RNAi-based functional pharmacogenomics

Methods in Molecular Biology

Volumn 700, Issue , 2011, Pages 271-290

  Tuzmen, Sukru ^a   Tuzmen, Pinar ^a   Arora, Shilpi ^a   Mousses, Spyro ^a   Azorsa, David ^a  

^a TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

Drug target; Functional pharmaco genomics; Genomics; Phenotypic screening; RNAi; siRNA

Indexed keywords

B RAF KINASE; BCR ABL PROTEIN; DOUBLE STRANDED RNA; EPIDERMAL GROWTH FACTOR RECEPTOR; HEAT SHOCK PROTEIN 27; K RAS PROTEIN; MULTIDRUG RESISTANCE PROTEIN 1; S PHASE KINASE ASSOCIATED PROTEIN 2; SHORT HAIRPIN RNA; SMALL INTERFERING RNA; VASCULOTROPIN;

ARTICLE; CANCER RESEARCH; DOWN REGULATION; DRUG DELIVERY SYSTEM; DRUG SENSITIVITY; DRUG TARGETING; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENETIC TRANSFECTION; HIGH THROUGHPUT SCREENING; HIGH THROUGHPUT SEQUENCING; HUMAN; NONHUMAN; PHARMACOGENOMICS; PHENOTYPE; PRIORITY JOURNAL; RNA ANALYSIS; RNA INTERFERENCE; TRANSCRIPTION REGULATION; DRUG DEVELOPMENT; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; METHODOLOGY; MICROARRAY ANALYSIS; PHARMACOGENETICS;

MAMMALIA;

DRUG DELIVERY SYSTEMS; DRUG DISCOVERY; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MICROARRAY ANALYSIS; PHARMACOGENETICS; RNA INTERFERENCE;

EID: 79955666238     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61737-954-3_18     Document Type: Article

References (101)

1. Elbashir SM, Harborth J, Weber K, Tuschl T (2002) Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 26:199-213
2. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806-811
3. Hannon GJ (2002) RNA interference. Nature 418:244-251
4. Huppi K, Martin SE, Caplen NJ (2005) Defining and assaying RNAi in mammalian cells. Mol Cell 17:1-10
5. Tuschl T (2001) RNA interference and small interfering RNAs. Chembiochem 2:239-245
6. Nakayashiki H, Nguyen QB (2008) RNA interference: roles in fungal biology. Curr Opin Microbiol 11:494-502
7. Travella S, Keller B (2009) Down-regulation of gene expression by RNA-induced gene silencing. Methods Mol Biol 478:185-199
8. Tomari Y, Du T, Zamore PD (2007) Sorting of Drosophila small silencing RNAs. Cell 130:299-308
9. Matranga C, Zamore PD (2007) Small silencing RNAs. Curr Biol 17:R789-R793
10. Zamore PD (2004) Plant RNAi: how a viral silencing suppressor inactivates siRNA. Curr Biol 14:R198-R200
11. Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, Ideker T, Grewal SI, Weissman JS, Krogan NJ (2008) Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322:405-410
12. Volpe T, Schramke V, Hamilton GL, White SA, Teng G, Martienssen RA, Allshire RC (2003) RNA interference is required for normal centromere function in fission yeast. Chromosome Res 11:137-146
13. Hamilton B, Dong Y, Shindo M, Liu W, Odell I, Ruvkun G, Lee SS (2005) A systematic RNAi screen for longevity genes in C. elegans. Genes Dev 19:1544-1555
14. Caplen NJ, Mousses S (2003) Short interfering RNA (siRNA)-mediated RNA interference (RNAi) in human cells. Ann N Y Acad Sci 1002:56-62
15. Haley B, Tang G, Zamore PD (2003) In vitro analysis of RNA interference in Drosophila melanogaster. Methods 30:330-336
16. Stroschein-Stevenson SL, Foley E, O'Farrell PH, Johnson AD (2009) Phagocytosis of Candida albicans by RNAi-treated Drosophila S2 cells. Methods Mol Biol 470:347-358
17. Grishok A (2005) RNAi mechanisms in Caenorhabditis elegans. FEBS Lett 579:5932-5939
18. Grishok A, Hoersch S, Sharp PA (2008) RNA interference and retinoblastomarelated genes are required for repression of endogenous siRNA targets in Caenorhabditis elegans. Proc Natl Acad Sci USA 105:20386-20391
19. Kamath RS, Ahringer J (2003) Genomewide RNAi screening in Caenorhabditis elegans. Methods 30:313-321
20. Kim JK, Gabel HW, Kamath RS, Tewari M, Pasquinelli A, Rual JF, Kennedy S, Dybbs M, Bertin N, Kaplan JM, Vidal M, Ruvkun G (2005) Functional genomic analysis of RNA interference in C. elegans. Science 308:1164-1167
21. Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, Artelt J, Bettencourt P, Cassin E, Hewitson M, Holz C, Khan M, Lazik S, Martin C, Nitzsche B, Ruer M, Stamford J, Winzi M, Heinkel R, Roder M, Finell J, Hantsch H, Jones SJ, Jones M, Piano F, Gunsalus KC, Oegema K, Gonczy P, Coulson A, Hyman AA, Echeverri CJ (2005) Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434:462-469
22. Mariotti M, Castiglioni S, Maier JA (2009) Inhibition of T24 human bladder carcinoma cell migration by RNA interference suppressing the expression of HD-PTP. Cancer Lett 273:155-163
23. Medarova Z, Kumar M, Ng SW, Yang J, Barteneva N, Evgenov NV, Petkova V, Moore A (2008) Multifunctional magnetic nanocarriers for image-tagged SiRNA delivery to intact pancreatic islets. Transplantation 86:1170-1177
24. Tuschl T, Zamore PD, Lehmann R, Bartel DP, Sharp PA (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 13:3191-3197
25. Sun X, Rogoff HA, Li CJ (2008) Asymmetric RNA duplexes mediate RNA interference in mammalian cells. Nat Biotechnol 26:1379-1382
26. Aleku M, Schulz P, Keil O, Santel A, Schaeper U, Dieckhoff B, Janke O, Endruschat J, Durieux B, Roder N, Loffler K, Lange C, Fechtner M, Mopert K, Fisch G, Dames S, Arnold W, Jochims K, Giese K, Wiedenmann B, Scholz A, Kaufmann J (2008) Atu027, a liposomal small interfering RNA formulation targeting protein kinase N3, inhibits cancer progression. Cancer Res 68:9788-9798
27. Rines DR, Gomez-Ferreria MA, Zhou Y, DeJesus P, Grob S, Batalov S, Labow M, Huesken D, Mickanin C, Hall J, Reinhardt M, Natt F, Lange J, Sharp DJ, Chanda SK, Caldwell JS (2008) Whole genome functional analysis identifies novel components required for mitotic spindle integrity in human cells. Genome Biol 9:R44
28. McManus MT, Sharp PA (2002) Gene silencing in mammals by small interfering RNAs. Nat Rev 3:737-747
29. Filipowicz W (2005) RNAi: the nuts and bolts of the RISC machine. Cell 122:17-20
30. Ohrt T, Mutze J, Staroske W, Weinmann L, Hock J, Crell K, Meister G, Schwille P (2008) Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells. Nucleic Acids Res 36:6439-6449
31. MacRae IJ, Ma E, Zhou M, Robinson CV, Doudna JA (2008) In vitro reconstitution of the human RISC-loading complex. Proc Natl Acad Sci USA 105:512-517
32. Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerkhoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W, Cavet G, Linsley PS, Beijersbergen RL, Bernards R (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428:431-437
33. Ganesan AK, Ho H, Bodemann B, Petersen S, Aruri J, Koshy S, Richardson Z, Le LQ, Krasieva T, Roth MG, Farmer P, White MA (2008) Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells. PLoS Genet 4:e1000298
34. Schlabach MR, Luo J, Solimini NL, Hu G, Xu Q, Li MZ, Zhao Z, Smogorzewska A, Sowa ME, Ang XL, Westbrook TF, Liang AC, Chang K, Hackett JA, Harper JW, Hannon GJ, Elledge SJ (2008) Cancer proliferation gene discovery through functional genomics. Science 319:620-624
35. Silva JM, Marran K, Parker JS, Silva J, Golding M, Schlabach MR, Elledge SJ, Hannon GJ, Chang K (2008) Profiling essential genes in human mammary cells by multiplex RNAi screening. Science 319:617-620
36. Paddison PJ, Hannon GJ (2003) siRNAs and shRNAs: skeleton keys to the human genome. Curr Opin Mol Ther 5:217-224
37. Amarzguioui M, Holen T, Babaie E, Prydz H (2003) Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res 31:589-595
38. Amarzguioui M, Prydz H (2004) An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun 316:1050-1058
39. Boden D, Pusch O, Lee F, Tucker L, Shank PR, Ramratnam B (2003) Promoter choice affects the potency of HIV-1 specific RNA interference. Nucleic Acids Res 31:5033-5038
40. Das AT, Brummelkamp TR, Westerhout EM, Vink M, Madiredjo M, Bernards R, Berkhout B (2004) Human immunodeficiency virus type 1 escapes from RNA interference-mediated inhibition. J Virol 78:2601-2605
41. Gitlin L, Karelsky S, Andino R (2002) Short interfering RNA confers intracellular antiviral immunity in human cells. Nature 418:430-434
42. Sano M, Sierant M, Miyagishi M, Nakanishi M, Takagi Y, Sutou S (2008) Effect of asymmetric terminal structures of short RNA duplexes on the RNA interference activity and strand selection. Nucleic Acids Res 36:5812-5821
43. Paddison PJ, Hannon GJ (2002) RNA interference: the new somatic cell genetics? Cancer Cell 2:17-23
44. Ui-Tei K, Naito Y, Saigo K (2007) Guidelines for the selection of effective short-interfering RNA sequences for functional genomics. Methods Mol Biol 361:201-216
45. Dykxhoorn DM, Novina CD, Sharp PA (2003) Killing the messenger: short RNAs that silence gene expression. Nat Rev Mol Cell Biol 4:457-467
46. Jones SW, Souza PM, Lindsay MA (2004) siRNA for gene silencing: a route to drug target discovery. Curr Opin Pharmacol 4:522-527
47. Rossi JJ (2008) Expression strategies for short hairpin RNA interference triggers. Hum Gene Ther 19:313-317
48. Han SE, Kang H, Shim GY, Suh MS, Kim SJ, Kim JS, Oh YK (2008) Novel cationic cholesterol derivative-based liposomes for serumenhanced delivery of siRNA. Int J Pharm 353:260-269
49. Sun TM, Du JZ, Yan LF, Mao HQ, Wang J (2008) Self-assembled biodegradable micellar nanoparticles of amphiphilic and cationic block copolymer for siRNA delivery. Biomaterials 29:4348-4355
50. Medarova Z, Pham W, Farrar C, Petkova V, Moore A (2007) In vivo imaging of siRNA delivery and silencing in tumors. Nat Med 13:372-377
51. Kuuselo R, Savinainen K, Azorsa DO, Basu GD, Karhu R, Tuzmen S, Mousses S, Kallioniemi A (2007) Intersex-like (IXL) is a cell survival regulator in pancreatic cancer with 19q13 amplification. Cancer Res 67:1943-1949
52. Ovcharenko D, Jarvis R, Hunicke-Smith S, Kelnar K, Brown D (2005) High-throughput RNAi screening in vitro: from cell lines to primary cells. RNA 11:985-993
53. Favard C, Dean DS, Rols MP (2007) Electrotransfer as a non viral method of gene delivery. Curr Gene Ther 7:67-77
54. Anderson E, Boese Q, Khvorova A, Karpilow J (2008) Identifying siRNA-induced offtargets by microarray analysis. Methods Mol Biol 442:45-63
55. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21:635-637
56. Scacheri PC, Rozenblatt-Rosen O, Caplen NJ, Wolfsberg TG, Umayam L, Lee JC, Hughes CM, Shanmugam KS, Bhattacharjee A, Meyerson M, Collins FS (2004) Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells. Proc Natl Acad Sci USA 101:1892-1897
57. Heidel JD, Hu S, Liu XF, Triche TJ, Davis ME (2004) Lack of interferon response in animals to naked siRNAs. Nat Biotechnol 22:1579-1582
58. Ma Z, Li J, He F, Wilson A, Pitt B, Li S (2005) Cationic lipids enhance siRNA-mediated interferon response in mice. Biochem Biophys Res Commun 330:755-759
59. Uprichard SL (2005) The therapeutic potential of RNA interference. FEBS Lett 579:5996-6007
60. Robbins MA, Rossi JJ (2005) Sensing the danger in RNA. Nat Med 11:250-251
61. Hornung V, Guenthner-Biller M, Bourquin C, Ablasser A, Schlee M, Uematsu S, Noronha A, Manoharan M, Akira S, de Fougerolles A, Endres S, Hartmann G (2005) Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med 11:263-270
62. Kim DH, Longo M, Han Y, Lundberg P, Cantin E, Rossi JJ (2004) Interferon induction by siRNAs and ssRNAs synthesized by phage polymerase. Nat Biotechnol 22:321-325
63. Caplen NJ (2002) A new approach to the inhibition of gene expression. Trends Biotechnol 20:49-51
64. Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA (2001) Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci USA 98:9742-9747
65. Scherr M, Battmer K, Winkler T, Heidenreich O, Ganser A, Eder M (2003) Specific inhibition of bcr-abl gene expression by small interfering RNA. Blood 101:1566-1569
66. Scherr M, Steinmann D, Eder M (2004) RNA interference (RNAi) in hematology. Ann Hematol 83:1-8
67. Scherr M, Venturini L, Eder M (2009) Knock-down of gene expression in hematopoietic cells. Methods Mol Biol 506:207-219
68. Bausero MA, Bharti A, Page DT, Perez KD, Eng JW, Ordonez SL, Asea EE, Jantschitsch C, Kindas-Muegge I, Ciocca D, Asea A (2006) Silencing the hsp25 gene eliminates migration capability of the highly metastatic murine 4T1 breast adenocarcinoma cell. Tumour Biol 27:17-26
69. Logashenko EB, Vladimirova AV, Repkova MN, Venyaminova AG, Chernolovskaya EL, Vlassov VV (2004) Silencing of MDR 1 gene in cancer cells by siRNA. Nucleosides Nucleotides Nucleic Acids 23:861-866
70. Nagy P, Arndt-Jovin DJ, Jovin TM (2003) Small interfering RNAs suppress the expression of endogenous and GFP-fused epidermal growth factor receptor (erbB1) and induce apoptosis in erbB1-overexpressing cells. Exp Cell Res 285:39-49
71. Stierle V, Laigle A, Jolles B (2005) Modulation of MDR1 gene expression in multidrug resistant MCF7 cells by low concentrations of small interfering RNAs. Biochem Pharmacol 70:1424-1430
72. Sumimoto H, Yamagata S, Shimizu A, Miyoshi H, Mizuguchi H, Hayakawa T, Miyagishi M, Taira K, Kawakami Y (2004) Gene therapy for human small-cell lung carcinoma by inactivation of Skp-2 with virally mediated RNA interference. Gene Ther 12:95-100
73. Wilda M, Fuchs U, Wossmann W, Borkhardt A (2002) Killing of leukemic cells with a BCR/ABL fusion gene by RNA interference (RNAi). Oncogene 21:5716-5724
74. Withey JM, Harvey AJ, Crompton MR (2006) RNA interference targeting of Bcr-Abl increases chronic myeloid leukemia cell killing by 17-allylamino-17- demethoxygeldanamycin. Leuk Res 30:553-560
75. Wu H, Hait WN, Yang JM (2003) Small interfering RNA-induced suppression of MDR1 (P-glycoprotein) restores sensitivity to multidrug-resistant cancer cells. Cancer Res 63:1515-1519
76. Zhang L, Yang N, Mohamed-Hadley A, Rubin SC, Coukos G (2003) Vector-based RNAi, a novel tool for isoform-specific knock-down of VEGF and anti-angiogenesis gene therapy of cancer. Biochem Biophys Res Commun 303:1169-1178
77. Brummelkamp TR, Bernards R, Agami R (2002) Stable suppression of tumorigenicity by virus-mediated RNA interference. Cancer Cell 2:243-247
78. Burgess DJ, Doles J, Zender L, Xue W, Ma B, McCombie WR, Hannon GJ, Lowe SW, Hemann MT (2008) Topoisomerase levels determine chemotherapy response in vitro and in vivo. Proc Natl Acad Sci USA 105:9053-9058
79. Frankish H (2003) Consortium uses RNAi to uncover genes' function. Lancet 361:584
80. Gobeil S, Zhu X, Doillon CJ, Green MR (2008) A genome-wide shRNA screen identifies GAS1 as a novel melanoma metastasis suppressor gene. Genes Dev 22:2932-2940
81. Ito M, Kawano K, Miyagishi M, Taira K (2005) Genome-wide application of RNAi to the discovery of potential drug targets. FEBS Lett 579:5988-5995
82. Chen M, Du Q, Zhang H, Wang X, Liang Z (2007) High-throughput screening using siRNA (RNAi) libraries. Expert Rev Mol Diagn 7:281-291
83. Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ, Hannon GJ (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature 428:427-431
84. Sachse C, Krausz E, Kronke A, Hannus M, Walsh A, Grabner A, Ovcharenko D, Dorris D, Trudel C, Sonnichsen B, Echeverri CJ (2005) High-throughput RNA interference strategies for target discovery and validation by using synthetic short interfering RNAs: functional genomics investigations of biological pathways. Methods Enzymol 392:242-277
85. Kimura J, Nguyen ST, Liu H, Taira N, Miki Y, Yoshida K (2008) A functional genome-wide RNAi screen identifies TAF1 as a regulator for apoptosis in response to genotoxic stress. Nucleic Acids Res 36:5250-5259
86. Dykxhoorn DM, Lieberman J (2005) The silent revolution: RNA interference as basic biology, research tool, and therapeutic. Annu Rev Med 56:401-423
87. Mousses S, Caplen NJ, Cornelison R, Weaver D, Basik M, Hautaniemi S, Elkahloun AG, Lotufo RA, Choudary A, Dougherty ER, Suh E, Kallioniemi O (2003) RNAi microarray analysis in cultured mammalian cells. Genome Res 13:2341-2347
88. Ortega-Paino E, Fransson J, Ek S, Borrebaeck CA (2008) Functionally associated targets in mantle cell lymphoma as defined by DNA microarrays and RNA interference. Blood 111:1617-1624
89. Semizarov D, Kroeger P, Fesik S (2004) siRNAmediated gene silencing: a global genome view. Nucleic Acids Res 32:3836-3845
90. Vanhecke D, Janitz M (2004) Highthroughput gene silencing using cell arrays. Oncogene 23:8353-8358
91. Wheeler DB, Carpenter AE, Sabatini DM (2005) Cell microarrays and RNA interference chip away at gene function. Nat Genet 37(Suppl):S25-S30
92. Castel D, Debily MA, Pitaval A, Gidrol X (2007) Cell microarray for functional exploration of genomes. Methods Mol Biol 381:375-384
93. Fjeldbo C, Misund K, Günther C, Langaas M, Steigedal T, Thommesen L, Laegreid A, Bruland T (2008) Functional studies on transfected cell microarray analysed by linear regression modelling. Nucleic Acids Res 36:e97
94. Whitehurst AW, Bodemann BO, Cardenas J, Ferguson D, Girard L, Peyton M, Minna JD, Michnoff C, Hao W, Roth MG, Xie XJ, White MA (2007) Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Nature 446:815-819
95. Zhang X, Yang X, Chung N, Gates A, Stec E, Kunapuli P, Holder D, Ferrer M, Espeseth A (2006) Robust statistical methods for hit selection in RNA interference high-throughput screening experiments. Pharmacogenomics 7:299-309
96. Thomas RK, Weir B, Meyerson M (2006) Genomic approaches to lung cancer. Clin Cancer Res 12:4384s-4391s
97. Ghosh D, Poisson L (2009) "Omics" data and levels of evidence for biomarker discovery. Genomics 93:13-16
98. Tuzmen S, Kiefer J, Mousses S (2007) Validation of short interfering RNA knockdowns by quantitative real-time PCR. Methods Mol Biol 353:177-203
99. Mehler MF (2008) Epigenetic principles and mechanisms underlying nervous system functions in health and disease. Prog Neurobiol 86:305-341
100. Meng F, Dong B, Li H, Fan D, Ding J (2009) RNAi-mediated inhibition of Raf-1 leads to decreased angiogenesis and tumor growth in gastric cancer. Cancer Biol Ther 8:174-179
101. Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N, Hahn WC, Jackson AL, Kiger A, Linsley PS, Lum L, Ma Y, Mathey-Prevot B, Root DE, Sabatini DM, Taipale J, Perrimon N, Bernards R (2006) Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods 3:777-779