructions. To measure luciferase activity, media is removed from HEK293 cells 24 hrs post-transfection, and 50 μl of Steady-GLO reagent (Promega) is added. After 5 minutes, plates are analyzed on a plate reader.
Example I. Sequences Used to Develop the Algorithm. Anti-Firefly and anti-Cyclophilin siRNAs panels (Figure 5a, b) sorted according to using Formula VIII predicted values. All siRNAs scoring more than 0 (formula VIII) and more then 20 (formula IX) are fully functional. AU ninety sequences for each gene (and DBI) appear below in Table III.
TABLE III
Cyclo 1 SEQ. ID 0032 GUUCCAAAAACAGUGGAUA
Cyclo 2 SEQ. ID 0033 UCCAAAAACAGUGGAUAAU
Cyclo 3 SEQ. ID 0034 CAAAAACAGUGGAUAAUUU
Cyclo 4 SEQ. ID 0035 AAAACAGUGGAUAAUUUUG
Cyclo 5 SEQ. ID 0036 AACAGUGGAUAAUUUUGUG
Cyclo 6 SEQ. ID 0037 CAGUGGAUAAUUUUGUGGC
Cyclo 7 SEQ. ID 0038 GUGGAUAAUUUUGUGGCCU
Cyclo 8 SEQ. ID 0039 GGAUAAUUUUGUGGCCUUA
Cyclo 9 SEQ. ID 0040 AUAAUUUUGUGGCCUUAGC
Cyclo 10 SEQ. ID 0041 AAUUUUGUGGCCUUAGCUA
Cyclo 11 SEQ. ID 0042 UUUUGUGGCCUUAGCUACA
Cyclo 12 SEQ. ID 0043 UUGUGGCCUUAGCUACAGG
Cyclo 13 SEQ. ID 0044 GUGGCCUUAGCUACAGGAG
Cyclo 14 SEQ. ID 0045 GGCCUUAGCUACAGGAGAG
Cyclo 15 SEQ. ID 0046 CCUUAGCUACAGGAGAGAA Cyclo 16 SEQ. ED 0047 UUAGCUACAGGAGAGAAAG
Cyclo 17 SEQ. ID 0048 AGCUACAGGAGAGAAAGGA
Cyclo 18 SEQ. ED 0049 CUACAGGAGAGAAAGGAUU
Cyclo 19 SEQ. ED 0050 ACAGGAGAGAAAGGAUUUG
Cyclo 20 SEQ. ED 0051 AGGAGAGAAAGGAUUUGGC
Cyclo 21 SEQ. ED 0052 GAGAGAAAGGAUUUGGCUA
Cyclo 22 SEQ. ID 0053 GAGAAAGGAUUUGGCUACA
Cyclo 23 SEQ. ID 0054 GAAAGGAUUUGGCUACAAA
Cyclo 24 SEQ. ID 0055 AAGGAUUUGGCUACAAAAA
Cyclo 25 SEQ. ED 0056 GGAUUUGGCUACAAAAACA
Cyclo 26 SEQ. ED 0057 AUUUGGCUACAAAAACAGC
Cyclo 27 SEQ. ID 0058 UUGGCUACAAAAACAGCAA
Cyclo 28 SEQ. ED 0059 GGCUACAAAAACAGCAAAU
Cyclo 29 SEQ. ID 0060 CUACAAAAACAGCAAAUUC
Cyclo 30 SEQ. ID 0061 ACAAAAACAGCAAAUUCCA
Cyclo 31 SEQ. ID 0062 AAAAACAGCAAAUUCCAUC
Cyclo 32 SEQ. ED 0063 AAACAGCAAAUUCCAUCGU
Cyclo 33 SEQ. ID 0064 ACAGCAAAUUCCAUCGUGU
Cyclo 34 SEQ. ID 0065 AGCAAAUUCCAUCGUGUAA
Cyclo 35 SEQ. ID 0066 CAAAUUCCAUCGUGUAAUC
Cyclo 36 SEQ. ED 0067 AAUUCCAUCGUGUAAUCAA
Cyclo 37 SEQ. ID 0068 UUCCAUCGUGUAAUCAAGG
Cyclo 38 SEQ. ID 0069 CCAUCGUGUAAUCAAGGAC
Cyclo 39 SEQ. ED 0070 AUCGUGUAAUCAAGGACUU
Cyclo 40 SEQ. ID 0071 CGUGUAAUCAAGGACUUCA
Cyclo 41 SEQ. ED 0072 UGUAAUCAAGGACUUCAUG
Cyclo 42 SEQ. ID 0073 UAAUCAAGGACUUCAUGAU
Cyclo 43 SEQ. ID 0074 AUCAAGGACUUCAUGAUCC
Cyclo 44 SEQ. ED 0075 CAAGGACUUCAUGAUCCAG
Cyclo 45 SEQ. ID 0076 AGGACUUCAUGAUCCAGGG
Cyclo 46 SEQ. ED 0077 GACUUCAUGAUCCAGGGCG
Cyclo 47 SEQ. ID 0078 CUUCAUGAUCCAGGGCGGA
Cyclo 48 SEQ. ED 0079 UCAUGAUCCAGGGCGGAGA
Cyclo 49 SEQ. ID 0080 AUGAUCCAGGGCGGAGACU
Cyclo 50 SEQ. ED 0081 GAUCCAGGGCGGAGACUUC
Cyclo 51 SEQ. ED 0082 UCCAGGGCGGAGACUUCAC
Cyclo 52 SEQ. ED 0083 CAGGGCGGAGACUUCACCA
Cyclo 53 SEQ. ID 0084 GGGCGGAGACUUCACCAGG
SEQ. ED 0085
Cyclo 54 GCGGAGACUUCACCAGGGG Cyclo 55 SEQ. ID 0086 GGAGACUUCACCAGGGGAG
Cyclo 56 SEQ. ID 0087 AGACUUCACCAGGGGAGAU
Cyclo 57 SEQ. ID 0088 ACUUCACCAGGGGAGAUGG
Cyclo 58 SEQ. ID 0089 UUCACCAGGGGAGAUGGCA
Cyclo 59 SEQ. ID 0090 CACCAGGGGAGAUGGCACA
Cyclo 60 SEQ. ID 0091 CCAGGGGAGAUGGCACAGG
Cyclo 61 SEQ. ID 0092 AGGGGAGAUGGCACAGGAG
Cyclo 62 SEQ. ID 0093 GGGAGAUGGCACAGGAGGA
Cyclo 63 SEQ. ID 0094 GAGAUGGCACAGGAGGAAA
Cyclo 64 SEQ. ID 0095 GAUGGCACAGGAGGAAAGA
Cyclo 65 SEQ. ID 0431 UGGCACAGGAGGAAAGAGC
Cyclo 66 SEQ. ID 0096 GCACAGGAGGAAAGAGCAU
Cyclo 67 SEQ. ID 0097 ACAGGAGGAAAGAGCAUCU
Cyclo 68 SEQ. ID 0098 AGGAGGAAAGAGCAUCUAC
Cyclo 69 SEQ. ID 0099 GAGGAAAGAGCAUCUACGG
Cyclo 70 SEQ. ID OlOO GGAAAGAGCAUCUACGGUG
Cyclo 71 SEQ. ID 0101 AAAGAGCAUCUACGGUGAG
Cyclo 72 SEQ. ID 0102 AGAGCAUCUACGGUGAGCG
Cyclo 73 SEQ. ID 0103 AGCAUCUACGGUGAGCGCU
Cyclo 74 SEQ. BD 0104 CAUCUACGGUGAGCGCUUC
Cyclo 75 SEQ. ID 0105 UCUACGGUGAGCGCUUCCC
Cyclo 76 SEQ. EO 0106 UACGGUGAGCGCUUCCCCG
Cyclo 77 SEQ. ID 0107 CGGUGAGCGCUUCCCCGAU
Cyclo 78 SEQ. ID 0108 GUGAGCGCUUCCCCGAUGA
Cyclo 79 SEQ. ID 0109 GAGCGCUUCCCCGAUGAGA
Cyclo 80 SEQ. ID OI lO GCGCUUCCCCGAUGAGAAC
Cyclo 81 SEQ. ID 0111 GCUUCCCCGAUGAGAACUU
Cyclo 82 SEQ. ID 0112 UUCCCCGAUGAGAACUUCA
Cyclo 83 SEQ. ID 0113 CCCCGAUGAGAACUUCAAA
Cyclo 84 SEQ. ID 0114 CCGAUGAGAACUUCAAACU
Cyclo 85 SEQ. ID 0115 GAUGAGAACUUCAAACUGA
Cyclo 86 SEQ. ID 0116 UGAGAACUUCAAACUGAAG
Cyclo 87 SEQ. ID 0117 AGAACUUCAAACUGAAGCA
Cyclo 88 SEQ. ID 0118 AACUUCAAACUGAAGCACU
Cyclo 89 SEQ. ID 0119 CUUCAAACUGAAGCACUAC
Cyclo 90 SEQ. ID 0120 UCAAACUGAAGCACUACGG
DB 1 SEQ. ID 0121 ACGGGCAAGGCCAAGUGGG
DB 2 SEQ. ID 0122 CGGGCAAGGCCAAGUGGGA
DB 3 SEQ. ID 0123 GGGCAAGGCCAAGUGGGAU
DB 4 SEQ. ID 0124 GGCAAGGCCAAGUGGGAUG DB 5 SEQ.ID0125 GCAAGGCCAAGUGGGAUGC
DB 6 SEQ.ID0126 CAAGGCCAAGUGGGAUGCC
DB 7 SEQ.ID0127 AAGGCCAAGUGGGAUGCCU
DB 8 SEQ.ID0128 AGGCCAAGUGGGAUGCCUG
DB 9 SEQ.ID0129 GGCCAAGUGGGAUGCCUGG
DB 10 SEQ.ID0130 GCCAAGUGGGAUGCCUGGA
DB 11 SEQ.ID0131 CCAAGUGGGAUGCCUGGAA
DB 12 SEQ.ID0132 CAAGUGGGAUGCCUGGAAU
DB 13 SEQ.ID0133 AAGUGGGAUGCCUGGAAUG
DB 14 SEQ.ID0134 AGUGGGAUGCCUGGAAUGA
DB 15 SEQ.ID0135 GUGGGAUGCCUGGAAUGAG
DB 16 SEQ.ID0136 UGGGAUGCCUGGAAUGAGC
DB 17 SEQ.ID0137 GGGAUGCCUGGAAUGAGCU
DB 18 SEQ.ID0138 GGAUGCCUGGAAUGAGCUG
DB 19 SEQ.ID0139 GAUGCCUGGAAUGAGCUGA
DB 20 SEQ.ID0140 AUGCCUGGAAUGAGCUGAA
DB 21 SEQ.ID0141 UGCCUGGAAUGAGCUGAAA
DB 22 SEQ.ID0142 GCCUGGAAUGAGCUGAAAG
DB 23 SEQ.ID0143 CCUGGAAUGAGCUGAAAGG
DB 24 SEQ.ID0144 CUGGAAUGAGCUGAAAGGG
DB 25 SEQ.ID0145 UGGAAUGAGCUGAAAGGGA
DB 26 SEQ.ID0146 GGAAUGAGCUGAAAGGGAC
DB 27 SEQ.ID0147 GAAUGAGCUGAAAGGGACU
DB 28 SEQ.ID0148 AAUGAGCUGAAAGGGACUU
DB 29 SEQ.ID0149 AUGAGCUGAAAGGGACUUC
DB 30 SEQ.ID0150 UGAGCUGAAAGGGACUUCC
DB 31 SEQ.ID0151 GAGCUGAAAGGGACUUCCA
DB 32 SEQ.ID0152 AGCUGAAAGGGACUUCCAA■
DB 33 SEQ.ID0153 GCUGAAAGGGACUUCCAAG
DB 34 SEQ.ID0154 CUGAAAGGGACUUCCAAGG
DB 35 SEQ.ID0155 UGAAAGGGACUUCCAAGGA
DB 36 SEQ.ID0156 GAAAGGGACUUCCAAGGAA
DB 37 SEQ.ID0157 AAAGGGACUUCCAAGGAAG
DB 38 SEQ.ID0158 AAGGGACUUCCAAGGAAGA
DB 39 SEQ.ID0159 AGGGACUUCCAAGGAAGAU
DB 40 SEQ.ID0160 GGGACUUCCAAGGAAGAUG
DB 41 SEQ.ID0161 GGACUUCCAAGGAAGAUGC
DB 42 SEQ.ID0162 GACUUCCAAGGAAGAUGCC
DB 43 SEQ.ID0163 •ACUUCCAAGGAAGAUGCCA
DB 44 SEQ.ID0164 CUUCCAAGGAAGAUGCCAU DB 45 SEQ.ID0165 UUCCAAGGAAGAUGCCAUG
DB 46 SEQ.ID0166 UCCAAGGAAGAUGCCAUGA
DB 47 SEQ.ID0167 CCAAGGAAGAUGCCAUGAA
DB 48 SEQ.ID0168 CAAGGAAGAUGCCAUGAAA
DB 49 SEQ.ID0169 AAGGAAGAUGCCAUGAAAG
DB 50 SEQ.ID0170 AGGAAGAUGCCAUGAAAGC
DB 51 SEQ.ID0171 GGAAGAUGCCAUGAAAGCU
DB 52 SEQ.ID0172 GAAGAUGCCAUGAAAGCUU
DB 53 SEQ.ID0173 AAGAUGCCAUGAAAGCUUA
DB 54 SEQ.ID0174 AGAUGCCAUGAAAGCUUAC
DB 55 SEQ.ID0175 GAUGCCAUGAAAGCUUACA
DB 56 SEQ.ID0176 AUGCCAUGAAAGCUUACAU
DB 57 SEQ.ID0177 UGCCAUGAAAGCUUACAUC
DB 58 SEQ.ID0178 GCCAUGAAAGCUUACAUCA
DB 59 SEQ.ID0179 CCAUGAAAGCUUACAUCAA
DB 60 SEQ.ID0180 CAUGAAAGCUUACAUCAAC
DB 61 SEQ.ID0181 AUGAAAGCUUACAUCAACA
DB 62 SEQ.ID0182 UGAAAGCUUACAUCAACAA
DB 63 SEQ.ID0183 GAAAGCUUACAUCAACAAA
DB 64 SEQ.ID0184 AAAGCUUACAUCAACAAAG
DB 65 SEQ.ID0185 AAGCUUACAUCAACAAAGU
DB 66 SEQ.ID0186 AGCUUACAUCAACAAAGUA
DB 67 SEQ.ID0187 GCUUACAUCAACAAAGUAG
DB 68 SEQ.ID0188 CUUACAUCAACAAAGUAGA
DB 69 SEQ.ID0189 UUACAUCAACAAAGUAGAA
DB 70 SEQ.ID0190 UACAUCAACAAAGUAGAAG
DB 71 SEQ.ID0191 ACAUCAACAAAGUAGAAGA
DB 72 SEQ.ID0192 CAUCAACAAAGUAGAAGAG
DB 73 SEQ.ID0193 AUCAACAAAGUAGAAGAGC
DB 74 SEQ.BD0194 UCAACAAAGUAGAAGAGCU
DB 75 SEQ.ID0195 CAACAAAGUAGAAGAGCUA
DB 76 SEQ.ID0196 AACAAAGUAGAAGAGCUAA
DB 77 SEQ.ID0197 ACAAAGUAGAAGAGCUAAA
DB 78 SEQ.ID0198 CAAAGUAGAAGAGCUAAAG
DB 79 SEQ.ID0199 AAAGUAGAAGAGCUAAAGA
DB 80 SEQ.ID0200 AAGUAGAAGAGCUAAAGAA
DB 81 SEQ.ID0201 AGUAGAAGAGCUAAAGAAA
DB 82 SEQ.ID0202 GUAGAAGAGCUAAAGAAAA
DB 83 SEQ.ID0203 UAGAAGAGCUAAAGAAAAA
DB 84 SEQ.ID0204 AGAAGAGCUAAAGAAAAAA DB 85 SEQ.ID0205 GAAGAGCUAAAGAAAAAAU
DB 86 SEQ.ID0206 AAGAGCUAAAGAAAAAAUA
DB 87 SEQ.ID0207 AGAGCUAAAGAAAAAAUAC
DB 88 SEQ.ID0208 GAGCUAAAGAAAAAAUACG
DB 89 SEQ.ID0209 AGCUAAAGAAAAAAUACGG
DB 90 SEQ.ID0210 GCUAAAGAAAAAAUACGGG
Luc 1 SEQ.ID0211 AUCCUCAUAAAGGCCAAGA
Luc 2 SEQ.ID0212 AGAUCCUCAUAAAGGCCAA
Luc 3 SEQ.ID0213 AGAGAUCCUCAUAAAGGCC
Luc 4 SEQ.ID0214 AGAGAGAUCCUCAUAAAGG
Luc 5 SEQ.ID0215 UCAGAGAGAUCCUCAUAAA
Luc 6 SEQ.ID0216 AAUCAGAGAGAUCCUCAUA
Luc 7 SEQ.ID0217 AAAAUCAGAGAGAUCCUCA
Luc 8 SEQ.ID0218 GAAAAAUCAGAGAGAUCCU
Luc 9 SEQ.ID0219 AAGAAAAAUCAGAGAGAUC
Luc 10 SEQ.ID0220 GCAAGAAAAAUCAGAGAGA
Luc 11 SEQ.ID0221 ACGCAAGAAAAAUCAGAGA
Luc 12 SEQ.ID0222 CGACGCAAGAAAAAUCAGA
Luc 13 SEQ.ID0223 CUCGACGCAAGAAAAAUCA
Luc 14 SEQ.ID0224 AACUCGACGCAAGAAAAAU
Luc 15 SEQ.ID0225 AAAACUCGACGCAAGAAAA
Luc 16 SEQ.ID0226 GGAAAACUCGACGCAAGAA
Luc 17 SEQ.ED0227 CCGGAAAACUCGACGCAAG
Luc 18 SEQ.ID0228 UACCGGAAAACUCGACGCA
Luc 19 SEQ.ID0229 CUUACCGGAAAACUCGACG
Luc 20 SEQ.ID0230 GUCUUACCGGAAAACUCGA
Luc 21 SEQ.ED0231 AGGUCUUACCGGAAAACUC
Luc 22 SEQ.ID0232 AAAGGUCUUACCGGAAAAC
Luc 23 SEQ.ID0233 CGAAAGGUCUUACCGGAAA
Luc 24 SEQ.ID0234 ACCGAAAGGUCUUACCGGA
Luc 25 SEQ.ID0235 GUACCGAAAGGUCUUACCG
Luc 26 SEQ.ID0236 AAGUACCGAAAGGUCUUAC
Luc 27 SEQ.ED0237 CGAAGUACCGAAAGGUCUU
Luc 28 SEQ.ED0238 GACGAAGUACCGAAAGGUC
Luc 29 SEQ.ID0239 UGGACGAAGUACCGAAAGG
Luc 30 SEQ.ID0240 UGUGGACGAAGUACCGAAA
Luc 31 SEQ.ID0241 UUUGUGGACGAAGUACCGA
Luc 32 SEQ.ID0242 UGUUUGUGGACGAAGUACC
Luc 33 SEQ.ED0243 UGUGUUUGUGGACGAAGUA
Luc 34 SEQ.ED0244 GUUGUGUUUGUGGACGAAG Luc 35 SEQ.ID0245 GAGUUGUGUUUGUGGACGA
Luc 36 SEQ.ID0246 AGGAGUUGUGUUUGUGGAC
Luc 37 SEQ.ID0247 GGAGGAGUUGUGUUUGUGG
Luc 38 SEQ.ID0248 GCGGAGGAGUUGUGUUUGU
Luc 39 SEQ.ID0249 GCGCGGAGGAGUUGUGUUU
Luc 40 SEQ.ID0250 UUGCGCGGAGGAGUUGUGU
Luc 41 SEQ.ID0251 AGUUGCGCGGAGGAGUUGU
Luc 42 SEQ.ID0252 AAAGUUGCGCGGAGGAGUU
Luc 43 SEQ.ID0253 AAAAAGUUGCGCGGAGGAG
Luc 44 SEQ.ID0254 CGAAAAAGUUGCGCGGAGG
Luc 45 SEQ.ID0255 CGCGAAAAAGUUGCGCGGA
Luc 46 SEQ.ID0256 ACCGCGAAAAAGUUGCGCG
Luc 47 SEQ.ID0257 CAACCGCGAAAAAGUUGCG
Luc 48 SEQ.ID0258 AACAACCGCGAAAAAGUUG
Luc 49 SEQ.ID0259 GUAACAACCGCGAAAAAGU
Luc 50 SEQ.ID0260 AAGUAACAACCGCGAAAAA
Luc 51 SEQ.ID0261 UCAAGUAACAACCGCGAAA
Luc 52 SEQ.ID0262 AGUCAAGUAACAACCGCGA
Luc 53 SEQ.ID0263 CCAGUCAAGUAACAACCGC
Luc 54 SEQ.ID0264 CGCCAGUCAAGUAACAACC
Luc 55 SEQ.ID0265 GUCGCCAGUCAAGUAACAA
Luc 56 SEQ.ID0266 ACGUCGCCAGUCAAGUAAC
Luc 57 SEQ.ID0267 UUACGUCGCCAGUCAAGUA
Luc 58 SEQ.ID0268 GAUUACGUCGCCAGUCAAG
Luc 59 SEQ.ID0269 UGGAUUACGUCGCCAGUCA
Luc 60 SEQ.ID0270 CGUGGAUUACGUCGCCAGU
Luc 61 SEQ.ID0271 AUCGUGGAUUACGUCGCCA
Luc 62 SEQ.ID0272 AGAUCGUGGAUUACGUCGC
Luc 63 SEQ.ID0273 AGAGAUCGUGGAUUACGUC
Luc 64 SEQ.ID0274 AAAGAGAUCGUGGAUUACG
Luc 65 SEQ.ID0275 AAAAAGAGAUCGUGGAUUA
Luc 66 SEQ.ID0276 GGAAAAAGAGAUCGUGGAU
Luc 67 SEQ.ID0277 ACGGAAAAAGAGAUCGUGG
Luc 68 SEQ.ID0278 UGACGGAAAAAGAGAUCGU
Luc 69 SEQ.ID0279 GAUGACGGAAAAAGAGAUC
Luc 70 SEQ.ID0280 ACGAUGACGGAAAAAGAGA
Luc 71 SEQ.ID0281 AGACGAUGACGGAAAAAGA
Luc 72 SEQ.ID0282 AAAGACGAUGACGGAAAAA
Luc 73' SEQ.ID0283 GGAAAGACGAUGACGGAAA
Luc 74 SEQ.ID0284 ACGGAAAGACGAUGACGGA Luc 75 SEQ.ID0285 GCACGGAAAGACGAUGACG
Luc 76 SEQ.ID0286 GAGCACGGAAAGACGAUGA
Luc 77 SEQ.ID0287 UGGAGCACGGAAAGACGAU
Luc 78 SEQ.ID0288 UUUGGAGCACGGAAAGACG
Luc 79 SEQ.ID02S9 GUUUUGGAGCACGGAAAGA
Luc 80 SEQ.ID0290 UUGUUUUGGAGCACGGAAA
Luc 81 SEQ.ID0291 UGUUGUUUUGGAGCACGGA
Luc 82 SEQ.ID0292 GUUGUUGUUUUGGAGCACG
Luc 83 SEQ.ID0293 CCGUUGUUGUUUUGGAGCA
Luc 84 SEQ.ID0294 CGCCGUUGUUGUUUUGGAG
Luc 85 SEQ.ID0295 GCCGCCGUUGUUGUUUUGG
Luc 86 SEQ.ID0296 CCGCCGCCGUUGUUGUUUU
Luc 87 SEQ.ID0297° UCCCGCCGCCGUUGUUGUU
Luc 88 SEQ.ID0298 CUUCCCGCCGCCGUUGUUG
Luc 89 SEQ.ID0299 AACUUCCCGCCGCCGUUGU
Luc 90 SEQ.ID0300 UGAACUUCCCGCCGCCGUU
Example II. Validation of the Algorithm using DBI, Luciferase, PLK, EGFR, and SEAP. The algorithm (Formula VIII) identified siRNAs for five genes, human DBI, firefly luciferase (fLuc), renilla luciferase (rLuc), human PLK, and human secreted alkaline phosphatase (SEAP). Four individual siRNAs were selected on the basis of their SMARTscores™ derived by analysis of their sequence using Formula VIII (all of the siRNAs would be selected with Formula IX as well) and analyzed for their ability to silence their targets' expression. In addition to the scoring, a BLAST search was conducted for each siRNA. To minimize the potential for off-target silencing effects, only those target sequences with more than three mismatches against un¬ related sequences were selected. Semizarov, et al, Specificity of short interfering ENA determined through gene expression signatures. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:6347. These duplexes were analyzed individually and in pools of 4 and compared with several siRNAs that were randomly selected. The functionality was measured as a percentage of targeted gene knockdown as compared to controls. All siRNAs were transfected as described by the methods above at 100 nM concentration into HEK293 using Lipofectamine 2000. The level of the targeted gene expression was evaluated by B-DNA as described above and normalized to the non-specific control. Figure 10 shows that the siRNAs selected by the algorithm disclosed herein were significantly more potent than randomly selected siRNAs. The algorithm increased the chances of identifying an F50 siRNA from 48% to 91%, and an F80 siRNA from 13% to 57%. In addition, pools of SMART siRNA silence the selected target better than randomly selected pools (see Figure 10F).
Example III. Validation of the Algorithm Using Genes Involved in Clathrin- Dependent Endocytosis.
Components of clathrin-mediated endocytosis pathway are key to modulating intracellular signaling and play important roles in disease. Chromosomal rearrangements that result in fusion transcripts between the Mixed-Lineage Leukemia gene (MLL) and CALM (clathrin assembly lymphoid myeloid leukemia gene) are believed to play a role in leukemogenesis. Similarly, disruptions in Rab7 and Rab9, as well as HIPl (Huntingtin-interacting protein), genes that are believed to be involved in endocytosis, are potentially responsible for ailments resulting in lipid storage, and neuronal diseases, respectively. For these reasons, siRNA directed against clathrin and other genes involved in the clathrin-mediated endocytotic pathway are potentially important research and therapeutic tools.
siRNAs directed against genes involved in the clathrin-mediated endocytosis pathways were selected using Formula VIII. The targeted genes were clathrin heavy chain (CHC, accession # NM_004859), clathrin light chain A (CLCa, NM_001833), clathrin light chain B (CLCb, NM_001834), CALM (U45976), β2 subunit of AP-2 (β2, NM_001282), Epsl5 (NM_001981), Epsl5R (NMJD21235), dynamin II (DYNII, NM_004945), Rab5a (BC001267), Rab5b (NM_002868), Rab5c (AF141304), and EEA.l (XM_018197).
For each gene, four siRNAs duplexes with the highest scores were selected and a BLAST search was conducted for each of them using the Human EST database. In order to minimize the potential for off-target silencing effects, only those sequences with more than three mismatches against un-related sequences were used. All duplexes were synthesized at Dharmacon, Inc. as 21-mers with 3'-UU overhangs using a modified method of 2'-ACE chemistry, Scaringe, Advanced 5'-silyl-2'- orthoester approach to RNA oligonucleotide synthesis, Methods Enzymol 2000, 317:3, and the antisense strand was chemically phosphorylated to insure maximized activity.
HeLa cells were grown in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum, antibiotics and glutamine. siRNA duplexes were resuspended in IX siRNA Universal buffer (Dharmacon, Inc.) to 20μM prior to transfection. HeLa cells in 12-well plates were transfected twice with 4μl of 20μM siRNA duplex in 3μl Lipofectamine 2000 reagent (Invitrogen, Carlsbad, California, USA) at 24-hour intervals. For the transfections in which 2 or 3 siRNA duplexes were included, the amount of each duplex was decreased, so that the total amount was the same as in transfections with single siRNAs. Cells were plated into normal culture medium 12 hours prior to experiments, and protein levels were measured 2 or 4 days after the first transfection.
Equal amounts of lysates were resolved by electrophoresis, blotted, and stained with the antibody specific to targeted protein, as well as antibodies specific to unrelated proteins, PPl phosphatase and TsglOl (not shown). The cells were lysed in Triton X-100/glycerol solubilization buffer as described previously. Tebar, Bohlander, & Sorkin, Clathrin Assembly Lymphoid Myeloid Leukemia (CALM) Protein: Localization in Endocytic-coated Pits, Interactions with Clathrin, and the Impact of Overexpression on Clathrin-mediated Traffic, MoI. Biol. Cell Aug 1999, 10:2687. Cell lysates were electrophoresed, transferred to nitrocellulose membranes, and Western blotting was performed with several antibodies followed by detection using enhanced chemiluminescence system (Pierce, Inc). Several x-ray films were analyzed to determine the linear range of the chemiluminescence signals, and the quantifications were performed using densitometry and Alphalmager v5.5 software (Alpha Innotech Corporation). In experiments with Epsl5R-targeted siRNAs, cell lysates were subjected to immunoprecipitation with Ab860, and Epsl5R was detected in immunoprecipitates by Western blotting as described above.
The antibodies to assess the levels of each protein by Western blot were obtained from the following sources: monoclonal antibody to clathrin heavy chain (TD.1) was obtained from American Type Culture Collection (Rockville, MD, USA); polyclonal antibody to dynamin II was obtained from Affinity Bioreagents, Inc. (Golden, CO, USA); monoclonal antibodies to EEA.1 and Rab5a were purchased from BD Transduction Laboratories (Los Angeles, CA, USA); the monoclonal antibody to TsglOl was purchased from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA); the monoclonal antibody to GFP was from ZYMED Laboratories Inc. (South San Francisco, CA, USA); the rabbit polyclonal antibodies Ab32 specific to α- adaptins and Ab20 to CALM were described previously Sorkin, et al, Stoichiometric Interaction of the Epidermal Growth Factor Receptor with the Clathrin-associated Protein Complex AP-2, J. Biol. Chem. Jan 1995, 270:619, the polyclonal antibodies to clathrin light chains A and B were kindly provided by Dr. F. Brodsky (UCSF); monoclonal antibodies to PPl (BD Transduction Laboratories) and α-Actinin (Chemicon) were kindly provided by Dr. M. Dell'Acqua (University of Colorado); Eρsl5 Ab577 and Eρsl5R Ab860 were kindly provided by Dr. P.P. Di Fiore (European Cancer Institute).
Figure 11 demonstrates the in vivo functionality of 48 individual siRNAs, selected using Formula VIII (most of them will meet the criteria incorporated by Formula IX as well) targeting 12 genes. Various cell lines were transfected with siRNA duplexes (Dupl-4) or pools of siRNA duplexes (Pool), and the cells were lysed 3 days after transfection with the exception of CALM (2 days) and β2 (4 days).
Note a βl-adaptin band (part of AP-I Golgi adaptor complex) that runs slightly slower than β2 adaptin. CALM has two splice variants, 66 and 72 kD. The full-length Eps 15R (a doublet of ~130 kD) and several truncated spliced forms of ~ 100 kD and ~70 kD were detected in Epsl5R immunoprecipitates (shown by arrows). The cells were lysed 3 days after transfection. Equal amounts of lysates were resolved by electrophoresis and blotted with the antibody specific to a targeted protein (GFP antibody for YFP fusion proteins) and the antibody specific to unrelated proteins PPl phosphatase or α-actinin, and TSGlOl. The amount of protein in each specific band was normalized to the amount of non-specific proteins in each lane of the gel. Nearly all of them appear to be functional, which establishes that Formula VIII and IX can be used to predict siRNAs' functionality in general in a genome wide manner.
To generate the fusion of yellow fluorescent protein (YFP) with Rab5b or Rab5c (YFP-Rab5b or YFP-Rab5c), a DNA fragment encoding the full-length human Rab5b or Rab5c was obtained by PCR using Pfu polymerase (Stratagene) with a Sad restriction site introduced into the 5' end and a Kpnl site into the 3' end and cloned into pEYFP-Cl vector (CLONTECH, Palo Alto, CA, USA). GFP-CALM and YFP- Rab5a were described previously Tebar, Bohlander, & Sorkin, Clathrin Assembly Lymphoid Myeloid Leukemia (CALM) Protein: Localization in Endocytic-coated Pits, Interactions with Clathrin, and the Impact of Overexpression on Clathrin-mediated Traffic, MoI. Biol. Cell Aug 1999, 10:2687.
Example IV. Validation of the Algorithm Using Eg5, GADPH, ATEl, MEK2, MEKl, QB, LaminA/C, c-myc, human cyclophilin, and mouse cyclophilin.
A number of genes have been identified as playing potentially important roles in disease etiology. Expression profiles of normal and diseased kidneys has implicated Edg5 in immunoglobulin A neuropathy, a common renal glomerular disease. Mycl , MEK1/2 and other related kinases have been associated with one or more cancers, while lamins have been implicated in muscular dystrophy and other diseases. For these reasons, siRNA directed against the genes encoding these classes of molecules would be important research and therapeutic tools.
Figure 12 illustrates four siRNAs targeting 10 different genes (Table V for sequence and accession number information) that were selected according to the Formula VIII and assayed as individuals and pools in HEK293 cells. The level of siRNA induced silencing was measured using the B-DNA assay. These studies demonstrated that thirty- six out of the forty individual SMART-selected siRNA tested are functional (90%) and all 10 pools are fully functional.
Example V. Validation of the Algorithm Using Bcl2.
Bcl-2 is a ~25kD, 205-239 amino acid, anti-apoptotic protein that contains considerable homology with other members of the BCL family including BCLX, MCLl, BAX, BAD, and BIK. The protein exists in at least two forms (Bcl2a, which has a hydrophobic tail for membrane anchorage, and Bcl2b, which lacks the hydrophobic tail) and is predominantly localized to the mitochondrial membrane. While Bcl2 expression is widely distributed, particular interest has focused on the expression of this molecule in B and T cells. Bcl2 expression is down-regulated in normal germinal center B cells yet in a high percentage of follicular lymphomas, Bcl2 expression has been observed to be elevated. Cytological studies have identified a common translocation ((14;18)(q32;q32)) amongst a high percentage (>70%) of these lymphomas. This genetic lesion places the Bcl2 gene in juxtaposition to immunoglobulin heavy chain gene (IgH) encoding sequences and is believed to enforce inappropriate levels of gene expression, and resistance to programmed cell death in the follicle center B cells. In other cases, hypomethylation of the Bcl2 promoter leads to enhanced expression and again, inhibition of apoptosis. In addition to cancer, dysregulated expression of Bcl-2 has been correlated with multiple sclerosis and various neurological diseases.
The correlation between Bcl-2 translocation and cancer makes this gene an attractive target for RNAi. Identification of siRNA directed against the bcl2 transcript (or Bcl2-IgH fusions) would further our understanding Bcl2 gene function and possibly provide a future therapeutic agent to battle diseases that result from altered expression or function of this gene.
In Silico Identification of Functional siRNA.
To identify functional and hyperfunctional siRNA against the Bcl2 gene, the sequence for Bcl-2 was downloaded from the NCBI Unigene database and analyzed using the Formula VIII algorithm. As a result of these procedures, both the sequence and SMARTscores™ of the Bcl2 siRNA were obtained and ranked according to their functionality. Subsequently, these sequences were BLAST' ed (database) to insure that the selected sequences were specific and contained minimal overlap with unrealated genes. The SMARTscores™ for the top 10 Bcl-2 siRNA are identified in Figure 13. In Vivo Testing of Bcl-2 SiRNA
Bcl-2 siRNAs having the top ten SMARTscores™ were selected and tested in a functional assay to determine silencing efficiency. To accomplish this, each of the ten duplexes were synthesized using 2'-0-ACE chemistry and transfected at 10OnM concentrations into cells. Twenty-four hours later assays were performed on cell extracts to assess the degree of target silencing. Controls used in these experiments included mock transfected cells, and cells that were transfected with a non-specific siRNA duplex.
The results of these experiments are presented below (and in Figure 14) and show that all ten of the selected siRNA induce 80% or better silencing of the Bcl2 message at 10OnM concentrations. These data verify that the algorithm successfully identified functional Bcl2 siRNA and provide a set of functional agents that can be used in experimental and therapeutic environments.
siRNA 1 GGGAGAUAGUGAUGAAGUA SEQ. ID NO. 301 siRNA 2 GAAGUACAUCCAUUAUAAG SEQ. ID NO. 302 siRNA 3 GUACGACAACCGGGAGAUA SEQ. ID NO. 303 siRNA 4 AGAUAGUGAUGAAGUACAU SEQ. ID NO. 304 siRNA 5 UGAAGACUCUGCUCAGUUU SEQ. ID NO. 305 siRNA 6 GCAUGCGGCCUCUGUUUGA SEQ. ID NO. 306 siRNA 7 UGCGGCCUCUGUUUGAUUU SEQ. ID NO. 307 siRNA 8 GAGAUAGUGAUGAAGUACA SEQ. ID NO. 308 siRNA 9 GGAGAUAGUGAUGAAGUAC SEQ. ID NO. 309 siRNA 10 GAAGACUCUGCUCAGUUUG SEQ. ID NO. 310
Bcl2 siRNA: Sense Strand, 5'→ 3'
Example VI. Sequences Selected by the Algorithm. Sequences of the siRNAs selected using Formulas (Algorithms) VIII and IX with their corresponding ranking, which have been evaluated for the silencing activity in vivo in the present study (Formula VIII and DC, respectively) are shown in Table V. It should be noted that the "t" residues in Table V, and elsewhere, when referring to siRNA, should be replaced by "u" residues. TABLE V
Gene Accession Formula Formula Name Number SEQ. ID NO. FTUSeqTence VIII DC
CLTC NM_004859 SEQ. ID NO. 2400 GAAAGAATCTGTAGAGAAA 76 94.2
CLTC NM_004859 SEQ. ID NO. 2401 GCAATGAGCTGTTTGAAGA 65 39.9
CLTC NM_004859 SEQ. ID NO. 2402 TGACAAAGGTGGATAAATT 57 38.2
CLTC NM_004859 SEQ. ID NO. 2403 GGAAATGGATCTCTTTGAA 54 49.4
CLTA NM_001833 SEQ. ID NO. 2404 GGAAAGTAATGGTCCAACA 22 55.5
CLTA NM_001833 SEQ. ID NO. 2405 AGACAGTTATGCAGCTATT 4 22.9
CLTA NMJ)01833 SEQ. ID NO. 2406 CCAATTCTCGGAAGCAAGA 1 17
CLTA NM_001833 SEQ. ID NO. 2407 GAAAGTAATGGTCCAACAG -1 -13
CLTB NMJ)01834 SEQ. ID NO. 2408 GCGCCAGAGTGAACAAGTA 17 57.5
CLTB NM_001834 SEQ. ID NO. 2409 GAAGGTGGCCCAGCTATGT 15 -8.6
CLTB NM_001834 SEQ. ID NO. 0311 GGAACCAGCGCCAGAGTGA 13 40.5
CLTB NMJ)01834 SEQ. ID NO. 0312 GAGCGAGATTGCAGGCATA 20 61.7
CALM U45976 SEQ. ID NO. 0313 GTTAGTATCTGATGACTTG 36 -34.6
CALM U45976 SEQ. ID NO. 0314 GAAATGGAACCACTAAGAA 33 46.1
CALM U45976 SEQ. ID NO. 0315 GGAAATGGAACCACTAAGA 30 61.2
CALM U45976 SEQ. ID NO. 0316 CAACTACACTTTCCAATGC 28 6.8
EPS 15 NM_001981 SEQ. ID NO. 0317 CCACCAAGATTTCATGATA 48 25.2
EPS 15 NM_001981 SEQ. ID NO. 0318 GATCGGAACTCCAACAAGA 43 49.3
EPS 15 NMJ)01981 SEQ. ID NO. 0319 AAACGGAGCTACAGATTAT 39 11.5
EPS 15 NM_001981 SEQ. ID NO. 0320 CCACACAGCATTCTTGTAA 33 -23.6
EPS15R NM_021235 SEQ. ID NO. 0321 GAAGTTACCTTGAGCAATC 48 33
EPS15R NMJ021235 SEQ. ID NO. 0322 GGACTTGGCCGATCCAGAA 27 33
EPS15R NM_021235 SEQ. ID NO. 0323 GCACTTGGATCGAGATGAG 20 1.3
EPS15R NM_021235 SEQ. ID NO. 0324 CAAAGACCAATTCGCGTTA 17 27.7
DNM2 NM_004945 SEQ. ID NO. 0325 CCGAATCAATCGCATCTTC 6 -29.6
DNM2 NM_004945 SEQ. ID NO. 0326 GACATGATCCTGCAGTTCA 5 -14
DNM2 NM_004945 SEQ. ID NO. 0327 GAGCGAATCGTCACCACTT 5 24
DNM2 NM_004945 SEQ. ID NO. 0328 CCTCCGAGCTGGCGTCTAC -4 -63.6
ARF6 AF93885 SEQ. ID NO. 0329 TCACATGGTTAACCTCTAA 27 -21.1
ARF6 AF93885 SEQ. ID NO. 0330 GATGAGGGACGCCATAATC 7 -38.4
ARF6 AF93885 SEQ. ID NO. 0331 CCTCTAACTACAAATCTTA 4 16.9
ARF6 AF93885 SEQ. ID NO. 0332 GGAAGGTGCTATCCAAAAT 4 11.5
RAB5A BC001267 SEQ. ID NO. 0333 GCAAGCAAGTCCTAACATT 40 25.1
RAB5A BCOO 1267 SEQ. ID NO. 0334 GGAAGAGGAGTAGACCTTA 17 50.1
RAB5A BCOO 1267 SEQ. ED NO. 0335 AGGAATCAGTGTTGTAGTA 16 11.5 TABLE V
Gene Accession Formula Formula
Name Number SEQ. ID NO. FTllSeqTence VIII IX
RAB5A BC001267 SEQ. ID NO. 0336 GAAGAGGAGTAGACCTTAC 12 7
RAB5B NM_002868 SEQ. ID NO. 0337 GAAAGTCAAGCCTGGTATT 14 18.1
RAB5B NM_002868 SEQ. ID NO. 0338 AAAGTCAAGCCTGGTATTA 6 -17.8
RAB5B NM_002868 SEQ. ID NO. 0339 GCTATGAACGTGAATGATC 3 -21.1
RAB5B NM_002868 SEQ. ID NO. 0340 CAAGCCTGGTATTACGTTT -7 -37.5
RAB5C AF141304 SEQ. ID NO. 0341 GGAACAAGATCTGTCAATT 38 51.9
RAB5C AF141304 SEQ. ID NO. 0342 GCAATGAACGTGAACGAAA 29 43.7
RAB5C AF141304 SEQ. ID NO. 0343 CAATGAACGTGAACGAAAT 18 43.3
RAB5C AF141304 SEQ. ID NO. 0344 GGACAGGAGCGGTATCACA 6 18.2
EEAl XM_018197 SEQ. ID NO. 0345 AGACAGAGCTTGAGAATAA 67 64.1
EEAl XM_018197 SEQ. ID NO. 0346 GAGAAGATCTTTATGCAAA 60 48.7
EEAl XM_018197 SEQ. ID NO. 0347 GAAGAGAAATCAGCAGATA 58 45.7
EEAl XM_018197 SEQ. ID NO. 0348 GCAAGTAACTCAACTAACA 56 72.3
AP2B1 NM_001282 SEQ. ID NO. 0349 GAGCTAATCTGCCACATTG 49 -12.4
AP2B1 NM_001282 SEQ. ID NO. 0350 GCAGATGAGTTACTAGAAA 44 48.9
AP2B1 NM_001282 SEQ. ID NO. 0351 CAACTTAATTGTCCAGAAA 41 28.2
AP2B1 NM_001282 SEQ. ID NO. 0352 CAACACAGGATTCTGATAA 33 -5.8
PLK NM_005030 SEQ. ID NO. 0353 AGATTGTGCCTAAGTCTCT -35 -3.4
PLK NM_005030 SEQ. ID NO. 0354 ATGAAGATCTGGAGGTGAA 0 -4.3
PLK NM_005030 SEQ. ID NO. 0355 TTTGAGACTTCTTGCCTAA -5 -27.7
PLK NM_005030 SEQ. ID NO. 0356 AGATCACCCTCCTTAAATA 15 72.3
GAPDH NM_002046 SEQ. ID NO. 0357 CAACGGATTTGGTCGTATT 27 -2.8
GAPDH NM_002046 SEQ. ID NO. 0358 GAAATCCCATCACCATCTT 24 3.9
GAPDH NM_002046 SEQ. ID NO. 0359 GACCTCAACTACATGGTTT ' 22 -22.9
GAPDH NM_002046 SEQ. ID NO. 0360 TGGTTTACATGTTCCAATA 9 9.8 c-Myc SEQ. ID NO. 0361 GAAGAAATCGATGTTGTTT 31 -11.7 c-Myc SEQ. ID NO. 0362 ACACAAACTTGAACAGCTA 22 51.3 c-Myc SEQ. ID NO. 0363 GGAAGAAATCGATGTTGTT 18 26 c-Myc SEQ. ID NO. 0364 GAAACGACGAGAACAGTTG 18 -8.9
MAP2K1 NM_002755 SEQ. ID NO. 0365 GCACATGGATGGAGGTTCT 26 .16
MAP2K1 NM_002755 SEQ. ID NO. 0366 GCAGAGAGAGCAGATTTGA 16 0.4
MAP2K1 NM_002755 SEQ. ID NO. 0367 GAGGTTCTCTGGATCAAGT 14 15.5
MAP2K1 NM_002755 SEQ. ID NO. 0368 GAGCAGATTTGAAGCAACT 14 18.5
MAP2K2 NM_030662 SEQ. ID NO. 0369 CAAAGACGATGACTTCGAA 37 26.4
MAP2K2 NM_030662 SEQ. ID NO. 0370 GATCAGCATTTGCATGGAA 24 -0.7
MAP2K2 NM_030662 SEQ. ID NO. 0371 TCCAGGAGTTTGTCAATAA 17 -4.5
MAP2K2 NM_030662 SEQ. ID NO. 0372 GGAAGCTGATCCACCTTGA 16 59.2 TABLE V
Gene Accession Formula Formula
Name Number SEQ. ID NO. FTllSeqTence vπi LX
KNSLl (EG5) NM_004523 SEQ. ID NO. 0373 GCAGAAATCTAAGGATATA 53 35.8
KNSLl (EG5) NM_004523 SEQ. ID NO. 0374 CAACAAGGATGAAGTCTAT 50 18.3
KNSL1(EG5) NM_004523 SEQ. ID NO. 0375 CAGCAGAAATCTAAGGATA 41 32.7
KNSLl (EG5) NM_004523 SEQ. ID NO. 0376 CTAGATGGCTTTCTCAGTA 39 3.9
CyclophilinA_ NM_021130 SEQ. ID NO. 0377 AGACAAGGTCCCAAAGACA -16 58.1
CyclophilinA_ NM_021130 SEQ. ID NO. 0378 GGAATGGCAAGACCAGCAA -6 36
CyclophilinA_ NM_021130 SEQ. ID NO. 0379 AGAATTATTCCAGGGTTTA -3 ' 16.1
CyclophilinA_ NM_021130 SEQ. ID NO. 0380 GCAGACAAGGTCCCAAAGA 8 8.9
LAMIN A/C NM_170707 SEQ. ID NO. 0381 AGAAGCAGCTTCAGGATGA 31 38.8
LAMIN A/C NM_170707 SEQ. ID NO. 0382 GAGCTTGACTTCCAGAAGA 33 22.4
LAMIN A/C NM_170707 SEQ. ID NO. 0383 CCACCGAAGTTCACCCTAA 21 27.5
LAMIN A/C NM_170707 SEQ. ID NO. 0384 GAGAAGAGCTCCTCCATCA 55 30.1
CyclophilinB M60857 SEQ. ID NO. 0385 GAAAGAGCATCTACGGTGA 41 83.9
CyclophilinB M60857 SEQ. ID NO. 0386 GAAAGGATTTGGCTACAAA 53 59.1
CyclophilinB M60857 SEQ. ID NO. 0387 ACAGCAAATTCCATCGTGT -20 28.8
CyclophilinB M60857 SEQ. ID NO. 0388 GGAAAGACTGTTCCAAAAA 2 27
DBIl NM_020548 SEQ. ID NO. 0389 CAACACGCCTCATCCTCTA 27 -7.6
DBI2 NM_020548 SEQ. ID NO. 0390 CATGAAAGCTTACATCAAC 25 -30.8
DBB NM_020548 SEQ. ID NO. 0391 AAGATGCCATGAAAGCTTA 17 22
DBI4 NM_020548 SEQ. DD NO. 0392 GCACATACCGCCTGAGTCT 15 3.9 rLUCl SEQ. ID NO. 0393 GATCAAATCTGAAGAAGGA 57 49.2
I-LUC2 SEQ. ID NO. 0394 GCCAAGAAGTTTCCTAATA 50 13.7 rLUC3 SEQ. ID NO. 0395 CAGCATATCTTGAACCATT 41 -2.2 rLUC4 SEQ. ID NO. 0396 GAACAAAGGAAACGGATGA 39 29.2
SeAPl NM_031313 SEQ. BD NO. 0397 CGGAAACGGTCCAGGCTAT 6 26.9
SeAP2 NM_031313 SEQ. ID NO. 0398 GCTTCGAGCAGACATGATA 4 -11.2
SeAP3 NM_031313 SEQ. ID NO. 0399 CCTACACGGTCCTCCTATA 4 4.9
SeAP4 NM_031313 SEQ. ID NO. 0400 GCCAAGAACCTCATCATCT 1 -9.9 fLUCl SEQ. ID NO. 0401 GATATGGGCTGAATACAAA 54 40.4 fLUC2 SEQ. ID NO. 0402 GCACTCTGATTGACAAATA 47 54.7 fLUC3 SEQ. ID NO. 0403 TGAAGTCTCTGATTAAGTA 46 34.5 fLUC4 SEQ. ID NO. 0404 TCAGAGAGATCCTCATAAA 40 11.4 mCyclo_l NM_008907 SEQ. DD NO. 0405 GCAAGAAGATCACCATTTC 52 46.4 mCyclo__2 NM_008907 SEQ. DD NO. 0406 GAGAGAAATTTGAGGATGA 36 70.7 mCyclo_3 NM_008907 SEQ. ID NO. 0407 GAAAGGATTTGGCTATAAG 35 -1.5 mCyclo_4 NM_008907 SEQ. DD NO. 0408 GAAAGAAGGCATGAACATT 27 10.3
BCL2_1 NM_000633 SEQ. DD NO. 0409 GGGAGATAGTGATGAAGTA 21 72 TABLE V
Gene Accession Formula Formula Name Number SEQ. ID NO. FTUSeqTence VIII IX
BCL2_2 NM_000633 SEQ. ID NO. 0410 GAAGTACATCCATTATAAG 1 3.3
BCL2_3 NM_000633 SEQ. ID NO. 0411 GTACGACAACCGGGAGATA 1 35.9
BCL2_4 NM_000633 SEQ. ID NO. 0412 AGATAGTGATGAAGTACAT -12 22.1
BCL2_5 NM_000633 SEQ. ID NO. 0413 TGAAGACTCTGCTCAGTTT 36 19.1
BCL2_6 NM_000633 SEQ. ID NO. 0414 GCATGCGGCCTCTGTTTGA 5 -9.7
QBl NM_003365.1 SEQ. ID NO. 0415 GCACACAGCUUACUACAUC 52 -4.8
QB2 NM_003365.1 SEQ. ID NO. 0416 GAAAUGCCCUGGUAUCUCA 49 22.1
QB3 NM_003365.1 SEQ. ID NO. 0417 GAAGGAACGUGAUGUGAUC 34 22.9
QB4 NM_003365.1 SEQ. ID NO. 0418 GCACUACUCCUGUGUGUGA 28 20.4
ATEl-I NM_007041 SEQ. ID NO. 0419 GAACCCAGCUGGAGAACUU 45 15.5
ATE1-2 NM_007041 SEQ. ID NO. 0420 GAUAUACAGUGUGAUCUUA 40 12.2
ATE1-3 NM_007041 SEQ. ID NO. 0421 GUACUACGAUCCUGAUUAU 37 32.9
ATE1-4 NM_007041 SEQ. ID NO. 0422 GUGCCGACCUUUACAAUUU 35 18.2
EGFR-I NM_005228 SEQ. ID NO. 0423 GAAGGAAACTGAATTCAAA 68 79.4
EGFR-I NM_005228 SEQ. ID NO. 0424 GGAAATATGTACTACGAAA 49 49.5
EGFR-I NM_005228 SEQ. ID NO. 0425 CCACAAAGCAGTGAATTTA 41 7.6
EGFR-I NM_005228 SEQ. ID NO. 0426 GTAACAAGCTCACGCAGTT 40 25.9
Example VII. Genome- Wide Application of Formula VIII or Formula X
The examples described above demonstrate that the algorithm(s) can successfully identify functional siRNA and that these duplexes can be used to induce the desirable phenotype of transcriptional knockdown or knockout. Each gene or family of genes in each organism plays an important role in maintaining physiological homeostasis and the algorithm can be used to develop functional, highly functional, or hyperfunctional siRNA to each gene. In one example of how this is accomplished, the entire online ncbi refseq, locuslink, and/or unigene database for the human genome is first downloaded to local servers. Concommitantly, the most current version of the BLAST algorithm/program is also downloaded to enable analysis of all siRNA identified by the algorithm. Prior to applying the algorithm, sequences are filtered to eliminate all non-coding sequences {e.g., 3' and 5' UTRs) and sequences that contain single nucleotide polymorphisms (SNPs). In addition, in one version of the siRNA selection process, only those sequences that are associated with all isoforms (e.g., splice variants) of a given gene are reserved and considered for targeting. Subsequently, a list of all potential siRNAs (including a 19 basepair "core" sequence with two basepair 3' overhangs) is generated for each gene sequence. This group is then filtered to eliminate sequences that contain any one of a number of undesirable traits including, but not limited to: 1) sequences that contain more than two GC basepairs in the last 5 nucleotides of the 3' end of the sense strand, and 2) sequences that contained internal repeats that could potentially form hairpin structures. The output of these procedures are then submitted for scoring by the algorithm. In this example, the pre- filtered database was processed with Formula VIII or Formula X and the top 5-100 siRNAs having scores of 75 (adjusted) or greater were selected. If desired, the sequences of these siRNA can be BLAST' ed against the Unigene database containing all sequences in the genome of choice (e.g. , the human genome) to eliminate any duplexes that show undesirable degrees of homology to sequences other than the intended target. The sequences of the (roughly) top 100 sequences for each gene are provided on the enclosed CDs in electronic form. In this example, the Formula X sequences were first generated using the procedures described above and subsequently compared to Formula VIII generated sequences. Formula VIII sequences that were also identified by Formula X were then removed (subtracted) from this database (Table XIH) to eliminate duplications.
With respect to the material on disk which is part of this disclosure, there are two tables provided in text format. Table XII, which is located in a file entitled table- xii.txt, created 26 April 2004, with a file size of 110,486 kb, provides a list of the 5- 100 sequences for each target, identified by Formula VIII as having the highest relative SMARTscores™ for the target analyzed. Table XIII, which is located in a file entitled table-xiii.txt, created 26 April 2004, with a file size of 23,146 kb, provides a list of the 5-100 sequences for each target identified by Formula X. In addition, each table provides information concerning: the gene name, an NCBI accession number, an adjusted SMARTscore, and a sequence ID number. Any of the provided sequences can be used for gene silencing either alone or in combination with other sequences. The information contained on the disks is part of this patent application and is incorporated into the specification by reference. One may use these tables in order to identify functional siRNAs for the gene provided therein, by simply looking for the gene of interest and an siRNA that is listed as functional. Preferably, one would select one or more of the siRNAs that is most optimized for the target of interest and is denoted as a pool pick. Table XII: siRNA Selected by Formula VIII
See data submitted herewith on a CD-ROM in accordance with PCT Administrative Instructions Part 8. Table XII is included on the compact disk labeled COPY 1 - TABLES PART DISK 1/1 , TABLES XII and XIII (provided in triplicate, which copies are identical), in a file entitled table-xii.txt, date of creation 26 April 2004, with a size of 110,486 kb.
Table XIII: siRNA Selected by Formula X See data submitted herewith on a CD-ROM in accordance with PCT
Administrative Instructions Part 8. Table XIII is included on the compact disk labeled COPY 1 - TABLES PART DISK 1/1, TABLES XII and XIII (provided in triplicate, which copies are identical), in file entitled table-xiii.txt, date of creation 26 April 2004, with a size of 23,146 kb.
Many of the genes to which the described siRNA are directed play critical roles in disease etiology. For this reason, the siRNAs listed in the accompanying compact disk may potentially act as therapeutic agents. A number of prophetic examples follow and should be understood in view of the siRNA that are identified on the accompanying CD. To isolate these siRNAs, the appropriate message sequence for each gene is analyzed using one of the before mentioned formulas (preferably formula VIII) to identify potential siRNA targets. Subsequently these targets are BLAST'ed to eliminate homology with potential off-targets.
The list of potential disease targets is extensive. For instance, over-expression of BcIlO has been implicated in the development of MALT lymphoma (mucosa associated lymphoid tissue lymphoma) and thus, functional, highly functional, or hyperfunctional siRNA directed against that gene (e.g., SEQ. ID NO. 0427: GGAAACCUCUCAUUGCUAA; SEQ. ID NO. 0428: GAAAGAACCUUGCCGAUCA; SEQ. ID NO. 0429: GGAAAUACAUCAGAGCUUA, or SEQ. ID NO. 0430: GAAAGUAUGUGUCUUAAGU) may contribute to treatment of this disorder. In another example, studies have shown that molecules that inhibit glutamine:fructose-6-phosphate aminotransferase (GFA) may act to limit the symptoms suffered by Type II diabetics. Thus, functional, highly functional, or hyperfunctional siRNA directed against GFA (also known as GFPTl : siRNA = SEQ. ID NO. 0433 UGAAACGGCUGCCUGAUUU; SEQ. ID NO. 0434 GAAGUUACCUCUUACAUUU; SEQ. ID NO. 0435 GUACGAAACUGUAUGAUUA; SEQ. ID NO. 0436 GGACGAGGCUAUCAUUAUG) may contribute to treatment of this disorder.
In another example, the von Hippel-Lindau (VHL) tumor suppressor has been observed to be inactivated at a high frequency in sporadic clear cell renal cell carcinoma (RCC) and RCCs associated with VHL disease. The VHL tumor suppressor targets hypoxia-inducible factor-1 alpha (HIF-I alpha), a transcription factor that can induce vascular endothelial growth factor (VEGF) expression, for ubiquitination and degradation. Inactivation of VHL can lead to increased levels of HIF-I alpha, and subsequent VEGF over expression. Such over expression of VEGF has been used to explain the increased (and possibly necessary) vascularity observed in RCC. Thus, functional, highly functional, or hyperfunctional siRNAs directed against either HIF-I alpha (SEQ. ID NO. 0437 GAAGGAACCUGAUGCUUUA; SEQ.IDNO.0438GCAUAUAUCUAGAAGGUAU;SEQ.IDNO.0439 GAACAAAUACAUGGGAUUA;SEQ.IDNO.0440 GGACACAGAUUUAGACUUG)orVEGF(SEQ.IDNO.0441 GAACGUACUUGCAGAUGUG;SEQ.IDNO.0442 GAGAAAGCAUUUGUUUGUA;SEQ.IDNO.0443 GGAGAAAGCAUUUGUUUGU;SEQ.IDNO.0444
CGAGGCAGCUUGAGUUAAA) may be useful in the treatment of renal cell carcinoma.
In another example, gene expression of platelet derived growth factor A and B (PDGF-A and PDGF-B) has been observed to be increased 22- and 6-fold, respectively, in renal tissues taken from patients with diabetic nephropathy as compared with controls. These findings suggest that over expression of PDGF A and B may play a role in the development of the progressive fibrosis that characterizes human diabetic kidney disease. Thus, functional, highly functional, or hyperfunctional siRNAs directed against either PDGF A (SEQ. ID NO. 0445: GGU AAGAU AUUGUGCUUUA; SEQ. ID NO. 0446: CCGCAAAUAUGCAGAAUUA; SEQ. ID NO. 0447: GGAUGUACAUGGCGUGUUA; SEQ. ID NO. 0448: GGUGAAGUUUGUAUGUUUA) or
PDGF B
(SEQ.IDNO.0449:CCGAGGAGCUUUAUGAGAU; SEQ.IDNO.0450:GCUCCGCGCUUUCCGAUUU;
SEQ.IDNO.0451 GAGCAGGAAUGGUGAGAUG;
SEQ.IDNO.0452:GAACUUGGGAUAAGAGUGU;
SEQ.IDNO.0453CCGAGGAGCUUUAUGAGAU;
SEQ. ID NO. 0454 UUUAUGAGAUGCUGAGUGA) may be useful in the treatment of this form of kidney disorder:
In another example, a strong correlation exists between the over-expression of glucose transporters (e.g., GLUT12) and cancer cells. It is predicted that cells undergoing uncontrolled cell growth up-regulate GLUT molecules so that they can cope with the heightened energy needs associated with increased rates of proliferation and metastasis. Thus, siRNA-based therapies that target the molecules such as
GLUTl (also known as SLC2A1: siRNA =
SEQ.IDNO.:0455GCAAUGAUGUCCAGAAGAA;
SEQ.IDNO.:0456GAAGAAUAUUCAGGACUUA; SEQ.IDNO.:0457GAAGAGAGUCGGCAGAUGA;
SEQ.IDNO.:0458CCAAGAGUGUGCUAAAGAA)
GLUT12(alsoknownasSLCA12:siRNA= SEQ.IDNO.0459:GAGACACUCUGAAAUGAUA; SEQ.IDNO.0460:GAAAUGAUGUGGAUAAGAG; SEQ.IDNO.0461:GAUCAAAUCCUCCCUGAAA;
SEQ. ID NO. 0462: UGAAUGAGCUGAUGAUUGU) and other related transporters, maybe of value in treating a multitude of malignancies. The siRNA sequences listed above are presented in a 5'-^ 3' sense strand direction. In addition, siRNA directed against the targets listed above as well as those directed against other targets and listed in the accompanying compact disk may be useful as therapeutic agents.
Example VUI. Evidence for the Benefits of Pooling
Evidence for the benefits of pooling have been demonstrated using the reporter gene, luciferase. Ninety siRNA duplexes were synthesized using Dharmacon proprietary ACE® chemistry against one of the standard reporter genes: firefly luciferase. The duplexes were designed to start two base pairs apart and to cover approximately 180 base pairs of the luciferase gene (see sequences in Table III). Subsequently, the siRNA duplexes were co-transfected with a luciferase expression reporter plasmid into HEK293 cells using standard transfection protocols and luciferase activity was assayed at 24 and 48 hours.
Transfection of individual siRNAs showed standard distribution of inhibitory effect. Some duplexes were active, while others were not. Figure 15 represents a typical screen of ninety siRNA duplexes (SEQ. ID NO. 0032- 0120) positioned two base pairs apart. As the figure suggests, the functionality of the siRNA duplex is determined more by a particular sequence of the oligonucleotide than by the relative oligonucleotide position within a gene or excessively sensitive part of the mRNA, which is important for traditional anti-sense technology.
When two continuous oligonucleotides were pooled together, a significant increase in gene silencing activity was observed. (See Figure 16) A gradual increase in efficacy and the frequency of pools functionality was observed when the number of siRNAs increased to 3 and 4. (Figures 16, 17). Further, the relative positioning of the oligonucleotides within a pool did not determine whether a particular pool was functional (see Figure 18, in which 100% of pools of oligonucleotides distanced by 2, 10 and 20 base pairs were functional).
However, relative positioning may nonetheless have an impact. An increased functionality may exist when the siRNA are positioned continuously head to toe (5' end of one directly adjacent to the 3' end of the others). Additionally, siRNA pools that were tested performed at least as well as the best oligonucleotide in the pool, under the experimental conditions whose results are depicted in Figure 19. Moreover, when previously identified non- functional and marginally (semi) functional siRNA duplexes were pooled together in groups of five at a time, a significant functional cooperative action was observed. (See Figure 20) In fact, pools of semi-active oligonucleotides were 5 to 25 times more functional than the most potent oligonucleotide in the pool. Therefore, pooling several siRNA duplexes together does not interfere with the functionality of the most potent siRNAs within a pool, and pooling provides an unexpected significant increase in overall functionality
Example IX. Additional Evidence of the Benefits of Pooling
Experiments were performed on the following genes: β-galactosidase, Renilla luciferase, and Secreted alkaline phosphatase, which demonstrates the benefits of pooling, (see Figure 21). Individual and pools of siRNA (described in Figure legend 21) were transfected into cells and tested for silencing efficiency. Approximately 50% of individual siRNAs designed to silence the above-specified genes were functional, while 100% of the pools that contain the same siRNA duplexes were functional.
Example X. Highly Functional siRNA
Pools of five siRNAs in which each two siRNAs overlap to 10-90% resulted in 98% functional entities (>80% silencing). Pools of siRNAs distributed throughout the mRNA that were evenly spaced, covering an approximate 20 - 2000 base pair range, were also functional. When the pools of siRNA were positioned continuously head to tail relative to mRNA sequences and mimicked the natural products of Dicer cleaved long double stranded RNA, 98% of the pools evidenced highly functional activity (>95% silencing).
Example XI. Human cyclophilin B Table III above lists the siRNA sequences for the human cyclophilin B protύn.
Figure imgf000094_0001
siRNA may be selected by applying these sequences to any of Formula I to VII above.
Alternatively, one could pool 2, 3, 4, 5 or more of these sequences to create a kit for silencing a gene. Preferably, within the kit there would be at least one sequence that has a relatively high predicted functionality when any of Formulas I - VII is applied.
Example XII. Sample Pools of siRNAs and Their Application to Human Disease
The genetic basis behind human disease is well documented and siRNA may be used as both research or diagnostic tools and therapeutic agents, either individually or in pools. Genes involved in signal transduction, the immune response, apoptosis, DNA repair, cell cycle control, and a variety of other physiological functions have clinical relevance and therapeutic agents that can modulate expression of these genes may alleviate some or all of the associated symptoms, hi some instances, these genes can be described as a member of a family or class of genes and siRNA (randomly, conventionally, or rationally designed) can be directed against one or multiple members of the family to induce a desired result.
To identify rationally designed siRNA to each gene, the sequence was analyzed using Formula VIII or Formula X to identify rationally designed siRNA. To confirm the activity of these sequences, the siRNA are introduced into a cell type of choice (e.g., HeLa cells, HEK293 cells) and the levels of the appropriate message are analyzed using one of several art proven techniques. siRNA having heightened levels of potency can be identified by testing each of the before mentioned duplexes at increasingly limiting concentrations. Similarly, siRNA having increased levels of longevity can be identified by introducing each duplex into cells and testing functionality at 24, 48, 72, 96, 120, 144, 168, and 192 hours after transfection. Agents that induce >95% silencing at sub-nanomolar concentrations and/or induce functional levels of silencing for >96 hours are considered hyperfunctional. Example XIII
The information presented in Tables XII and XIII provides the siRNA sequence (sense strand), the gene name, the NCBI accession number, the adjusted algorithm score, and the sequence ID number. All sequences have an adjusted score 5 of 75 or above. For Table XIII, Formula X derived sequences were compared with Formula VIII sequences. Sequences that were in common with both were eliminated from Table XIII. Pool picks are typically identified as gene specific siRNA that have the hightest adjusted scores.
10 The following are non-limiting examples of families of proteins to which siRNA described in this document are targeted against:
Transporters, Pumps, and Channels
15
Transporters, pumps, and channels represent one class of genes that are attractive targets for siRNAs. One major class of transporter molecules are the ATP- binding cassette (ABC) transporters. To date, nearly 50 human ABC-transporter genes have been characterized and have been shown to be involved in a variety of
20 physiological functions including transport of bile salts, nucleosides, chloride ions, cholesterol, toxins, and more. Predominant among this group are MDRl (which encodes the P-glycoprotein, NP_000918), the MDR-related proteins (MRP 1-7), and the breast cancer resistance protein (BCRP). In general, these transporters share a common structure, with each protein containing a pair of ATP -binding domains (also
25 known as nucleotide binding folds, NBF) and two sets of transmembrane (TM) domains, each of which typically contains six membrane-spanning α-helices. The genes encoding this class of transporter are organized as either full transporters (i.e., containing two TM and two NBF domains) or as half transporters that assemble as either homodimers or heterodimers to create functional transporters. As a whole,
30. members of the family are widely dispersed throughout the genome and show a high degree of amino acid sequence identify among eukaryotes.
ABC-transporters have been implicated in several human diseases. For instance, molecular efflux pumps of this type play a major role in the development of 35 drug resistance exhibited by a variety of cancers and pathogenic microorganisms. In the case of human cancers, increased expression of the MDRl gene and related pumps have been observed to generate drug resistance to a broad collection of commonly used chemotherapeutics including doxorubicin, daunorubicin, vinblastine, vincristine, colchicines. In addition to the contribution these transporters make to the development of multi-drug resistance, there are currently 13 human genetic diseases associated with defects in 14 different transporters. The most common of these conditions include cystic fibrosis, Stargardt disease, age-related macular degeneration, adrenoleukodystrophy, Tangier disease, Dubin- Johnson syndrome and progressive familial intrahepatic cholestasis. For this reason, siRNAs directed against members of this, and related, families are potentially valuable research and therapeutic tools.
With respect to channels, analysis of Drosophila mutants has enabled the initial molecular isolation and characterization of several distinct channels including (but not limited to) potassium (K+) channels. This list includes shaker (Sh), which encodes a voltage activated K+ channel, slowpoke (SIo), a Ca2+ activated K+ channel, and ether-a-go-go (Eag). The Eag family is further divided into three subfamilies: Eag, Elk (eag-like K channels), and Erg (Eag related genes).
The Erg subfamily contains three separate family members (Ergl-3) that are distantly related to the sh family of voltage activated K channels. Like sh, erg polypetides contain the classic six membrane spanning architecture of K+ channels (S1-S6) but differ in that each includes a segment associated with the C-terminal cytoplasmic region that is homologous to cyclic nucleotide binding domains (cNBD). Like many isolated ion channel mutants, erg mutants are temperature-sensitive paralytics, a phenotype caused by spontaneous repetitive firing (hyperactivity) in neurons and enhanced transmitter release at the neuromuscular junction.
Initial studies on the tissue distribution of all three members of the erg subfamily show two general patterns of expression. Ergl and erg3 are broadly expressed throughout the nervous system and are observed in the heart, the superior mesenteric ganglia, the celiac ganglia, the retina, and the brain. In contrast, erg2 shows a much more restricted pattern of expression and is only observed in celiac ganglia and superior mesenteric ganglia. Similarly, the kinetic properties of the three erg potassium channels are not homogeneous. Ergl and erg2 channels are relatively slow activating delayed rectifiers whereas the erg3 current activates rapidly and then exhibits a predominantly transient component that decays to a sustained plateau. The current properties of all three channels are sensitive to methanesulfonanilides, suggesting a high degree of conservation in the pore structure of all three proteins.
Recently, the erg family of K channels has been implicated in human disease. Consistent with the observation that ergl is expressed in the heart, single strand conformation polymorphism and DNA sequence analyses have identified HERG (human ergl) mutations in six long-QT-syndrome (LQT) families, an inherited disorder that results in sudden death from a ventricular tachyarrythmia. Thus siRNA directed against this group of molecules (e.g., KCNHl-8) will be of extreme therapeutic value.
Another group of channels that are potential targets of siRNAs are the CLCA family that mediate a Ca2+-activated Cl~ conductance in a variety of tissues. To date, two bovine (bCLCl; bCLCA2 (Lu-ECAM-I)), three mouse (mCLCAl; mCLCA2; mCLCA3) and four human (hCLCAl; hCLCA2; hCLCA3; hCLCA4) CLCA family members have been isolated and patch-clamp studies with transfected human embryonic kidney (HEK-293) cells have shown that bCLCAl, mCLCAl, and hCLCAl mediate a Ca2+-activated CF conductance that can be inhibited by the anion channel blocker DIDS and the reducing agent dithiothreitol (DTT).
The protein size, structure, and processing seem to be similar among different CLCA family members and has been studied in greatest detail for Lu-ECAM-I . The Lu-ECAM-I open reading frame encodes a precursor glycoprotein of 130 kDa that is processed to a 90-kDa amino-terminal cleavage product and a group of 30- to 40-kDa glycoproteins that are glycosylation variants of a single polypeptide derived from its carboxy terminus. Both subunits are associated with the outer cell surface, but only the 90-kDa subunit is thought to be anchored to the cell membrane via four transmembrane domains.
Although the protein processing and function appear to be conserved among CLCA homologs, significant differences exist in their tissue expression patterns. For example, bovine Lu-ECAM-I is expressed primarily in vascular endothelia, bCLCAl is exclusively detected in the trachea, and hCLCAl is selectively expressed in a subset of human intestinal epithelial cells. Thus the emerging picture is that of a multigene family with members that are highly tissue specific, similar to the ClC family of voltage-gated CF channels. The human channel, hCLCA2, is particular interesting from a medical and pharmacological standpoint. CLC A2 is expressed on the luminal surface of lung vascular endothelia and serves as an adhesion molecule for lung metastatic cancer cells, thus mediating vascular arrest and lung colonization. Expression of this molecule in normal mammary epithelium is consistently lost in human breast cancer and in nearly all tumorigenic breast cancer cell lines. Moreover, re-expression of hCLCA2 in human breast cancer cells abrogates tumorigenicity in nude mice, implying that hCLCA2 acts as a tumour suppressor in breast cancer. For these reasons, siRNA directed against CLCA family members and related channels may prove to be valuable in research and therapeutic venues.
Transporters Involved in Synaptic Transmission
Synaptic transmission involves the release of a neurotransmitter into the synaptic cleft, interaction of that transmitter with a postsynaptic receptor, and subsequent removal of the transmitter from the cleft. In most synapses the signal is terminated by a rapid reaccumulation of the neurotransmitter into presynaptic terminals. This process is catalyzed by specific neurotransmitter transporters that are often energized by the electrochemical gradient of sodium across the plasma membrane of the presynaptic cells.
Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the central nervous system. The inhibitory action of GABA, mediated through GABAA/ GABAB receptors, and is regulated by GABA transporters (GATs), integral membrane proteins located perisynaptically on neurons and glia. So far four different carriers (GAT1-GAT4) have been cloned and their cellular distribution has been partly worked out. Comparative sequence analysis has revealed that GABA transporters are related to several other proteins involved in neurotransmitter uptake including gamma-aminobutyric acid transporters, monoamine transporters, amino acid transporters, certain "orphan" transporters, and the recently discovered bacterial transporters. Each of these proteins has a similar 12 transmembrane helices topology and relies upon the Na+/Cl- gradient for transport function. Transport rates are dependent on substrate concentrations, with half-maximal effective concentrations for transport frequently occurring in the submicromolar to low micromolar range. In addition, transporter function is bidirectional, and non- vesicular efflux of transmitter may contribute to ambient extracellular transmitter levels.
Recent evidence suggests that GABA transporters, and neurotransmitter transporters in general, are not passive players in regulating neuronal signaling; rather, transporter function can be altered by a variety of initiating factors and signal transduction cascades. In general, this functional regulation occurs in two ways, either by changing the rate of transmitter flux through the transporter or by changing the number of functional transporters on the plasma membrane. A recurring theme in transporter regulation is the rapid redistribution of the transporter protein between intracellular locations and the cell surface, hi general, this functional modulation occurs in part through activation of second messengers such as kinases, phosphatases, arachidonic acid, and pH. However, the mechanisms underlying transporter phosphorylation and transporter redistribution have yet to be fully elucidated.
GABA transporters play a pathophysiological role in a number of human diseases including temporal lobe epilepsy and are the targets of pharmacological interventions. Studies in seizure sensitive animals show some (but not all) of the GAT transporters have altered levels of expression at times prior to and post seizure, suggesting this class of transporter may affect epileptogenesis, and that alterations following- seizure may be compensatory responses to modulate seizure activity. For these reasons, siRNAs directed against members of this family of genes (including but not limited to SLCG6A1-12) may prove to be valuable research and therapeutic tools.
Organic Ion Transporters
The human body is continuously exposed to a great variety of xenobiotics, via food, drugs, occupation, and environment. Excretory organs such as kidney, liver, and intestine defend the body against the potentially harmful effects of these compounds by transforming them into less active metabolites that are subsequently secreted from the system. Carrier-mediated transport of xenobiotics and their metabolites exist for the active secretion of organic anions and cations. Both systems are characterized by a high clearance capacity and tremendous diversity of substances accepted, properties that result from the existance of multiple transporters with overlapping substrate specificities. The class of organic anion transporters plays a critical role in the elimination of a large number of drugs (e.g., antibiotics, chemotherapeutics, diuretics, nonsteroidal anti-inflammatory drugs, radiocontrast agents, cytostatics); drug metabolites (especially conjugation products with glutathione, glucuronide, glycine, sulfate, acetate); and toxicants and their metabolites (e.g., mycotoxins, herbicides, plasticizers, glutathione .S-conjugates of polyhaloalkanes,polyhaloalkenes, hydroquinones, aminophenols), many of which are specifically harmful to the kidney.
Over the past couple of years the number of identified anion transporting molecules has grown tremendously. Uptake of organic anions (OA") across the basolateral membrane is mediated by the classic sodium-dependent organic anion transport system, which includes α-ketoglutarate (ct-KG2~)/OA~ exchange via the organic anion transporter (OATl) and sodium-ketoglutarate cotransport via the Na+/dicarboxylate cotransporter (SDCT2). The organic anion transporting polypetide, Oatpl, and the kidney-specific OAT-Kl and OAT-K2 are seen as potential molecules that mediate facilitated OA" efflux but could also be involved in reabsorption via an exchange mechanism. Lastly the PEPTl and PEPT2 mediate luminal uptake of peptide drugs, whereas CNTl and CNT2 are involved in reabsorption of nucleosides.
The organic anion-transporting polypeptide 1 (Oatpl) is a Na+- and ATP- independent transporter originally cloned from rat liver. The tissue distribution and transport properties of the Oatpl gene product are complex. Oatpl is localized to the basolateral membrane of hepatocytes, and is found on the apical membrane of S3 proximal tubules. Studies with transiently transfected cells (e.g., HeLa cells) have indicated that Oatpl mediates transport of a variety of molecules including taurocholate, estrone-3 -sulfate, aldosterone, Cortisol, and others. The observed uptake of taurocholate by Oatpl expressed in X. laevis oocytes is accompanied by efflux of GSH, suggesting that transport by this molecule may be glutathione dependent. Computer modeling suggests that members of the Oatp family are highly conserved, hydrophobic, and have 12 transmembrane domains. Decreases in expression of Oatp family members have been associated with cholestatic liver diseases and human hepatoblastomas, making this family of proteins of key interest to researchers and the medical community. For these reasons, siRNAs directed against OAT family members (including but not limited to SLC21 A2, 3, 6, 8, 9, 11, 12, 14, 15, and related transporters) are potentially useful as research and therapeutic tools.
Nucleoside transporters Nucleoside transporters play key roles in physiology and pharmacology.
Uptake of exogenous nucleosides is a critical first step of nucleotide synthesis in tissues such as bone marrow and intestinal epithelium and certain parasitic organisms that lack de novo pathways for purine biosynthesis. Nucleoside transporters also control the extracellular concentration of adenosine in the vicinity of its cell surface receptors and regulate processes such as neurotransmission and cardiovascular activity. Adenosine itself is used clinically to treat cardiac arrhythmias, and nucleoside transport inhibitors such as dipyridamole, dilazep, and draflazine function as coronary vasodilators.
In mammals, plasma membrane transport of nucleosides is brought about by members of the concentrative, Na+-dependent (CNT) and equilibrative, Na+- independent (ENT) nucleoside transporter families. CNTs are expressed in a tissue- specific fashion; ENTs are present inmost, possibly all, cell types and are responsible for the movement of hydrophilic nucleosides and nucleoside analogs down their concentration gradients. In addition, structure/function studies of ENT family members have predicted these molecules to contain eleven transmembrane helical segments with an amino terminus that is intracellular and a carboxyl terminus that is extracellular. The proteins have a large glycosylated loop between TMs 1 and 2 and a large cytoplasmic loop between TMs 6 and 7. Recent investigations have implicated the TM 3-6 region as playing a central role in solute recognition. The medical importance of the ENT family of proteins is broad. In humans adenosine exerts a range of cardioprotective effects and inhibitors of ENTs are seen as being valuable in alleviating a variety of cardio/cardio vascular ailments. In addition, responses to nucleoside analog drugs has been observed to vary considerably amongst, e.g., cancer patients. While some forms of drug resistance have been shown to be tied to the up-regulation of ABC-transporters (e.g., MDRl), resistance may also be the result of reduced drug uptake (i.e., reduced ENT expression). Thus, a clearer understanding of ENT transporters may aid in optimizing drug treatments for patients suffering a wide range of malignancies. For these reasons, siRNAs directed against this class of molecules (including SLC28A1-3, SLC29A1-4, and related molecules) may be useful as therapeutic and research tools.
Sulfate Transporters All cells require inorganic sulfate for normal function. Sulfate is the fourth most abundant anion in human plasma and is the major source of sulfur in many organisms. Sulfation of extracellular matrix proteins is critical for maintaining normal cartilage metabolism and sulfate is an important constituent of myelin membranes found in the brain
Because sulfate is a hydrophilic anion that cannot passively cross the lipid bilayer of cell membranes, all cells require a mechanism for sulfate influx and efflux to ensure an optimal supply. To date, a variety of sulfate transporters have been identified in tissues from many origins. These include the renal sulfate transporters (NaSi-I and Sat-1), the ubiquitously expressed diastrophic dysplasia sulfate transporter (DTDST), the intestinal sulfate transporter (DRA), and the erythrocyte anion exchanger (AEl). Most, if not all, of these molecules contain the classic 12 transmembrane spanning domain architecture commonly found amongst members of the anion transporter superfamily.
Recently three different sulfate transporters have been associated with specific human genetic diseases. Family members SLC26A2, SLC26A3, and SLC26A4 have been recognized as the disease genes mutated in diastrophic dysplasia, congenital chloride diarrhea (CLD), and Pendred syndrome (PDS), respectively. DTDST is a particularly complex disorder. The gene encoding this molecule maps to chromosome 5q, and encodes two distinct transcripts due to alternative exon usage. In contrast to other sulfate transporters (e.g., Sat-1) anion movement by the DTDST protein is markedly inhibited by either extracellular chloride or bicarbonate. Impaired function of the DTDST gene product leads to undersulfation of proteoglycans and a complex family of recessively inherited osteochondrodysplasias (achondrogenesis type IB, atelosteogenesis type II, and diastrophic dysplasia) with clinical features including but not limited to, dwarfism, spinal deformation, and specific joint abnormalities. Interestingly, while epidemiological studies have shown that the disease occurs in most populations, it is particularly prevalent in Finland owing to an apparent founder effect. For these reasons, siRNAs directed against this class of genes (including but not limited to SLC26A1-9, and related molecules) may be potentially helpful in both therapeutic and research venues.
Ion Exchangers
Intracellular pH regulatory mechanisms are critical for the maintenance of countless cellular processes. For instance, in muscle cells, contractile processes and metabolic reactions are influenced by pH. During periods of increased energy demands and ischemia, muscle cells produce large amounts of lactic acid that, without quick and efficient disposal, would lead to acidification of the sarcoplasm.
Several different transport mechanisms have evolved to maintain a relatively constant intracellular pH. The relative contribution of each of these processes varies with cell type, the metabolic requirements of the cell, and the local environmental conditions. Intracellular pH regulatory processes that have been characterized functionally include but are not limited to the Na+/H+ exchange, the Na(HCO3 )„ cotransport, and the Na+-dependent and -independent Cl^ase exchangers. As bicarbonate and CO2 comprise the major pH buffer of biological fluids, sodium biocarbonate cotransporters (NBCs) are critical. Studies have shown that these molecules exist in numerous tissues including the kidney, brain, liver, cornea, heart, and lung, suggesting that NBCs play an important role in mediating HCO3 " transport in both epithelial as well as nonepithelial cells.
Recent molecular cloning experiments have identified the existence of four NBC isoforms (NBCl, 2, 3 and 4) and two NBC-related proteins, AE4 and NCBE (Anion Exchanger 4 and Na-dependent Chloride-Bicarbonate Exchanger). The secondary structure analyses and hydropathy profile of this family predict them to be intrinsic membrane proteins with 12 putative transmembrane domains and several family members exhibit iV-linked glycosylation sites, protein kinases A and C, casein kinase II, and ATP/GTP -binding consensus phosphorylation sites, as well as potential sites for myristylation and amidation. AE4 is a relatively recent addition to this family of proteins and shows between 30-48% homology with the other family members. When expressed in COS-7 cells and Xenopus oocytes AE4 exhibits sodium-independent and DIDS-insensitive anion exchanger activity. Exchangers have been shown to be responsible for a variety of human diseases. For instance, mutations in three genes of the anion transporter family (SLC) are believed to cause known hereditary diseases, including chondrodysplasia (SLC26A2, DTD), diarrhea (A3, down-regulated in adenoma/chloride-losing diarrhea protein: DRA/CLD), and goiter/deafness syndrome (A4, pendrin). Moreover, mutations in Na+/HCO3 co- transporters have also been associated with various human maladies. For these reasons, siRNAs directed against these sorts of genes {e.g., SLC4A4-10, and related genes) may be useful for therapeutic and research purposes.
Receptors Involved in Synaptic Transmission hi all vertebrates, fast inhibitory synaptic transmission is the result of the interaction between the neurotransmitters glycine (GIy) and γ-aminobutyric acid (GABA) and their respective receptors. The strychnine-sensitive glycine receptor is especially important in that it acts in the mammalian spinal cord and brain stem and has a well-established role in the regulation of locomotor behavior.
Glycine receptors display significant sequence homology to several other receptors including the nicotinic acetylcholine receptor, the aminobutyric acid receptor type A (GABAAR), and the serotonin receptor type 3 (5-HT3R) subunits. As members of the superfamily of ligand-gated ion channels, these polypeptides share common topological features. The glycine receptor is composed of two types of glycosylated integral membrane proteins (αl-α4 and β) arranged in a pentameric suprastructure. The alpha subunit encodes a large extracellular, N-terminal domain that carries the structural determinants essential for agonist and antagonist binding, followed by four transmembrane spanning regions (TMl -TM4), with TM2 playing the critical role of forming the inner wall of the chloride channel. The density, location, and subunit composition of glycine neurotransmitter receptors changes over the course of development. It has been observed that the amount of GIyR gene translation (assessed by the injection of developing rat cerebral cortex rnRNA into Xenopus oocytes) decreases with age, whereas that of GABARs increases. In addition, the type and location of mRNAs coding for GIyR changes over the course of development. For instance in a study of the expression of alpha 1 and alpha 2 subunits in the rat, it was observed that (in embryonic periods El 1-18) the mantle zone was scarce in the alpha 1 mRNA, but the germinal zone (matrix layer) at El 1-14 expressed higher levels of the message. At postnatal day 0 (PO), the alpha 1 signals became manifested throughout the gray matter of the spinal cord. By contrast, the spinal tissues at PO exhibited the highest levels of alpha 2 mRNA, which decreased with the postnatal development.
In both, man and mouse mutant lines, mutations of GIyR subunit genes result in hereditary motor disorders characterized by exaggerated startle responses and increased muscle tone. Pathological alleles of the Glral gene are associated with the murine phenotypes oscillator (spd01) and spasmodic (spd). Similarly, a mutant allele of Glrb has been found to underly the molecular pathology of the spastic mouse (spa). Resembling the situation in the mouse, a variety of GLRAl mutant alleles have been shown to be associated with the human neurological disorder hyperekplexia or startle disease. For these reasons, siRNA directed against glycine receptors (GLRA 1-3, GLRB, and related molecules), glutamate receptors, GABA receptors, ATP receptors, and related neurotransmitter receptor molecules may be valuable therapeutic and research reagents.
Proteases Kallikreins
One important class of proteases are the kallikreins, serine endopeptidases that split peptide substrates preferentially on the C-terminal side of internal arginyl and lysyl residues. Kallikreins are generally divided into two distinct groups, plasma kallikreins and tissue kallikreins. Tissue kallikreins represent a large group of enzymes that have substantial similarities at both the gene and protein level. The genes encoding this group are frequently found on a single chromosome, are organized in clusters, and are expressed in a broad range of tissues {e.g., pancreas, ovaries, breast). In contrast, the plasma form of the enzyme is encoded by a single gene (e.g., KLK3) that has been localized to chromosome 4q34-35 in humans. The gene encoding plasma kallikrein is expressed solely in the liver, contains 15 exons, and encodes a glycoprotein that is translated as a preprotein called prekallikrein.
Kallikreins are believed to play an important role in a host of physiological events. For instance, the immediate consequence of plasma prekallikrein activation is the cleavage of high molecular weight kininogen (HK) and the subsequent liberation of bradykinin, a nine amino acid vasoactive peptide that is an important mediator of inflammatory responses. Similarly, plasma kallikrein promotes single-chain urokinase activation and subsequent plasminogen activation, events that are critical to blood coaggulation and wound healing.
Disruptions in the function of kallikreins have been implicated in a variety of pathological processes including imbalances in renal function and inflammatory processes. For these reasons, siRNAs directed against this class of genes (e.g., KLKl -15) may prove valuable in both research and therapeutic settings.
ADAM Proteins The process of fertilization takes place in a series of discrete steps whereby the sperm interacts with, i) the cumulus cells and the hyaluronic acid extracellular matrix (ECM) in which they are embedded, ii) the egg's own ECM, called the zona pellucida (ZP), and iii) the egg plasma membrane. During the course of these interactions, the "acrosome reaction," the exocytosis of the acrosome vesicle on the head of the sperm, is induced, allowing the sperm to penetrate the ZP and gain access to the perivitelline space. This process exposes new portions of the sperm membrane, including the inner acrosomal membrane and the equatorial segment, regions of the sperm head that can participate in initial gamete membrane binding.
The interactions of the gamete plasma membranes appear to involve multiple ligands and receptors and are frequently compared to leukocyte-endothelial interactions. These interactions lead to a series of signal transduction events in the egg, known as collectively as egg activation and include the initiation of oscillations in intracellular calcium concentration, the exit from meiosis, the entry into the first embryonic mitosis, and the formation of a block to polyspermy via the release of ZP- modifying enzymes from the egg's cortical granules. Ultimately, sperm and egg not only adhere to each other but also go on to undergo membrane fusion, making one cell (the zygote) from two.
Studies on the process of sperm-egg interactions have identified a number of proteins that are crucial for fertilization. One class of proteins, called the ADAM family (A Disintegrin And Metalloprotease), has been found to be important in spermatogenesis and fertilization, as well as various developmental systems including myo genesis and neurogenesis. Members of the family contain a disintegrin and metalloprotease domain (and therefore have (potentially) both cell adhesion and protease activities), as well as cysteine-rich regions, epidermal growth factor (EGF)- like domains, a transmembrane region, and a cytoplasmic tail. Currently, the ADAM gene family has 29 members and constituents are widely distributed in many tissues including the brain, testis, epididymis, ovary, breast, placenta, liver, heart, lung, bone, and muscle.
One of the best-studied members of the ADAM family is fertilin, a heterodimeric protein comprised of at least two subunits, fertilin alpha and fertilin beta. The fertilin beta gene (AD AM2) has been disrupted with a targeting gene construct corresponding to the exon encoding the fertilin beta disintegrin domain. Sperm from males homozygous for disruptions in this region exhibit defects in multiple facets of sperm function including reduced levels of sperm transit from the uterus to the oviduct, reduced sperm-ZP binding, and reduced sperm-egg binding, all of which contribute to male infertility.
Recently, four new ADAM family members (ADAM 24-27) have been isolated. The deduced amino acid sequences show that all four contain the complete domain organization common to ADAM family members and Northern Blot analysis has shown all four to be specific to the testes. siRNAs directed against this class of genes (e.g., ADAM2 and related proteins) may be useful as research tools and therapeutics directed toward fertility and birth control. Aminopeptidases
Aminopeptidases are proteases that play critical roles in processes such as protein maturation, protein digestion in its terminal stage, regulation of hormone levels, selective or homeostatic protein turnover, and plasmid stabilization. These enzymes generally have broad substrate specificity, occur in several forms and play a major role in physiological homeostasis. For instance, the effects of bradykinin, angiotensin converting enzyme (ACE), and other vasoactive molecules are muted by one of several peptidases that cleave the molecule at an internal position and eliminate its ability to bind its cognate receptor (e.g., for bradykinin, the B2 -receptor).
Among the enzymes that can cleave bradykinin is the membrane bound aminopeptidase P, also referred to as aminoacylproline aminopeptidase, proline aminopeptidase; X-Pro aminopeptidase (eukaryote) and XPNPEP2. Aminopeptidase P is an aminoacylproline aminopeptidase specific for NH^-terminal Xaa-proline bonds. The enzyme i) is a mono-zinc-containing molecule that lacks any of the typical metal binding motifs found in other zinc metalloproteases, ii) has an active- site configuration similar to that of other members of the MG peptidase family, and iii) is present in a variety of tissues including but not limited to the lung, kidney, brain, and intestine.
Aminopeptidases play an important role in a diverse set of human diseases. Low plasma concentrations of aminopeptidase P are a potential predisposing factor for development of angio-oedema in patients treated with ACE inhibitors, and inhibitors of aminopeptidase P may act as cardioprotectors against other forms of illness including, but not limited to myocardial infarction. For these reasons, siRNAs directed against this family of proteins (including but not limited to XPNPEPl and related proteins) may be useful as research and therapeutic tools.
Serine Proteases One important class of proteases are the serine proteases. Serine proteases share a common catalytic triad of three amino acids in their active site (serine (nucleophile), aspartate (electrophile), and histidine (base)) and can hydrolyze either esters or peptide bonds utilizing mechanisms of covalent catalysis and preferential binding of the transition state. Based on the position of their introns serine proteases have been classified into a minimum of four groups including those in which 1) the gene has no introns interrupting the exon coding for the catalytic triad (e.g., the haptoglobin gene,); 2) each gene contains an intron just downstream from the codon for the histidine residue at the active site, a second intron downstream from the exon containing the aspartic acid residue of the active site and a third intron just upstream from the exon containing the serine of the active site (e.g., trypsinogen, chymotrypsinogen, kallikrein and proelastase); 3) the genes contain seven introns interrupting the exons coding the catalytic region (e.g., complement factor B gene); and 4) the genes contain two introns resulting in a large exon that contains both the active site aspartatic acid and serine residues (e.g., factor X, factor IX and protein C genes).
Cytotoxic lymphocytes (e.g., CD8(+) cytotoxic T cells and natural killer cells) form the major defense of higher organisms against virus-infected and transformed cells. A key function of these cells is to detect and eliminate potentially harmful cells by inducing them to undergo apoptosis. This is achieved through two principal pathways, both of which require direct but transient contact between the killer cell and its target. The first pathway involves ligation of TNF receptor-like molecules such as Fas/CD95 to their cognate ligands, and results in mobilization of conventional, programmed cell-death pathways centered on activation of pro-apoptotic caspases. The second mechanism consists of a pathway whereby the toxic contents of a specialized class of secretory vesicles are introduced into the target cell. Studies over the last two decades have identified the toxic components as Granzymes, a family of serine proteases that are expressed exclusively by cytotoxic T lymphocytes and natural killer (NK) cells. These agents are stored in specialized lytic granules and enter the target cell via endocytosis. Like caspases, cysteine proteases that play an important role in apoptosis, granzymes can cleave proteins after acidic residues, especially aspartic acid, and induce apoptosis in the recipient cell.
Granzymes have been grouped into three subfamilies according to substrate specificity. Members of the granzyme family that have enzymatic activity similar to the serine protease chymotrypsin are encoded by a gene cluster termed the 'chymase locus'. Similarly, granzymes with trypsin-like specificities are encoded by the 'tryptase locus', and a third subfamily cleaves after unbranched hydrophobic residues, especially methionine, and are encoded by the 'Met-ase locus'. All granzymes are synthesized as zymogens and, after clipping of the leader peptide, obtain maximal enzymatic activity subsequent to the removal of an amino-terminal dipeptide.
Granzymes have been found to be important in a number of important biological functions including defense against intracellular pathogens, graft versus host reactions, the susceptibility to transplantable and spontaneous malignancies, lymphoid homeostasis, and the tendency toward auto-immune diseases. For these reasons, siRNAs directed against granszymes (e.g., GZMA, GZMB, GZMH, GZHK, GZMM) and related serine proteases may be useful research and therapeutic reagents.
Kinases
Protein Kinases (PKs) have been implicated in a number of biological processes. Kinase molecules play a central role in modulating cellular physiology and developmental decisions, and have been implicated in a large list of human maladies including cancer, diabetes, and others.
During the course of the last three decades, over a hundred distinct protein kinases have been identified, all with presumed specific cellular functions. A few of these enzymes have been isolated to sufficient purity to perform in vitro studies, but most remain intractable due to the low abundance of these molecules in the cell. To counter this technical difficulty, a number of protein kinases have been isolated by molecular cloning strategies that utilize the conserved sequences of the catalytic domain to isolate closely related homologs. Alternatively, some kinases have been purified (and subsequently studied) based on their interactions with other molecules.
p58 is a member of the p34cdc2-related supergene family and contains a large domain that is highly homologous to the cell division control kinase, cdc2. This new cell division control-related protein kinase was originally identified as a component of semipurified galactosyltransferase; thus, it has been denoted galactosyltransferase- associated protein kinase (GTA-kinase). GTA-kinase has been found to be expressed in both adult and embryonic tissues and is known to phosphorylate a number of substrates, including histone Hl, and casein. Interestingly enough, over expression of this molecule in CHO cells has shown that elevated levels of p58 result in a prolonged late telophase and an early Gl phase, thus hinting of an important role for GTA- kinase in cell cycle regulation.
Cyclin Dependent Kinases The cyclin-dependent kinases (Cdks) are a family of highly conserved serine/threonine kinases that mediate many of the cell cycle transitions that occur during duplication. Each of these Cdk catalytic subunits associates with a specific subset of regulatory subunits, termed cyclins, to produce a distinct Cdk-cyclin kinase complex that, in general, functions to execute a unique cell cycle event.
Activation of the Cdk-cyclin kinases during cellular transitions is controlled by a variety of regulatory mechanisms. For the Cdc2-cyclin B complex, inhibition of kinase activity during S phase and G2 is accomplished by phosphorylation of two Cdc2 residues, Thr14 and Tyr15, which are positioned within the ATP-binding cleft. Phosphorylation of Thr14 and/or Tyr15 suppresses the catalytic activity of the molecule by disrupting the orientation of the ATP present within this cleft. In contrast, the abrupt dephosphorylation of these residues by the Cdc25 phosphatase results in the rapid activation of Cdc2-cyclin B kinase activity and subsequent downstream mitotic events. While the exact details of this pathway have yet to be elucidated, it has been proposed that Thr14/Tyr15 phosphorylation functions to permit a cell to attain a critical concentration of inactive Cdk-cyclin complexes, which, upon activation, induces a rapid and complete cell cycle transition. Furthermore, there is evidence in mammalian cells that Thr14/Tyr15 phosphorylation also functions to delay Cdk activation after DNA damage.
The Schizosaccharomycespom.be weel gene product was the first kinase identified that is capable of phosphorylating Tyr15 in Cdc2. Homologs of the Weel kinase have been subsequently identified and biochemically characterized from a wide range of species including human, mouse, frog, Saccharomyces cerevisiae, and Drosophila. In vertebrate systems, where Thr14 in Cdc2 is also phosphorylated, the Weel kinase was capable of phosphorylating Cdc2 on Tyr15, but not Thr14, indicating that another kinase was responsible for Thr14 phosphorylation. This gene, Mytl kinase, was recently isolated from the membrane fractions of Xenopus egg extracts and has been shown to be capable of phosphorylating Thr14 and, to a lessor extent, Tyr15 in Cdc2. A human Mytl homolog displaying similar properties has been isolated, as well as a non-membrane- associated molecule with Thr14 kinase activity.
In the past decade it has been shown that cancer can originate from overexpression of positive regulators, such as cyclins, or from underexpression of negative regulators (e.g., plό (INK4a), pl5 (INK4b), p21 (Cipl)). Inhibitors such as Mytl are the focus of much cancer research because they are capable of controlling cell cycle proliferation, now considered the Holy Grail for cancer treatment. For these reasons, siRNA directed against kinases and kinase inhibitors including but not limited to ABLl, ABL2, ACKl, ALK, AXL, BLK, BMX, BTK, C20orf64, CSFlR, SCK, DDRl, DDR2, DKFZp761P1010, EGFR, EPHAl, EPHA2, EPHA3, EPHA4, EPHA7, EPHA8, EPHBl, EPHB2, EPHB3, EPHB4. EPHB6, ERBB2, ERBB3, ERBB4, FER, FES, FGFRl, FGFR2, FGFR3, FGFR4, FGR, FLTl, FLT3, FLT4, FRK, FYN, HCK, IGFlR, INSR, ITK, JAKl, JAK2, JAK3, KDR, KIAA1079, KIT, LCK, LTK, LYN, MATK, MERTK, MET, MSTl R, MUSK, NTRKl , NTRK2, NTRK3, PDGFRA, PDGFRB, PTK2, PTK2B, PTK6, PTK7, PTK9, PTK9L, RET, RORl, ROR2, ROSl, RYK, SRC, SYK, TEC, TEK, TIE, TNKl, TXK, TYK2, TYRO3, YESl, and related proteins, may be useful for research and therapeutic purposes.
G Protein Coupled Receptors
One important class of genes to which siRNAs can be directed are G-protein coupled receptors (GPCRs). GPCRs constitute a superfamily of seven transmembrane spanning proteins that respond to a diverse array of sensory and chemical stimuli, such as light, odor, taste, pheromones, hormones and neurotransmitters. GPCRs play a central role in cell proliferation, differentiation, and have been implicated in the etiology of disease.
The mechanism by which G protein-coupled receptors translate extracellular signals into cellular changes was initially envisioned as a simple linear model: activation of the receptor by agonist binding leads to dissociation of the heterotrimeric GTP -binding G protein (Gs, Gi, or Gq) into its alpha and beta/gamma subunits, both of which can activate or inhibit various downstream effector molecules. More specifically, activation of the GPCR induces a conformational change in the Ga subunit, causing GDP to be released and GTP to be bound in its place. The Ga and Gβγ subunits then dissociate from the receptor and interact with a variety of effector molecules. For instance in the case of the Gs family, the primary function is to stimulate the intracellular messenger adenylate cyclase (AC), which catalyzes the conversion of cytoplasmic ATP into the secondary messenger cyclic AMP (cAMP). In contrast, the Gi family inhibits this pathway and the Gq family activates phospholipases C (PLC), which cleaves phosphatidylinositol 4,5, bisphosphate (PIP2) to generate inositol- 1,4,5-phosphate (IP3) and diacylglycerol (DAG).
More recently, studies have shown that the functions of GPCRs are not limited to their actions on G-proteins and that considerable cross-talk exists between this diverse group of receptor molecules and a second class of membrane bound proteins, the receptor tyrosine kinases (RTKs). A number of GPCRs such as endothelin-1, thrombin, bombesin, and dopamine receptors can activate MAPKs, a downstream effector of the RTK/Ras pathway. Interestingly, the interaction between these two families is not unidirectional and RTKs can also modulate the activity of signaling pathways traditionally thought to be controlled exclusively by ligands that couple to GPCRs. For instance, EGF, which normally activates the MAPK cascade via the EGF receptor can stimulate adenylate cyclase activity by activating Gas.
There are dozens of members of the G Protein-Coupled Receptor family that have emerged as prominent drug targets in the last decade. One non-limiting list of potential GPCR-siRNA targets is as follows:
CMKLRl
CMLl/ CMKLRl (Accession No. Q99788) is a member of the chemokine receptor family of GPCRs that may play a role in a number of diseases including those involved in inflammation and immunological responses (e.g., asthma, arthritis). For this reason, siRNA directed against this protein may prove to be important therapeutic reagents.
Ill Studies of juvenile-onset neuronal ceroid lipofuscinosis (JNCL, Batten disease), the most common form of childhood encephalopathy that is characterized by progressive neural degeneration, show that it is brought on by mutations in a novel lysosomal membrane protein (CLN3). In addition to being implicated in JNCL, CLN3 (GPCR-like protein, Accession No. A57219) expression studies have shown that the CLN3 mRNA and protein are highly over-expressed in a number of cancers (e.g., glioblastomas, neuroblastomas, as well as cancers of the prostate, ovaries, breast, and colon) suggesting a possible contribution of this gene to tumor growth. For this reason, siRNA directed against this protein may prove to be important therapeutic reagents.
CLACR
The calcitonin receptor (CTR/ CALCR, Accession No. NM_001742) belongs to "family B" of GPCRs which typically recognized regulatory peptides such as parathyroid hormone, secretin, glucagons and vasoactive intestinal polypeptide.
Although the CT receptor typically binds to calcitonin (CT), a 32 amino acid peptide hormone produced primarily by the thyroid, association of the receptor with RAMP (Receptor Activity Modulating Protein) enables it to readily bind other members of the calcitonin peptide family including amylin (AMY) and other CT gene-related peptides (e.g., αCGRP and βCGRP). While the primary function of the calcitonin receptor pertains to regulating osteoclast mediated bone resorption and enhanced Ca+2 excretion by the kidney, recent studies have shown that CT and CTRs may play an important role in a variety of processes as wide ranging as embryonic/fetal development and sperm function/physiology. In addition, studies have shown that patients with particular CTR genotypes may be at higher risk to lose bone mass and that this GPCR may contribute to the formation of calcium oxalate urinary stones. For this reason, siRNA directed against CTR may be useful as therapeutic reagents.
OXTR The human oxytocin receptor (OTR, OXTR) is a 389 amino acid polypeptide that exhibits the seven transmembrane domain structure and belongs to the Class-I (rhodopsin-type) family of G-protein coupled receptors. OTR is expressed in a wide variety of tissues throughout development and mediates physiological changes through G(q) proteins and phospholipase C-beta. Studies on the functions of oxytocin and the oxytocin receptor have revealed a broad list of duties. OT and OTR play a role in a host of sexual, maternal and social behaviors that include egg-laying, birth, milk-letdown, feeding, grooming, memory and learning. In addition, it has been hypothesized that abnormalities in the functionality of oxytocin-OTR receptor-ligand system can lead to a host of irregularities including compulsive behavior, eating disorders (such as anorexia), depression, and various forms of neurodegenerative diseases. For these reasons, siRNA directed against this gene (NM_000916) may play an important role in combating OTR-associated illnesses.
EDG GPCRs
Lysophosphatidic acid and other lipid-based hormones/growth factors induce their effects by activating signaling pathways through the G-protein coupled receptors (GPCRs) and have been observed to play important roles in a number of human diseases including cancer, asthma, and vascular pathologies. For instance, during studies of immunoglobulin A nephropathy (IgAN), researchers have observed an enhanced expression of EDG5 (NP_004221) suggesting a contribution of this gene product in the development of IgAN. For that reason, siRNA directed against Edg5 (NM_004230), Edg4 (NM_004720), Edg7 (Nm_012152) and related genes may play an important role in combating human disease.
Genes Involved in Cholesterol Signaling and Biosynthesis
Studies on model genetic organisms such as Drosophila and C. elegans have led to the identification of a plethora of genes that are essential for early development. Mutational analysis and ectopic expression studies have allowed many of these genes to be grouped into discreet signal transduction pathways and have shown that these elements play critical roles in pattern formation and cell differentiation. Disruption of one or more of these genes during early stages of development frequently leads to birth defects whereas as alteration of gene function at later stages in life can result in tumorigenesis.
One critical set of interactions known to exist in both invertebrates and vertebrates is the Sonic Hedgehog-Patched-Gli pathway. Originally documented as a Drosophila segmentation mutant, several labs have recently identified human and mouse orthologs of many of the pathways members and have successfully related disruptions in these genes to known diseases. Pathway activation is initiated with the secretion of Sonic hedgehog. There are three closely related members of the Shh family (Sonic hedgehog, Desert, and Indian) with Shh being the most widely expressed form of the group. The Shh gene product is secreted as a small pro-signal molecule. To successfully initiate its developmental role, Shh is first cleaved, whereupon the N-terminal truncated fragment is covalently modified with cholesterol. The addition of the sterol moiety promotes the interaction between Shh and its cognate membrane bound receptor, Patched (Ptch). There are at least two isoforms of the Patched gene, Ptchl and Ptch2. Both isoforms contain a sterol-sensing domain (SSD); a roughly 180 amino acid cluster that is found in at least seven different classes of molecules including those involved in cholesterol biosynthesis, vesicular traffic, signal transduction, cholesterol transport, and sterol homeostasis, hi the absence of Shh, the Patched protein is a negative regulator of the pathway. In contrast, binding of Shh-cholesterol to the Patched receptor releases the negative inhibition which that molecule enforces on a G-protein coupled receptor known as Smoothened. Subsequent activation of Smoothened (directly or indirectly) leads to the triggering of a trio of transcription factors that belong to the GIi family. All three factors are relatively large, contain a characteristic C2-H2 zinc-finger pentamer, and recognize one of two consensus sequences (SEQ. ID NO. 0463 GACCACCCA or SEQ. ID NO. 0464 GAACCACCCA). hi the absence of Shh, GIi proteins are cleaved by the proteosome and the C-terminally truncated fragment translocates to the nucleus and acts as a dominant transcription repressor. In the presence of Shh-cholesterol, GIi repressor formation is inhibited and full-length GIi functions as a transcriptional activator.
Shh and other members of the Shh-PTCH-Gli pathway are expressed in a broad range of tissues (e.g., the notochord, the floorplate of the neural tube, the brain, and the gut) at early stages in development. Not surprisingly, mutations that lead to altered protein expression or function have been shown to induce developmental abnormalities. Defects in the human Shh gene have been shown to cause holoprosencephaly, a midline defect that manifests itself as cleft lip or palate, CNS septation, and a wide range of other phenotypes. Interestingly, defects in cholesterol biosynthesis generate similar Shh-like disorders (e.g., Smith-Lemli-Opitz syndrome) suggesting that cholesterol modification of the Shh gene product is crucial for pathway function. Both the Patched and Smoothened genes have also been shown to be clinically relevant with Smoothened now being recognized as an oncogene that, like PTCH-I and PTCH-2, is believed to be the causative agent of several forms of adult tumors. For these reasons, siRNA directed against Smoothened (SMO,
NM_005631), Patched (PTCH, nm_000264), and additional genes that participate in cholesterol signaling, biosynthesis, and degradation, have potentially useful research and therapeutic applications.
Targeted Pathways.
In addition to targeting siRNA against one or more members of a family of proteins, siRNA can be directed against members of a pathway. Thus, for instance, siRNA can be directed against members of a signal transduction pathway (e.g., the insulin pathway, including AKTl -3, CBL, CBLB, EIF4EBP1, FOXOlA, FOXO3A, FRAPl, GSK3A, GSK3B, IGFl, IGFlR, INPP5D, INSR, IRSl, MLLT7, PDPKl, PIK3CA, PIK3CB, PIK3R1, PIK3R2, PPP2R2B, PTEN, RPS6, RPS6KA1, RPX6KA3, SGK, TSCl, TSC2, AND XPOl), an apoptotic pathway (CASP3,6,7,8,9, DSH1/2, PI lO, P85, PDK1/2, CATENIN, HSP90, CDC37, P23, BAD, BCLXL, BCL2, SMAC, and others), pathways, involved in DNA damage, cell cycle, and other physiological (p53 ,MDM2, CHKl/2, BRCAl/2, ATM, ATR, P 15INK4, P27, P21 , SKP2, CDC25C/A, 14-3-3, PLK, RB, CDK4, GLUT4, Inos, Mtor, FKBP, PPAR, RXR, ER). Similarly, genes involved in immune system function including TNFRl, IL-IR, IRAKI/2, TRAF2, TRAF6, TRADD, FADD, IKKε, IKKγ, IKKβ, IKKα, IkBa, IkBβ, p50, p65, Rac, RhoA, Cdc42, ROCK, Pakl/2/3/4/5/6, cIAP, HDACl/2, CBP, β-TrCP, Rip2/4, and others are also important targets for the siRNAs described in this document and may be useful in treating immune system disorders. Genes involved in apoptosis, such as Dshl/2,PTEN, PI lO (pan), P85, PDK1/2, Aktl, Akt2, Akt (pan), p70S6K, GSK3β, PP2A (cat), β-catenin, HSP90, Cdc37/ρ50, P23, Bad, BcIxL, Bcl2, Smac/Diablo, and Askl are potentially useful in the treatment of diseases that involve defects in programmed cell death (e.g., cancer), while siRNA agents directed against p53, MDM2, Chkl/2, BRCAl/2, ATM, ATR, p^11^4, P27, P21, Skp2, Cdc25C/A, 14-3-3σ/ε, PLK, Rb, Cdk4, Glut4, iNOS, mTOR, FKBP, PPARγ, RXRα,.ERq and related genes may play a critical role in combating diseases associated with disruptions in DNA repair, and cell cycle abnormalities.
Tables VI -Table X below provide examples of useful pools for inhibiting different genes in the human insulin pathway and tyrosine kinase pathways, proteins involved in the cell cycle, the production of nuclear receptors, and other genes. These particular pools are particularly useful in humans, but would be useful in any species that generates an appropriately homologous mRNA. Further, within each of the listed pools any one sequence maybe used independently but preferably at least two of the listed sequences, more preferably at least three, and most preferably all of the listed sequences- for a given gene is present.
Figure imgf000118_0001
Figure imgf000119_0001
Figure imgf000120_0001
Figure imgf000121_0001
Figure imgf000121_0002
Figure imgf000122_0001
Figure imgf000123_0001
Figure imgf000124_0001
Figure imgf000125_0001
Figure imgf000126_0001
Figure imgf000127_0001
Figure imgf000128_0001
Figure imgf000129_0001
Figure imgf000129_0002
Figure imgf000130_0001
Figure imgf000131_0001
Figure imgf000132_0001
Figure imgf000133_0001
Figure imgf000134_0001
Figure imgf000135_0001
Figure imgf000136_0001
Figure imgf000137_0001
Figure imgf000138_0001
Figure imgf000139_0001
Figure imgf000140_0001
Figure imgf000140_0002
Figure imgf000141_0001
Figure imgf000142_0001
Figure imgf000143_0001
Figure imgf000144_0001
Figure imgf000145_0001
Figure imgf000146_0001
Figure imgf000147_0001
Figure imgf000148_0001
Figure imgf000149_0001
Figure imgf000150_0001
Figure imgf000151_0001
Figure imgf000152_0001
Figure imgf000153_0001
Figure imgf000154_0001
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Figure imgf000159_0001
Figure imgf000160_0001
Figure imgf000161_0001
Figure imgf000162_0001
In addition, to identifying functional siRNA against gene families or pathways, it is possible to design duplexes against genes known to be involved in specific diseases. For example when dealing with human disorders associated with allergies, it will be beneficial to develop siRNA against a number of genes including but not limited to:
the interleukin 4 receptor gene (SEQ.IDNO.2224:UAGAGGUGCUCAUUCAUUU, SEQ.IDNO.2225:GGUAUAAGCCUUUCCAAGA, SEQ.IDNO.2412:ACACACAGCUGGAAGAAAU, SEQ.IDNO.2226:UAACAGAGCUUCCUUAGGU),
the Beta-arrestin-2 (SEQ. ID NO. 2227: GGAUGAAGGAUGACGACUA, SEQ. ID NO. 2228: ACACC AACCUCAUUGAAUU, SEQ. ID NO. 2229: CGAACAAGAUGACCAGGUA, SEQ. ID NO. 2230: GAUGAAGGAUGACGACUAU, ),
the interferon-gamma receptor 1 gene (SEQ. ID NO. 2231: CAGCAUGGCUCUCCUCUUU, SEQ. ID NO. 2232: GUAAAGAACUAUGGUGUUA, SEQ. ID NO. 2233: GAAACUACCUGUUACAUUA, SEQ. ID NO. 2234: GAAGUGAGAUCCAGUAUAA),
the matrix metalloproteinase MMP-9 (SEQ. ID NO. 2235: GGAACCAGCUGUAUUUGUU, SEQ. ID NO. 2236: GUUGGAGUGUUUCUAAUAA, SEQ. ID NO. 2237: GCGCUGGGCUUAGAUCAUU, SEQ. ID NO. 2238: GGAGCCAGUUUGCCGGAUA),
the Slcllal (Nrampl) gene
(SEQ.IDNO.2239:CCAAUGGCCUGCUGAACAA, SEQ.IDNO.2240:GGGCCUGGCUUCCUCAUGA, SEQ.IDNO.2241:GGGCAGAGCUCCACCAUGA, SEQ.IDNO.2242:GCACGGCCAUUGCAUUCAA),
SPINK5 (SEQ. ID NO. 2243: CCAACUGCCUGUUCAAUAA, SEQ. ID NO. 2244: GGAUACAUGUGAUGAGUUU, SEQ. ID NO. 2245: GGACGAAUGUGCUGAGUAU, SEQ. ID NO. 2246: GAGCUUGUCUUAUUUGCUA,),
the CYP 1A2 gene
(SEQ.IDNO.2247:GAAAUGCUGUGUCUUCGUA, SEQ.IDNO.2248:GGACAGCACUUCCCUGAGA, SEQ.IDNO.2249:GAAGACACCACCAUUCUGA, SEQ.IDNO.2250:GGCCAGAGCUUGACCUUCA), thymosin-beta4Y
(SEQ. ID NO. 2251: GGACAGGCCUGCGUUGUUU, SEQ. ID NO. 2252: GGAAAGAGGAAGCUCAUGA, SEQ. ID NO. 2253 : GCAAACACGUUGGAUGAGU, SEQ. ID NO. 2254: GGACUAUGCUGCCCUUUUG,
activin A receptor IB
(SEQ.IDNO.2255:ACAAGACGCUCCAGGAUCU, SEQ.IDNO.2413:GCAACAGGAUCGACUUGAG, SEQ.IDNO.2414:GAAGCUGCGUCCCAACAUC, SEQ.IDNO.2256:GCAUAGGCCUGUAAUCGUA, SEQ.IDNO.2257:UCAGAGAGUUCGAGACAAA, SEQ.IDNO.2258:UGCGAAAGGUUGUAUGUGA, SEQ.IDNO.2259:GCAACAGGAUCGACUUGAG, SEQ.IDNO.2260:GAAUAGCGUUGUGUGUUAU, SEQ.IDNO.2261:UGAAUAGCGUUGUGUGUUA, SEQ.IDNO.2262:GGGAUCAGUUUGUUGAAUA, SEQ.IDNO.2263:GAGCCUGAAUCAUCGUUUA,),
ADAM33
(SEQ.IDNO.2264:GGAAGUACCUGGAACUGUA, SEQ.IDNO.2265:GGACAGAGGGAACCAUUUA, SEQ.IDNO.2266:GGUGAGAGGUAGCUCCUAA, SEQ.IDNO.2267:AAAGACAGGUGGCCACUGA),
theTAPl gene
(SEQ.IDNO.2268:GAAAGAUGAUCAGCUAUUU, SEQ.IDNO.2269:CAACAGAACCAGACAGGUA, SEQ.IDNO.2270:UGAGAAAUGUUCAGAAUGU, SEQ.IDNO.2271:UACCUUCACUCGAAACUUA,
COX-2
(SEQ. ID NO. 2272: GAACGAAAGUAAAGAUGUU, SEQ.IDNO.2273:GGACUUAUGGGUAAUGUUA, SEQ.IDNO.2274:UGAAAGGACUUAUGGGUAA, SEQ.IDNO.2275:GAUCAGAGUUCACUUUCUU),
ADPRT
(SEQ.IDNO.2276:GGAAAGAUGUUAAGCAUUU,
SEQ.IDNO.2277:CAUGGGAGCUCUUGAAAUA,
SEQ.IDNO.2278:GAACAAGGAUGAAGUGAAG,
SEQ.IDNO.2279:UGAAGAAGCUCACAGUAAA,),
HDC
(SEQ. ID NO. 2280: CAGCAGACCUUCAGUGUGA,
SEQ. ID NO. 2281: GGAGAGAGAUGGUGGAUUA,
SEQ. ID NO. 2282: GUACAGAGCUGGAGAUGAA, SEQ. ID NO. 2283 : GAACGUCCCUUCAGUCUGU),
HnmT
(SEQ.IDNO.2284:CAAAUUCUCUCCAAAGUUC, SEQ.IDNO.2285:GGAUAUAUCUGACUGCUUU, SEQ.IDNO.2286:GAGCAGAGCUUGGGAAAGA, SEQ.IDNO.2287:GAUAUGAGAUGUAGCAAAU),
GATA-3
(SEQ.IDNO.2288:GAACUGCUUUCUUUCGUUU, SEQ.IDNO.2289:GCAGUAUCAUGAAGCCUAA, SEQ.IDNO.2290:GAAACUAGGUCUGAUAUUC, SEQ.IDNO.2291:GUACAGCUCCGGACUCUUC),
Gab2 (SEQ. ID NO. 2292: GCACAACCAUUCUGAAGUU, SEQ. ID NO. 2293: GGACUUAGAUGCCCAGAUG, SEQ. ID NO. 2294: GAAGGUGGAUUCUAGGAAA, SEQ. ID NO. 2295: GGACUAGCCCUGCUGUUUA), and STAT6
(SEQ.IDNO.2296:GAUAGAAACUCCUGCUAAU, SEQ.IDNO.2297:GGACAUUUAUUCCCAGCUA, SEQ.IDNO.2298:GGACAGAGCUACAGACCUA, SEQ.IDNO.2299:GGAUGGCUCUCCACAGAUA).
In addition, rationally designed siRNA or siRNA pools can be directed against genes involved in anemia, heniophila or hypercholesterolemia. Such genes would include, but are not be limited to: APOA5
(SEQ.IDNO.2300:GAAAGACAGCCUUGAGCAA,
SEQ.IDNO.2301:GGACAGGGAGGCCACCAAA,
SEQ.IDNO.2302:GGACGAGGCUUGGGCUUUG,
SEQ.IDNO.2303:AGCAAGACCUCAACAAUAU),
HMG-CoA reductase
(SEQ.IDNO.2304:GAAUGAAGCUUUGCCCUUU,
SEQ.IDNO.2305:GAACACAGUUUAGUGCUUU,
SEQ.IDNO.2306:UAUCAGAGCUCUUAAUGUU, SEQ.IDNO.2307:UGAAGAAUGUCUACAGAUA),
NOS3
(SEQ.IDNO.2308:UGAAGCACCUGGAGAAUGA, SEQ.IDNO.2309:CGGAACAGCACAAGAGUUA, SEQ.IDNO.2310:GGAAGAAGACCUUUAAAGA, SEQ.IDNO.2415:GCACAAGAGUUAUAAGAUC),
ARH
(SEQ.IDNO.2416:CGAUACAGCUUGGCACUUU, SEQ.IDNO.2311:GAGAAGCGCUGCCCUGUGA, SEQ.IDNO.2312:GAAUCAUGCUGUUCUCUUU, SEQ.IDNO.2313:GGAGUAACCGGACACCUUA),
CYP7A1 (SEQ. ID NO. 2314: UAAGGUGACUCGAGUGUUU, SEQ. ID NO. 2315: AAACGACACUUUCAUCAAA, SEQ. ID NO. 2316: GGACUCAAGUUAAAGUAUU, SEQ. ID NO. 2317: GUAAUGGACUCAAGUUAAA),
FANCA
(SEQ. ID NO. 2318: GGACAUCACUGCCCACUUC, SEQ. ID NO. 2319: AGAGGAAGAUGUUCACUUA, SEQ. ID NO. 2320: GAUCGUGGCUCUUCAGGAA, SEQ. ID NO. 2321 : GGACAGAGGCAGAUAAGAA),
FANCG
(SEQ. ID NO. 2322: GCACUAAGCAGCCUUCAUG, SEQ. ID NO. 2323: GCAAGCAGGUGCCUACAGA, SEQ. ID NO. 2324: GGAAUUAGAUGCUCCAUUG, SEQ. ID NO. 2325: GGACAUCUCUGCCAAAGUC),
ALAS
(SEQ.IDNO.2326:CAAUAUGCCUGGAAACUAU, SEQ.IDNO.2327:GGUUAAGACUCACCAGUUC, SEQ.IDNO.2328:CAACAGGACUUUAGGUUCA, SEQ.IDNO.2329:GCAUAAGAUUGACAUCAUC),
PIGA (SEQ.IDNO.2330:GAAAGAGGGCAUAAGGUUA, SEQ.IDNO.2331:GGACUGAUCUUUAAACUAU, SEQ.IDNO.2332: UCAAAUGGCUUACUUCAUC, SEQ.IDNO.2333:UCUAAGAACUGAUGUCUAA),and
factor VIII
(SEQ.IDNO.2334:GCAAAUAGAUCUCCAUUAC, SEQ.IDNO.2335:CCAGAUAUGUCGUUCUUUA, SEQ.IDNO.2336:GAAAGGCUGUGCUCUCAAA, SEQ.IDNO.2337:GGAGAAACCUGCAUGAAAG, SEQ.IDNO.2338:CUUGAAGCCUCCUGAAUUA, SEQ.IDNO.2339: GAGGAAGCAUCCAAAGAUU, SEQ.IDNO.2340:GAUAGGAGAUACAAACUUU).
Furthermore, rationally designed siRNA or siRNA pools can be directed against genes involved in disorders of the brain and nervous system. Such genes would include, but are not be limited to:
APBBl (SEQ.IDNO.2341:CUACGUAGCUCGUGAUAAG, SEQ.IDNO.2342:GCAGAGAUGUCCACACGUU, SEQ.IDNO.2343:CAUGAGAUCUGCUCUAAGA, SEQ.IDNO.2344:GGGCACCUCUGCUGUAUUG),
BACEl
(SEQ.IDNO.2345:CCACAGAGCAAGUGAUUUA,
SEQ.IDNO.2346:GCAGAAAGGAGAUCAUUUA,
SEQ.IDNO.2347:GUAGCAAGAUCUUUACAUA,
SEQ.IDNO.2348:UGUCAGAGCUUGAUUAGAA),
PSENl
(SEQ.IDNO.2349:GAGCUGACAUUGAAAUAUG,
SEQ.IDNO.2350:GUACAGCUAUUUCUCAUCA,
SEQ.IDNO.2351:GAGGUUAGGUGAAGUGGUU, SEQ.IDNO.2352:GAAAGGGAGUCACAAGACA,
SEQ.IDNO.2353:GAACUGGAGUGGAGUAGGA,
SEQ.IDNO.2354:CAGCAGGCAUAUCUCAUUA,
SEQ.IDNO.2355:UCAAGUACCUCCCUGAAUG),
PSEN2
(SEQ.IDNO.2356:GCUGGGAAGUGGCUUAAUA, SEQ.IDNO.2357:CAUAUUCCCUGCCCUGAUA, SEQ.IDNO.2358:GGGAAGUGCUCAAGACCUA, SEQ.IDNO.2359:CAUAGAAAGUGACGUGUUA), MASSl
(SEQ.IDNO.2360:GGAAGGAGCUGUUAUGAGA, SEQ.IDNO.2361:GAAAGGAGAAGCUAAAUUA, SEQ.IDNO.2362:GGAGGAAGGUCAAGAUUUA, SEQ.IDNO.2363:GGAAAUAGCUGAGAUAAUG,),
ARX
(SEQ.IDNO.2364:CCAGACGCCUGAUAUUGAA, SEQ.IDNO.2365:CAGCACCACUCAAGACCAA, SEQ.IDNO.2366:CGCCUGAUAUUGAAGUAAA, SEQ.IDNO.2367:CAACAUCCACUCUCUCUUG)and
NNMT (SEQ.IDNO.2368:GGGCAGUGCUCCAGUGGUA, SEQ.IDNO.2369:GAAAGAGGCUGGCUACACA, SEQ.IDNO.2370:GUACAGAAGUGAGACAUAA, SEQ.IDNO.2371:GAGGUGAUCUCGCAAAGUU).
In addition, rationally designed siRNA or siRNA pools can be directed against genes involved in hypertension and related disorders. Such genes would include, but are not be limited to:
angiotensin II type 1 receptor (SEQ. ID NO. 2372: CAAGAAGCCUGCACCAUGU,
SEQ.IDNO.2373:GCACUUCACUACCAAAUGA,
SEQ.IDNO.2374:GCACUGGUCCCAAGUAGUA,
SEQ.IDNO.2375:CCAAAGGGCAGUAAAGUUU,
SEQ.IDNO.2376:GCUCAGAGGAGGUGUAUUU, SEQ.IDNO.2377:GCACUUCACUACCAAAUGA,
SEQ.IDNO.2378:AAAGGGCAGUAAAGUUU),
AGTR2
(SEQ.IDNO.2379:GAACAUCUCUGGCAACAAU, SEQ. ID NO. 2380: GGUGAUAUAUCUCAAAUUG, SEQ. ID NO. 2381: GCAAGCAUCUUAUAUAGUU, SEQ. ID NO. 2382: GAACCAGUCUUUCAACUCA), and other related targets.
Example XIII: Validation of Multigene Knockout using Rab5 and Eps.
Two or more genes having similar, overlapping functions often leads to genetic redundancy. Mutations that knockout only one of, e.g., a pair of such genes (also referred to as homologs) results in little or no phenotype due to the fact that the remaining intact gene is capable of fulfilling the role of the disrupted counterpart. To fully understand the function of such genes in cellular physiology, it is often necessary to knockout or knockdown both homologs simultaneously. Unfortunately, concomitant knockdown of two or more genes is frequently difficult to achieve in higher organisms (e.g., mice) thus it is necessary to introduce new technologies dissect gene function. One such approach to knocking down multiple genes simultaneously is by using siRNA. For example, Figure 11 showed that rationally designed siRNA directed against a number of genes involved in the clathrin-mediated endocytosis pathway resulted in significant levels of protein reduction (e.g., >80%). To determine the effects of gene knockdown on clathrin-related endocytosis, internalization assays were performed using epidermal growth factor and transferrin. Specifically, mouse receptor-grade EGF (Collaborative Research Inc.) and iron- saturated human transferrin (Sigma) were iodinated as described previously (Jiang, X., Huang, F., Marusyk, A. & Sorkin, A. (2003) MoI Biol Cell 14, 858-70). HeLa cells grown in 12-well dishes were incubated with 125I-EGF (1 ng/ml) or I- transferrin (1 μg/ml) in binding medium (DMEM, 0.1% bovine serum albumin) at 370C, and the ratio of internalized and surface radioactivity was determined during 5- min time course to calculate specific internalization rate constant ke as described previously (Jiang, X et al). The measurements of the uptakes of radiolabeled transferrin and EGF were performed using short time-course assays to avoid influence of the recycling on the uptake kinetics, and using low ligand concentration to avoid saturation of the clathrin-dependent pathway (for EGF Lund, K. A., Opresko, L. K., Strarbuck, C, Walsh, B. J. & Wiley, H. S. (1990) J. Biol. Chem. 265, 15713-13723). The effects of knocking down Rab5a, 5b, 5c, Eps, or Eps 15R (individually) are shown in Figure 22 and demonstrate that disruption of single genes has little or no effect on EGF or Tfii internalization. In contrast, simultaneous knock down of Rab5a, 5b, and 5c, or Eps and Eps 15R, leads to a distinct phenotype (note: total concentration of siRNA in these experiments remained constant with that in experiments in which a single siRNA was introduced, see Figure 23). These experiments demonstrate the effectiveness of using rationally designed siRNA to knockdown multiple genes and validates the utility of these reagents to override genetic redundancy.
Example XIV. Validation of Multigene Targeting Using G6PD, GAPDH, PLK, and UQC.
Further demonstration of the ability to knock down expression of multiple genes using rationally designed siRNA was performed using pools of siRNA directed against four separate genes. To achieve this, siRNA were transfected into cells (total siRNA concentration of 10OnM) and assayed twenty-four hours later by B-DNA. Results shown in Figure 24 show that pools of rationally designed molecules are capable of simultaneously silencing four different genes.
Example XV. Validation of Multigene Knockouts As Demonstrated by Gene Expression Profiling, a Prophetic Example.
To further demonstrate the ability to concomitantly knockdown the expression of multiple gene targets, single siRNA or siRNA pools directed against a collection of genes (e.g., 4, 8, 16, or 23 different targets) are simultaneously transfected into cells and cultured for twenty-four hours. Subsequently, mRNA is harvested from treated (and untreated) cells and labeled with one of two fluorescent probes dyes (e.g., a red fluorescent probe for the treated cells, a green fluorescent probe for the control cells.). Equivalent amounts of labeled RNA from each sample is then mixed together and hybridized to sequences that have been linked to a solid support (e.g., a slide, "DNA CHIP"). Following hybridization, the slides are washed and analyzed to assess changes in the levels of target genes induced by siRNA.
Example XVI. Identifying Hyperfunctional siRNA. Identification of Hyperfunctional Bcl-2 siRNA
The ten rationally designed Bcl2 siRNA (identified in Figure 13, 14) were tested to identify hyperpotent reagents. To accomplish this, each of the ten Bcl-2 siRNA were individually transfected into cells at a 30OpM (0.3nM) concentrations. Twenty-four hours later, transcript levels were assessed by B-DNA assays and compared with relevant controls. As shown in Figure 25, while the majority of Bcl-2 siRNA failed to induce functional levels of silencing at this concentration, siRNA 1 and 8 induced >80% silencing, and siRNA 6 exhibited greater than 90% silencing at this subnanomolar concentration.
By way of prophetic examples, similar assays could be performed with any of the groups of rationally designed genes described in Example VII or Example VIII. Thus for instance, rationally designed siRNA sequences directed against PDGFA (SEQ. ID NO. 2383 : GGUAAGAUAUUGUGCUUUA, SEQ. ID NO. 2384: CCGCAAAUAUGCAGAAUUA, SEQ. ID NO. 2385: GGAUGUACAUGGCGUGUUA, SEQ. ID NO. 2386: GGUGAAGUUUGUAUGUUUA), or
PDGFB
(SEQ.IDNO.2387:GCUCCGCGCUUUCCGAUUU,
SEQ.IDNO.2388:GAGCAGGAAUGGUGAGAUG,
SEQ.IDNO.2389:GAACUUGGGAUAAGAGUGU,
SEQ.IDNO.2390:CCGAGGAGCUUUAUGAGAU, SEQ.IDNO.2391:UUUAUGAGAUGCUGAGUGA) could be introduced into cells at increasingly limiting concentrations to determine whether any of the duplexes are hyperfunctional. Similarly, rationally designed sequences directed against
HIFl alpha (SEQ. ID NO. 2392: GAAGGAACCUGAUGCUUUA,
SEQ. ID NO. 2393: GCAUAUAUCUAGAAGGUAU,
SEQ. ID NO. 2394: GAACAAAUACAUGGGAUUA,
SEQ. ID NO. 2395: GGACACAGAUUUAGACUUG), or VEGF
(SEQ.IDNO.2396:GAACGUACUUGCAGAUGUG, SEQ.IDNO.2397: GAGAAAGCAUUUGUUUGUA, SEQ.IDNO.2398:GGAGAAAGCAUUUGUUUGU, SEQ. ED NO. 2399: CGAGGCAGCUUGAGUUAAA) could be introduced into cells at increasingly limiting concentrations and screened for hyperfunctional duplexes.
Example XVII: Gene Silencing: Prophetic Example
Below is an example of how one might transfect a cell. a. Select a cell line. The selection of a cell line is usually determined by the desired application. The most important feature to RNAi is the level of expression of the gene of interest. It is highly recommended to use cell lines for which siRNA transfection conditions have been specified and validated.
b. Plate the cells. Approximately 24 hours prior to transfection, plate the cells at the appropriate density so that they will be approximately 70 - 90% confluent, or approximately 1 x 105 cells/ml at the time of transfection. Cell densities that are too low may lead to toxicity due to excess exposure and uptake of transfection reagent-siRNA complexes. Cell densities that are too high may lead to low transfection efficiencies and little or no silencing. Incubate the cells overnight. Standard incubation conditions for mammalian cells are 37°C in 5% CO2. Other cell types, such as insect cells, require different temperatures and CO2 concentrations that are readily ascertainable by persons skilled in the art. Use conditions appropriate for the cell type of interest.
c. siRNA re-suspension. Add 20 μl siRNA universal buffer to each siRNA to generate a final concentration of 50 μM.
d. SiRNA-lipid complex formation. Use RNase-free solutions and tubes. Using the following table, Table XI: e.
Figure imgf000174_0001
Transfection. Create a Mixture 1 by combining the specified amounts of OPTI-MEM serum free media and transfection reagent in a sterile polystyrene tube. Create a Mixture 2 by combining specified amounts of each siRNA with OPTI-MEM media in sterile 1 ml tubes. Create a Mixture 3 by combining specified amounts of Mixture 1 and Mixture 2. Mix gently (do not vortex) and incubate at room temperature for 20 minutes. Create a Mixture 4 by combining specified amounts of Mixture 3 to complete media. Add appropriate volume to each cell culture well. Incubate cells with transfection reagent mixture for 24 - 72 hours at 370C. This incubation time is flexible. The ratio of silencing will remain consistent at any point in the time period. Assay for gene silencing using an appropriate detection method such as RT-PCR, Western blot analysis, immunohistochemistry, phenotypic analysis, mass spectrometry, fluorescence, radioactive decay, or any other method that is now known or that comes to be known to persons skilled in the art and that from reading this disclosure would useful with the present invention. The optimal window for observing a knockdown phenotype is related to the mRNA turnover of the gene of interest, although 24 - 72 hours is standard. Final Volume reflects amount needed in each well for the desired cell culture format. When adjusting volumes for a Stock Mix, an additional 10% should be used to accommodate variability in pipetting, etc. Duplicate or triplicate assays should be carried out when possible.
While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departure from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth and as follows in the scope of the appended claims.

Claims

What is claimed is:
1. A kit for gene silencing, wherein said kit is comprised of a pool of at least two siRNA duplexes, each of which is comprised of a sequence that is complementary to a portion of the sequence of one or more target messenger RNA, and each of which is selected using non-target specific criteria.
2. A kit according to claim 1, wherein each of the at least two siRNA duplexes complementary to a portion of the sequence of one or more target mRNAs is selected using Formula X.
3. A method for selecting an siRNA, said method comprising: applying selection criteria to a set of potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; and determining the relative functionality of the at least two siRNAs.
4. A method according to claim 3, wherein said selection criteria are embodied in a formula comprising: Formula X
(-8)*Al+(-l)*A2+(12)*A3+(7)*A4+(18)*A5+(12)*A6+ (19)*A7+(6)*A8+(-4)*A9+(-5)*A10+(-2)*All+(- 5)*A12+(17)*A13+(-3)* A14+(4)* Al 5+(2)* Al 6+(8)* Al 7+ (l l)*A18+(30)*A19+(-13)*Ul+(-10)*U2+(2)*U3+(-2)*U4+(- 5)*U5+(5)*U6+(-2)*U7+(-l 0)*U8+(-5)*U9+(l 5)*U10+(- l)*Ul l+(0)*U12+(10);|:U13+(-9)*U14+(-13)*U15+(- 10)*U16+(3)*U17+(9):1:U18+(9):1:U19+(7)*Cl+(3)*C2+(- 21)*C3+(5)*C4+(-9)*C5+(-20)*C6+(-18)*C7+(- 5)*C8+(5)*C9+(l)*C10+(2)*Cll+(-5)*C124<-3)*C13+(-6)*C14+(- 2)*C15+(-5)*C16+(-3)*C17+(-12)*C18+(-
18)*C19+(14)*Gl+(8)*G2+(7)*G3+(-10)*G4+(- 4)*G5+(2)*G6+(l)*G7+(9)*G8+(5)*G9+(- ll)*G10+(l)*Gll+(9)*G12+(- 24)*G13+(18)*G14+(ll);|;G15+(13)*G16+(-7)*G17+(-9);1:G18+(- 22)*G19 + 6*(number of A+U in position 15-19) - 3*(number of G+C in whole siRNA), wherein position numbering begins at the 5 '-most position of a sense strand, and
A1 = 1 if A is the base at position 1 of the sense strand, otherwise its value is 0; A2 = 1 if A is the base at position 2 of the sense strand, otherwise its value is 0;
A3 = 1 if A is the base at position 3 of the sense strand, otherwise its value is 0;
A4 = 1 if A is the base at position 4 of the sense strand, otherwise its value is 0;
A5= 1 if A is the base at position 5 of the sense strand, otherwise its value is 0;
A6 = 1 if A is the base at position 6 of the sense strand, otherwise its value is 0; A7 = 1 if A is the base at position 7 of the sense strand, otherwise its value is 0;
A10= 1 if A is the base at position 10 of the sense strand, otherwise its value is 0;
An = 1 if A is the base at position 11 of the sense strand, otherwise its value is 0;
A13 = 1 if A is the base at position 13 of the sense strand, otherwise its value is 0;
Ai9 = 1 if A is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
C3 = 1 if C is the base at position 3 of the sense strand, otherwise its value is 0;
C4 = 1 if C is the base at position 4 of the sense strand, otherwise its value is 0;
C5 = 1 if C is the base at position 5 of the sense strand, otherwise its value is 0; C6 = 1 if C is the base at position 6 of the sense strand, otherwise its value is 0;
C7 = 1 if C is the base at position 7 of the sense strand, otherwise its value is 0;
C9 = 1 if C is the base at position 9 of the sense strand, otherwise its value is 0;
C17 = 1 if C is the base at position 17 of the sense strand, otherwise its value is 0;
Ci8 = 1 if C is the base at position 18 of the sense strand, otherwise its value is 0; C19 = 1 if C is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
G1 = 1 if G is the base at position 1 on the sense strand, otherwise its value is 0; G2 = 1 if G is the base at position 2 of the sense strand, otherwise its value is 0; Gg = 1 if G is the base at position 8 on the sense strand, otherwise its value is 0; G1O = 1 if G is the base at position 10 on the sense strand, otherwise its value is 0; G13 = 1 if G is the base at position 13 on the sense strand, otherwise its value is 0; G19= 1 if G is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0; U1 = 1 if U is the base at position 1 on the sense strand, otherwise its value is 0; U2 = 1 if U is the base at position 2 on the sense strand, otherwise its value is 0; U3 = 1 if U is the base at position 3 on the sense strand, otherwise its value is 0; U4 = 1 if U is the base at position 4 on the sense strand, otherwise its value is 0; U7 = 1 if U is the base at position 7 on the sense strand, otherwise its value is 0; U9 = 1 if U is the base at position 9 on the sense strand, otherwise its value is 0; U1O = 1 if U is the base at position 10 on the sense strand, otherwise its value is 0; U15 = 1 if U is the base at position 15 on the sense strand, otherwise its value is 0; U16 = 1 if U is the base at position 16 on the sense strand, otherwise its value is 0; U17 = 1 if U is the base at position 17 on the sense strand, otherwise its value is 0; U18 = 1 if U is the base at position 18 on the sense strand, otherwise its value is 0.
5. A method according to any of claims 3-4, further comprising comparing the internal stability profiles of said at least two siRNAs.
6. A method according to any of claims 3-4, further comprising selecting either for or against sequences that contain motifs that induce cellular stress.
7. A method according to any of claims 3-4, further comprising selecting either for or against sequences that comprise stability motifs.
8. A method of gene silencing, comprising introducing into a cell at least one siRNA selected according to a method of any of claims 1-5.
9. A method according to any of claims 1-6, wherein said introducing is by allowing passive uptake of the at least one siRNA.
10. A method according claim 8, wherein said introducing in through the use of a vector.
11. A method for developing an siRNA algorithm for selecting siRNA, said method comprising:
(a) selecting a set of siRNA; (b) measuring gene silencing ability of each siRNA from said set;
(c) determining relative functionality of each siRNA;
(d) determining improved functionality by the presence or absence of at least one variable selected from the group consisting of the presence or absence of a particular nucleotide at a particular position, the total number of As and Us in positions 15-19, the number of times that the same nucleotide repeats within a given sequence, and the total number of Gs and Cs; and
(e) developing an algorithm using the information of step (d).
12. A method of selecting an siRNA with improved functionality, said method comprising using the algorithm of claim 11.
13. A kit, wherein said kit is comprised of at least two siRNAs, wherein said at least two siRNAs comprise a first optimized siRNA and a second optimized siRNA, wherein said first optimized siRNA and said second optimized siRNA are optimized according a formula comprising: Formula X
(-8)*Al+(-l)*A2+(12)*A3+(7)*A4+(18)*A5+(12)*A6+ (19)*A7+(6)*A8+(-4)*A9+(-5)*A10+(-2)*Al l+(- 5)* Al 2+(l 7)* Al 3+(-3)* Al 4+(4)* Al 5+(2)* Al 6+(8)* Al 7+
(ll)*A18+(30):l!A19+(-13)*Ul+(-10)*U2+(2):f:U3+(-2)*U4+(- 5)*U5+(5)*U6+(-2)*U7+(-10)*U8+(-5)*U9+(15)*U10+(- l)*Ul l+(0)*U12+(10)*U13+(-9)*U14+(-13)*U15+(- 10)nJ16+(3)HJ17+(9)*U18+(9)*U19+(7)*Cl+(3)*C2+(- 21)*C3+(5)*C4+(-9)*C5+(-20)*C6+(-18)*C7+(-
5)*C84<5)*C9+(l)*C10+(2)*Cll+(-5)*C12+(-3)*C13+(-6)*C14+(- 2)*C15+(-5)*C16+(-3)*C17+(-12)*C18+(- 18)*C19+(14)*Gl+(8)*G2+(7)*G3+(-10)*G4+(- 4)*G5+(2)*G6+(l)*G7+(9)*G8+(5)*G9+(- ll)*G10+(l)*Gll+(9)*G12+(-
24)*G13+(18)*G14+(l l)*G15+(13)*G16+(-7)*G17+(-9)*G18+(- 22)*G19 + 6*(number of A+U in position 15-19) - 3*(number of G+C in whole siRNA), wherein position numbering begins at the 5 '-most position of a sense strand, and A1 = 1 if A is the base at position 1 of the sense strand, otherwise its value is 0; A2 = 1 if A is the base at position 2 of the sense strand, otherwise its value is 0; A3 = 1 if A is the base at position 3 of the sense strand, otherwise its value is 0; A4 = 1 if A is the base at position 4 of the sense strand, otherwise its value is 0; A5 = 1 if A is the base at position 5 of the sense strand, otherwise its value is 0; A6 = 1 if A is the base at position 6 of the sense strand, otherwise its value is 0; A7 = 1 if A is the base at position 7 of the sense strand, otherwise its value is 0; A1O = 1 if A is the base at position 10 of the sense strand, otherwise its value is 0; A11 = 1 if A is the base at position 11 of the sense strand, otherwise its value is 0; A13 = 1 if A is the base at position 13 of the sense strand, otherwise its value is 0; A\9 = 1 if A is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
C3 = 1 if C is the base at position 3 of the sense strand, otherwise its value is 0; C4 = 1 if C is the base at position 4 of the sense strand, otherwise its value is 0;
C5 = 1 if C is the base at position 5 of the sense strand, otherwise its value is 0;
C6 = 1 if C is the base at position 6 of the sense strand, otherwise its value is 0;
C7 = 1 if C is the base at position 7 of the sense strand, otherwise its value is 0;
C9 = 1 if C is the base at position 9 of the sense strand, otherwise its value is 0; C17 = 1 if C is the base at position 17 of the sense strand, otherwise its value is 0;
C18 = 1 if C is the base at position 18 of the sense strand, otherwise its value is 0;
C19 = 1 if C is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
G1 = 1 if G is the base at position 1 on the sense strand, otherwise its value is 0;
G2 = 1 if G is the base at position 2 of the sense strand, otherwise its value is 0;
G8 = 1 if G is the base at position 8 on the sense strand, otherwise its value is 0;
G10 = 1 if G is the base at position 10 on the sense strand, otherwise its value is 0;
G13 = 1 if G is the base at position 13 on the sense strand, otherwise its value is 0; G19 = 1 if G is the base at position 19 of the sense strand, otherwise if another base is present or the sense strand is only 18 base pairs in length, its value is 0;
U1 = 1 if U is the base at position 1 on the sense strand, otherwise its value is 0; U2 = 1 if U is the base at position 2 on the sense strand, otherwise its value is 0; U3 = 1 if U is the base at position 3 on the sense strand, otherwise its value is 0; U4 = 1 if U is the base at position 4 on the sense strand, otherwise its value is 0; U7 = 1 if U is the base at position 7 on the sense strand, otherwise its value is 0; U9 = 1 if U is the base at position 9 on the sense strand, otherwise its value is 0; U1O = 1 if U is the base at position 10 on the sense strand, otherwise its value is 0; U15 = 1 if U is the base at position 15 on the sense strand, otherwise its value is 0; U16 = 1 if U is the base at position 16 on the sense strand, otherwise its value is 0; U17 = 1 if U is the base at position 17 on the sense strand, otherwise its value is 0; U18 = 1 if U is the base at position 18 on the sense strand, otherwise its value is 0.
14. A method for identifying hyperfunctional siRNA, comprising: applying selection criteria to a set of potential siRNA that comprise 18-30 base pairs, wherein said selection criteria are non-target specific criteria, and said set comprises at least two siRNAs and each of said at least two siRNAs contains a sequence that is at least substantially complementary to a target gene; and determining the relative functionality of the at least two siRNAs and assigning each of the at least two siRNAs a functionality score; and selecting siRNAs from the at least two siRNAs that have a functionality score that reflects greater than 80 percent silencing at a concentration in the picomolar range, wherein said greater than 80 percent silencing endures for greater than 120 hours.
15. A hyperfunctional siRNA that is capable of silencing Bcl2.
16. A method according to any of claims 1-10 and 12-13, wherein said siRNA are unimolecular.
17. A method according to any of claims 1-10 and 12-13, wherein said siRNA are comprised of two separate polynucleotide strands.
18. A method according to any of claims 1-10 and 12-13, wherein said siRNA are expressed from one or more vectors.
19. A method according to any of claims 1-10 and 12-13, wherein two or more genes are silenced by a single administration of siRNA.
20. A kit according to claim 10, wherein one or more of said siRNA are unimolecular.
21. A kit according to claim 10, wherein one or more of said siRNA are comprised of two separate polynucleotide strands.
22. A kit according to claim 10, wherein one or more of said siRNA are capable of silencing the Bcl2 gene.
23. A method for developing an siRNA algorithm for selecting functional and hyperfunctional siRNAs for a given sequence, comprising: (a) selecting a set of siRNAs;
(b) measuring the gene silencing ability of each siRNA from said set;
(c) determining the relative functionality of each siRNA;
(d) determining the amount of improved functionality by the presence or absence of at least one variable selected from the group consisting of the total GC content, melting temperature of the siRNA, GC content at positions 15 -19, the presence or absence of a particular nucleotide at a particular position, relative thermodynamic stability at particular positions in a duplex, and the number of times that the same nucleotide repeats within a given sequence; and
(e) developing an algorithm using the information of step (d).
PCT/US2004/014885 2002-11-14 2004-05-12 METHODS AND COMPOSITIONS FOR SELECTING siRNA OF IMPROVED FUNCTIONALITY WO2006006948A2 (en)

Priority Applications (191)

Application Number Priority Date Filing Date Title
PCT/US2004/014885 WO2006006948A2 (en) 2002-11-14 2004-05-12 METHODS AND COMPOSITIONS FOR SELECTING siRNA OF IMPROVED FUNCTIONALITY
US10/940,892 US20120052487A9 (en) 2002-11-14 2004-09-14 Methods and compositions for selecting sirna of improved functionality
US11/593,100 US7615541B2 (en) 2002-11-14 2006-11-03 siRNA targeting TIE-2
US11/594,530 US7608706B2 (en) 2002-11-14 2006-11-08 siRNA targeting ras-related nuclear protein
US11/594,666 US20070128641A1 (en) 2002-11-14 2006-11-08 siRNA targeting hypoxia-inducible factor 1
US11/598,179 US7541453B2 (en) 2002-11-14 2006-11-09 siRNA targeting aquaporin 4
US11/595,698 US7598369B2 (en) 2002-11-14 2006-11-09 siRNA targeting histamine receptor H1
US11/595,112 US7605250B2 (en) 2004-05-12 2006-11-09 siRNA targeting cAMP-specific phosphodiesterase 4D
US11/726,245 US20070207491A1 (en) 2004-05-12 2007-03-21 siRNA targeting minichromosome maintenance deficient 4 (MCM4)
US11/729,388 US20070185317A1 (en) 2002-11-14 2007-03-28 siRNA targeting HtrA serine peptidase 1
US11/729,924 US20080015114A1 (en) 2002-11-14 2007-03-29 siRNA targeting connective tissue growth factor (CTGF)
US11/731,843 US7569684B2 (en) 2002-11-14 2007-03-30 siRNA targeting gremlin
US11/731,894 US7521191B2 (en) 2002-11-14 2007-03-30 siRNA targeting connexin 43
US11/731,890 US20080045703A1 (en) 2002-11-14 2007-03-30 siRNA targeting platelet-derived growth factor receptor beta polypeptide (PDGFR)
US11/731,875 US20070299253A1 (en) 2002-11-14 2007-03-30 siRNA targeting vacuolar ATPase
US11/732,457 US7638621B2 (en) 2002-11-14 2007-04-03 siRNA targeting insulin-like growth factor 1 receptor (IGF-1R)
US11/732,413 US20070238868A1 (en) 2002-11-14 2007-04-03 siRNA targeting chemokine (C-X-C motif) receptor 4 (CXCR4)
US11/732,810 US20070219362A1 (en) 2002-11-14 2007-04-04 siRNA targeting azurocidin 1 (Cartionic Antimicrobial protein 37)
US11/732,809 US20070255046A1 (en) 2002-11-14 2007-04-04 siRNA targeting spectrin SH3 domain binding protein 1 (SSH3BP1)
US11/784,559 US20070213520A1 (en) 2002-11-14 2007-04-06 siRNA targeting calcium/calmodulin dependent protein kinase IV (CAMK4)
US11/784,536 US20070179286A1 (en) 2002-11-14 2007-04-06 siRNA targeting testis-specific serine kinase 4
US11/784,752 US20070213521A1 (en) 2002-11-14 2007-04-09 siRNA targeting cell division cycle 25 (CDC25C)
US11/784,755 US7550572B2 (en) 2002-11-14 2007-04-09 siRNA targeting cell division cycle 20 homolog (CDC20)
US11/784,756 US20070232797A1 (en) 2002-11-14 2007-04-09 siRNA targeting cell division cycle 2-like 5(CDC2L5)
US11/807,530 US20070255047A1 (en) 2002-11-14 2007-05-29 siRNA targeting cell division cycle 6 homolog (CDC6)
US11/807,486 US7745610B2 (en) 2002-11-14 2007-05-29 siRNA targeting cyclin dependent kinase 11 (CDK11)
US11/807,577 US20070260048A1 (en) 2002-11-14 2007-05-29 siRNA targeting centromere protein E, 312kDa (CENPE)
US11/807,836 US7619081B2 (en) 2002-11-14 2007-05-30 siRNA targeting coatomer protein complex, subunit beta 2 (COPB2)
US11/809,909 US20070255048A1 (en) 2002-11-14 2007-06-01 siRNA targeting discoidin domain receptor family, member 1 (DDR1)
US11/810,074 US20070276135A1 (en) 2002-11-14 2007-06-04 siRNA targeting dual specificity phosphate 5 (DUSP5)
US11/810,383 US7595388B2 (en) 2002-11-14 2007-06-05 siRNA targeting EPH receptor A3 (EPHA3)
US11/810,381 US20080221316A1 (en) 2002-11-14 2007-06-05 siRNA targeting ethanolamine Kinase I1 (EKI1)
US11/810,384 US20070260049A1 (en) 2002-11-14 2007-06-05 siRNA targeting MAD2 mitotic arrest deficient-like (MAD2L2)
US11/810,382 US20070260047A1 (en) 2002-11-14 2007-06-05 siRNA targeting EPH receptor A4 (EPHA4)
US11/810,673 US20070293664A1 (en) 2002-11-14 2007-06-06 siRNA targeting minichromosome maintenance deficient 5 (MCM5)
US11/810,672 US20070255050A1 (en) 2002-11-14 2007-06-06 siRNA targeting minichromosome maintenance deficient 2, mitotin (MCM2)
US11/810,670 US20090043084A1 (en) 2002-11-14 2007-06-06 siRNA targeting minichromosome maintenance deficient 3 (MCM3)
US11/811,003 US20070287833A1 (en) 2002-11-14 2007-06-07 siRNA targeting minichromosome maintenance deficient 6 (MCM6)
US11/811,005 US20070265437A1 (en) 2002-11-14 2007-06-07 siRNA targeting testes development-related NYD-SP21 (NYD-SP21)
US11/811,012 US20070260050A1 (en) 2002-11-14 2007-06-07 siRNA targeting minichromosome maintenance deficient 7 (MCM7)
US11/811,209 US20080085997A1 (en) 2002-11-14 2007-06-08 siRNA targeting phosphoinositide-3-kinase, class 2, beta polypeptide (PIK3C2B)
US11/811,424 US20070244312A1 (en) 2002-11-14 2007-06-08 siRNA targeting phosphoinositide-3-kinase, class 2, alpha polypeptide (PIK3C2A)
US11/811,423 US7645870B2 (en) 2002-11-14 2007-06-08 siRNA targeting proteasome 26S subunit, non-ATPase, 10 (Gankyrin or PSMD10)
US11/811,954 US20070249819A1 (en) 2002-11-14 2007-06-12 siRNA targeting WEE1 homolog (WEE1)
US11/811,929 US20070255051A1 (en) 2002-11-14 2007-06-12 siRNA targeting serine/threonine kinase 22B (STK22B)
US11/811,925 US20070260051A1 (en) 2002-11-14 2007-06-12 siRNA targeting pituitary tumor-transforming 1 (PTTG1)
US11/811,950 US20070260052A1 (en) 2002-11-14 2007-06-12 siRNA targeting RAD1 homolog (RAD1)
US11/818,555 US7592442B2 (en) 2002-11-14 2007-06-13 siRNA targeting ribonucleotide reductase M2 polypeptide (RRM2 or RNR-R2)
US11/818,547 US20070255052A1 (en) 2002-11-14 2007-06-14 siRNA targeting v-myc myelocytomatosis viral oncogene homolog (MYC)
US11/818,936 US7598370B2 (en) 2002-11-14 2007-06-15 siRNA targeting polo-like kinase-1 (PLK-1)
US11/818,938 US7678896B2 (en) 2002-11-14 2007-06-15 siRNA targeting serine/threonine kinase 12 (STK12 or aurora B kinase)
US11/880,628 US7595389B2 (en) 2002-11-14 2007-07-23 siRNA targeting casitas B cell lymphoma-B (CBL-B)
US11/880,623 US20090023907A1 (en) 2002-11-14 2007-07-23 siRNA targeting kinesin spindle protein (KSP)
US11/880,624 US20080027215A1 (en) 2002-11-14 2007-07-23 siRNA targeting vascular endothelial growth factor (VEGF)
US11/880,622 US20080161547A1 (en) 2002-11-14 2007-07-23 siRNA targeting serine/threonine protein kinase AKT
US11/880,776 US20080207884A1 (en) 2002-11-14 2007-07-24 siRNA targeting 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC)
US11/880,794 US7635770B2 (en) 2002-11-14 2007-07-24 siRNA targeting protein kinase N-3 (PKN-3)
US11/880,775 US7655788B2 (en) 2002-11-14 2007-07-24 siRNA targeting DNA-damage-inducible transcript 4 (DDIT4)
US11/880,755 US20080293595A1 (en) 2002-11-14 2007-07-24 siRNA targeting protein tyrosine phosphatase-1B (PTP1B)
US11/880,777 US20080188648A1 (en) 2002-11-14 2007-07-24 siRNA targeting human hairless protein (HR)
US11/880,855 US20080300395A1 (en) 2002-11-14 2007-07-24 siRNA targeting vascular endothelial growth factor receptor 1 (VEGFR1)
US11/881,385 US20080306015A1 (en) 2002-11-14 2007-07-25 siRNA targeting proprotein convertase subtilisin/kexin type 9 (PCSK9)
US11/880,965 US7579458B2 (en) 2002-11-14 2007-07-25 siRNA targeting synuclein, alpha (SNCA-1)
US11/881,386 US20080221317A1 (en) 2002-11-14 2007-07-25 siRNA targeting cystic fibrosis transmembrane conductance regulator (CFTR)
US11/881,777 US20090005548A1 (en) 2002-11-14 2007-07-27 siRNA targeting nuclear receptor interacting protein 1 (NRIP1)
US11/881,768 US20090030190A1 (en) 2002-11-14 2007-07-27 siRNA targeting 1-acylglycerol-3-phosphate O-acyltransferase 2 (AGPAT2)
US11/881,771 US20090005547A1 (en) 2002-11-14 2007-07-27 siRNa targeting neuropilin 1 (NRP1)
US11/881,767 US20080039617A1 (en) 2002-11-14 2007-07-27 siRNA targeting neuropeptide Y (NPY)
US11/881,773 US20090023908A1 (en) 2002-11-14 2007-07-27 siRNA targeting ribosomal protein S2 (RPS2)
US11/881,772 US20080027216A1 (en) 2002-11-14 2007-07-27 siRNA targeting sodium channel, voltage-gated, type X, alpha (SCN10A)
US11/975,902 US20080097091A1 (en) 2002-11-14 2007-10-22 siRNA targeting TNFalpha
US11/977,128 US20080097092A1 (en) 2002-11-14 2007-10-23 siRNA targeting kinases
US11/977,347 US20080076908A1 (en) 2002-11-14 2007-10-24 siRNA targeting nuclear receptors
US11/977,406 US20090182134A1 (en) 2002-11-14 2007-10-24 siRNA targeting phosphatases
US11/977,558 US20080097089A1 (en) 2002-11-14 2007-10-25 siRNA targeting deubiqutination enzymes
US11/977,675 US20080071073A1 (en) 2002-11-14 2007-10-25 siRNA targeting ubiquitin ligases
US11/978,125 US20080086002A1 (en) 2002-11-14 2007-10-26 siRNA targeting secreted frizzled-related protein 1 (sFRP1)
US11/978,070 US7582746B2 (en) 2002-11-14 2007-10-26 siRNA targeting complement component 3 (C3)
US11/978,097 US7638622B2 (en) 2002-11-14 2007-10-26 SiRNA targeting intercellular adhesion molecule 1 (ICAM1)
US11/978,106 US7655789B2 (en) 2002-11-14 2007-10-26 siRNA targeting transient receptor potential cation channel, subfamily V, member 1 (TRPV1)
US11/978,120 US20080081904A1 (en) 2002-11-14 2007-10-26 siRNA targeting carbonic anhydrase 4(CA4)
US11/978,107 US7605252B2 (en) 2002-11-14 2007-10-26 siRNA targeting kinase insert domain receptor (KDR)
US11/978,518 US7632938B2 (en) 2002-11-14 2007-10-29 siRNA targeting superoxide dismutase 1 (SOD1)
US11/978,487 US20080113374A1 (en) 2002-11-14 2007-10-29 siRNA targeting fructose-1,6-bisphosphatase 1 (FBP1)
US11/978,475 US20080113372A1 (en) 2002-11-14 2007-10-29 siRNA targeting glucagon receptor (GCGR)
US11/978,476 US7635771B2 (en) 2002-11-14 2007-10-29 siRNA targeting amyloid beta (A4) precursor protein (APP)
US11/978,455 US7795421B2 (en) 2002-11-14 2007-10-29 siRNA targeting apolipoprotein B (APOB)
US11/978,457 US20080113371A1 (en) 2002-11-14 2007-10-29 siRNA targeting beta secretase (BACE)
US11/978,398 US7709629B2 (en) 2002-11-14 2007-10-29 siRNA targeting diacylglycerol O-acyltransferase homolog 2 (DGAT2)
US11/980,210 US8198427B1 (en) 2002-11-14 2007-10-30 SiRNA targeting catenin, beta-1 (CTNNB1)
US11/980,102 US7662950B2 (en) 2002-11-14 2007-10-30 siRNA targeting myeloid differentiation primary response gene (88) (MYD88)
US11/978,900 US7612196B2 (en) 2002-11-14 2007-10-30 siRNA targeting cyclin-dependent kinase inhibitor 1B (p27, Kip1) (CDKN1B)
US11/980,263 US7632939B2 (en) 2002-11-14 2007-10-30 siRNA targeting proto-oncogene MET
US11/980,300 US7592443B2 (en) 2002-11-14 2007-10-30 siRNA targeting interleukin-1 receptor-associated kinase 4 (IRAK4)
US12/157,151 US7582747B2 (en) 2002-11-14 2008-06-06 siRNA targeting inner centromere protein antigens (INCENP)
US12/157,152 US20080268457A1 (en) 2002-11-14 2008-06-06 siRNA targeting forkhead box P3 (FOXP3)
US12/157,137 US7642349B2 (en) 2002-11-14 2008-06-06 siRNA targeting TATA box binding protein (TBP)-associated factor (TAF1)
US12/157,289 US7691998B2 (en) 2002-11-14 2008-06-09 siRNA targeting nucleoporin 62kDa (Nup62)
US12/209,698 US7977471B2 (en) 2002-11-14 2008-09-12 siRNA targeting TNFα
US12/287,757 US7576196B2 (en) 2002-11-14 2008-10-14 siRNA targeting transducin (beta)-like 3 (TBL3)
US12/321,749 US7666853B2 (en) 2002-11-14 2009-01-23 siRNA targeting connective tissue growth factor (CTGF)
US12/322,387 US7589191B2 (en) 2002-11-14 2009-02-02 siRNA targeting hypoxia-inducible factor 1
US12/384,768 US8030474B2 (en) 2002-11-14 2009-04-08 siRNA targeting cyclin-dependent kinase 4 (CDK4)
US12/454,055 US20090275640A1 (en) 2002-11-14 2009-05-12 siRNA targeting inner centromere protein antigens (INCENP)
US12/454,271 US20090227780A1 (en) 2002-11-14 2009-05-14 siRNA targeting connexin 43
US12/455,098 US7741470B2 (en) 2002-11-14 2009-05-28 siRNA targeting gremlin
US12/456,424 US7951935B2 (en) 2002-11-14 2009-06-16 siRNA targeting v-myc myelocytomatosis viral oncogene homolog (MYC)
US12/459,489 US20090291497A1 (en) 2002-11-14 2009-07-01 siRNA targeting transducin (beta)-like 3 (TBL3)
US12/460,876 US20100004141A1 (en) 2002-11-14 2009-07-24 siRNA targeting polo-like Kinase-1 (PLK-1)
US12/462,029 US7745612B2 (en) 2002-11-14 2009-07-28 siRNA targeting interleukin-1 receptor-associated kinase 4 (IRAK4)
US12/462,420 US7737267B2 (en) 2002-11-14 2009-08-04 siRNA targeting hypoxia-inducible factor 1
US12/462,776 US20100248990A1 (en) 2002-11-14 2009-08-07 siRNA targeting ribonucleotide reductase M2 polypeptide (RRM2 or RNR-R2)
US12/462,820 US8022198B2 (en) 2002-11-14 2009-08-10 siRNA targeting histamine receptor H1
US12/584,352 US8222395B2 (en) 2002-11-14 2009-09-03 siRNA targeting kinase insert domain receptor (KDR)
US12/584,850 US7897754B2 (en) 2002-11-14 2009-09-11 SiRNA targeting ras-related nuclear protein RAN
US12/584,899 US8013145B2 (en) 2002-11-14 2009-09-14 SiRNA targeting cyclin-dependent kinase inhibitor 1B (p27, Kip1) (CDKN1B)
US12/586,167 US7855186B2 (en) 2002-11-14 2009-09-17 siRNA targeting TIE-2
US12/586,271 US7781575B2 (en) 2002-11-14 2009-09-18 siRNA targeting tumor protein 53 (p53)
US12/586,999 US20100056395A1 (en) 2002-11-14 2009-09-30 siRNA targeting coatomer protein complex, subunit beta 2 (CPOB2)
US12/589,879 US8039610B2 (en) 2002-11-14 2009-10-29 siRNA targeting superoxide dismutase 1 (SOD1)
US12/590,097 US7816512B2 (en) 2002-11-14 2009-11-02 siRNA targeting proto-oncogene MET
US12/590,252 US7829696B2 (en) 2002-11-14 2009-11-04 siRNA targeting amyloid beta (A4) precursor protein (APP)
US12/590,707 US7803933B2 (en) 2002-11-14 2009-11-12 siRNA targeting TATA box binding protein (TBP)-associated factor (TAF1)
US12/592,872 US8304528B2 (en) 2002-11-14 2009-12-03 SiRNA targeting fructose-1, 6-bisphosphatase 1 (FBP1)
US12/653,120 US8022199B2 (en) 2002-11-14 2009-12-08 SiRNA targeting myeloid differentiation primary response gene (88) (MYD88)
US12/653,402 US7807820B2 (en) 2002-11-14 2009-12-11 siRNA targeting beta secretase (BACE)
US12/653,530 US20100113307A1 (en) 2002-11-14 2009-12-15 siRNA targeting vascular endothelial growth factor (VEGF)
US12/655,107 US7833989B2 (en) 2002-11-14 2009-12-23 siRNA targeting connective tissue growth factor (CTGF)
US12/657,448 US8067576B2 (en) 2002-11-14 2010-01-21 siRNA targeting serine/threonine kinase 12 (STK12 or aurora B kinase)
US12/657,721 US20100145039A1 (en) 2002-11-14 2010-01-26 siRNA targeting nucleoporin 62kDa (Nup62)
US12/660,582 US8247169B2 (en) 2002-11-14 2010-03-01 SiRNA targeting diacylglycerol O-acyltransferase homolog 2 (DGAT2)
US12/798,603 US8030476B2 (en) 2002-11-14 2010-04-07 siRNA targeting gremlin
US12/798,802 US7935813B2 (en) 2002-11-14 2010-04-12 siRNA target hypoxia-inducible factor 1
US12/798,906 US8236942B2 (en) 2002-11-14 2010-04-13 SiRNA targeting glucagon receptor (GCGR)
US12/799,758 US8217162B2 (en) 2002-11-14 2010-04-30 siRNA targeting interleukin-1 receptor-associated kinase 4(IRAK4)
US12/799,975 US20100267587A1 (en) 2002-11-14 2010-05-05 siRNA targeting cyclin dependent kinase 11 (CDK11)
US12/802,647 US8000902B2 (en) 2002-11-14 2010-06-11 Methods and compositions for selecting siRNA of improved functionality
US12/804,014 US8071754B2 (en) 2002-11-14 2010-07-12 siRNA targeting apolipoprotein B (APOB)
US12/806,320 US7985854B2 (en) 2002-11-14 2010-08-10 siRNA targeting TATA box binding protein (TBP)-associated factor (TAF1)
US12/806,570 US7999097B2 (en) 2002-11-14 2010-08-17 siRNA targeting beta secretase (BACE)
US12/807,526 US8222396B2 (en) 2002-11-14 2010-09-08 SiRNA targeting proto-oncogene MET
US12/924,078 US8268985B2 (en) 2002-11-14 2010-09-20 siRNA targeting amyloid beta (A4) precursor protein (APP)
US12/924,653 US8138329B2 (en) 2002-11-14 2010-10-01 siRNA targeting connective tissue growth factor (CTGF)
US12/927,144 US8314229B2 (en) 2002-11-14 2010-11-08 siRNA targeting tie-2
US12/928,950 US20110105363A1 (en) 2002-11-14 2010-12-23 siRNA targeting TNFa
US13/135,336 US8293887B2 (en) 2002-11-14 2011-07-01 SiRNA targeting beta secretase (BACE)
US13/135,443 US8232385B2 (en) 2002-11-14 2011-07-05 siRNA targeting cyclin-dependent kinase inhibitor 1B (p27, Kip1) (CDKN1B)
US13/136,780 US8633306B2 (en) 2002-11-14 2011-08-10 SiRNA targeting histamine receptor H1
US13/136,812 US8426579B2 (en) 2002-11-14 2011-08-11 SiRNA targeting myeloid differentiation primary response gene (88) (MYD88)
US13/199,001 US20110319474A1 (en) 2002-11-14 2011-08-17 siRNA targeting cyclin-dependent kinase 4 (CDK4)
US13/199,240 US20110319297A1 (en) 2002-11-14 2011-08-23 siRNA targeting gremlin
US13/199,946 US20120015850A1 (en) 2002-11-14 2011-09-13 siRNA targeting Superoxide
US13/317,752 US8232386B2 (en) 2002-11-14 2011-10-27 SiRNA targeting apolipoprotein B (APOB)
US13/385,320 US8461326B2 (en) 2002-11-14 2012-02-14 SiRNA targeting connective tissue growth factor (CTGF)
US13/466,631 US8399654B2 (en) 2002-11-14 2012-05-08 siRNA targeting catenin, Beat-1 (CTNNB1)
US13/489,725 US20120252873A1 (en) 2002-11-14 2012-06-06 siRNA Targeting Interleukin-1 Receptor-associated Kinase 4 (IRAK4)
US13/494,360 US20120258888A1 (en) 2002-11-14 2012-06-12 siRNA Targeting Proto-oncogene MET
US13/524,015 US8575329B2 (en) 2002-11-14 2012-06-15 siRNA targeting kinase insert domain receptor (KDR)
US13/531,657 US8445667B2 (en) 2002-11-14 2012-06-25 SiRNA targeting cyclin-dependent kinase inhibitor 1B (p27, Kip1) (CDKN1B)
US13/536,005 US8445668B2 (en) 2002-11-14 2012-06-28 SiRNA targeting apolipoprotein (APOB)
US13/539,630 US20120270751A1 (en) 2002-11-14 2012-07-02 siRNA Targeting Diacylglycerol O-Acyltransferase Homolog 2 (DGAT2)
US13/542,332 US20120283311A1 (en) 2002-11-14 2012-07-05 siRNA Targeting Glucagon Receptor (GCCR)
US13/551,794 US8658784B2 (en) 2002-11-14 2012-07-18 siRNA targeting amyloid beta (A4) precursor protein (APP)
US13/613,910 US20130023446A1 (en) 2002-11-14 2012-09-13 siRNA Targeting Beta Secretase (BACE)
US13/632,519 US20130059760A1 (en) 2002-11-14 2012-10-01 siRNA Targeting Fructose-1, 6-bisphosphatase 1 (FBP1)
US13/647,869 US8658785B1 (en) 2002-11-14 2012-10-09 siRNA targeting tie-2
US13/764,825 US8937172B2 (en) 2002-11-14 2013-02-12 siRNA targeting catenin, beta-1 (CTNNB1)
US13/847,544 US8883998B2 (en) 2002-11-14 2013-03-20 siRNA targeting myeloid differentiation primary response gene (88) (MYD88)
US13/867,175 US20130225447A1 (en) 2002-11-14 2013-04-22 siRNA Targeting Apolipoprotein B (APOB)
US13/867,168 US20130225667A1 (en) 2002-11-14 2013-04-22 siRNA Targeting Cyclin-dependent Kinase Inhibitor 1B (p27, Kip1) (CDKN1B)
US14/097,551 US9228186B2 (en) 2002-11-14 2013-12-05 Methods and compositions for selecting siRNA of improved functionality
US14/099,339 US8907077B2 (en) 2002-11-14 2013-12-06 siRNA targeting TIE-2
US14/936,403 US10011836B2 (en) 2002-11-14 2015-11-09 Methods and compositions for selecting siRNA of improved functionality
US14/936,395 US9839649B2 (en) 2002-11-14 2015-11-09 Methods and compositions for selecting siRNA of improved functionality
US14/937,607 US9879266B2 (en) 2002-11-14 2015-11-10 Methods and compositions for selecting siRNA of improved functionality
US14/965,816 US9777270B2 (en) 2002-11-14 2015-12-10 Methods and compositions for selecting siRNA of improved functionality
US15/254,524 US9771586B2 (en) 2002-11-14 2016-09-01 RNAi targeting ZNF205
US15/255,973 US9719094B2 (en) 2002-11-14 2016-09-02 RNAi targeting SEC61G
US15/255,829 US9719092B2 (en) 2002-11-14 2016-09-02 RNAi targeting CNTD2
US15/679,097 US20170349904A1 (en) 2002-11-14 2017-08-16 Methods and Compositions for Selecting siRNA of Improved Functionality
US15/705,650 US10233449B2 (en) 2002-11-14 2017-09-15 Methods and compositions for selecting siRNA of improved functionality
US15/823,415 US10765695B2 (en) 2002-11-14 2017-11-27 Methods and compositions for selecting siRNA of improved functionality
US15/862,479 US10696968B2 (en) 2002-11-14 2018-01-04 Methods and compositions for selecting siRNA of improved functionality
US16/038,029 US20180320182A1 (en) 2002-11-14 2018-07-17 Methods and Compositions for Selecting siRNA of Improved Functionality
US16/171,166 US10920226B2 (en) 2002-11-14 2018-10-25 siRNA targeting LDHA
US16/256,933 US20190316139A1 (en) 2002-11-14 2019-01-24 Methods and Compositions for Selecting siRNA of Improved Functionality
US16/378,629 US10421970B2 (en) 2004-05-12 2019-04-09 Methods and compositions for selecting siRNA of improved functionality
US16/379,273 US20190270995A1 (en) 2002-11-14 2019-04-09 Methods and Compositions for Selecting siRNA of Improved Functionality
US16/680,340 US20200123550A1 (en) 2002-11-14 2019-11-11 siRNA Targeting LDHA
US16/782,976 US11198870B2 (en) 2002-11-14 2020-02-05 Methods and compositions for selecting siRNA of improved functionality
US17/520,530 US20220315922A1 (en) 2002-11-14 2021-11-05 Methods and Compositions for Selecting siRNA of Improved Functionality

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US42613702P 2002-11-14 2002-11-14
US50205003P 2003-09-10 2003-09-10
US10/714,333 US8090542B2 (en) 2002-11-14 2003-11-14 Functional and hyperfunctional siRNA
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US10/940,892 US20120052487A9 (en) 2002-11-14 2004-09-14 Methods and compositions for selecting sirna of improved functionality
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