In vitro high-throughput RNAI screening to accelerate the process of target identification and drug development

Methods in Molecular Biology

Volumn 1470, Issue , 2016, Pages 137-149

  Yin, Hongwei ^a   Kassner, Michelle ^a  

^a NONE

Author keywords

Drug development; Drug sensitizer; Essential gene; Functional genomics; Gene knockdown; Gene silencing; High throughput; RNA interference (RNAi); siRNA; Synthetic lethal; Target discovery

Indexed keywords

BIOLOGICAL MARKER; SMALL INTERFERING RNA;

CENTRIFUGE; DRUG SENSITIVITY; DRUG SENSITIZATION; ESSENTIAL GENE; GENE SILENCING; GENETIC SCREENING; HIGH THROUGHPUT SCREENING; IN VITRO STUDY; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; RNA INTERFERENCE; SYNTHESIS; WESTERN BLOTTING; DRUG DEVELOPMENT; PROCEDURES;

DRUG DISCOVERY; GENE KNOCKDOWN TECHNIQUES; GENE SILENCING; GENES, ESSENTIAL; HIGH-THROUGHPUT SCREENING ASSAYS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 84985020366     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-6337-9_11     Document Type: Chapter

References (29)

1. Agrawal N, Dasaradhi PV et al (2003) RNA interference: biology, mechanism, and applications. Microbiol Mol Biol Rev 67(4):657–685
2. Boutros M, Ahringer J (2008) The art and design of genetic screens: RNA interference. Nat Rev Genet 9(7):554–566
3. Caplen NJ, Parrish S et al (2001) Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci U S A 98(17):9742–9747
4. Duxbury MS, Whang EE (2004) RNA interference: a practical approach. J Surg Res 117(2):339–344
5. Elbashir SM, Harborth J et al (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411(6836):494–498
6. Bartlett DW, Davis ME (2006) Insights into the kinetics of siRNA-mediated gene silencing from live-cell and live-animal bioluminescent imaging. Nucleic Acids Res 34(1):322–333
7. Life Technologies. Duration of siRNA induced silencing: your questions answered. https://www.lifetechnologies.com/us/en/home/references/ambion-tech-support/rnai-sirna/tech-notes/duration-of-sirna-induced-silencing.html. Accessed 30 Jul 2015
8. Ganesan AK, Ho H et al (2008) Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells. PLoS Genet 4(12):e1000298
9. Henderson-Smith A, Chow D et al (2013) SMG1 identified as a regulator of Parkinson’s disease-associated alpha-synuclein through siRNA screening. PLoS One 8(10):e77711
10. Petrocca F, Altschuler G et al (2013) A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basal-like triple-negative breast cancer cells. Cancer Cell 24(2):182–196
11. Tiedemann RE, Zhu YX et al (2011) Identification of molecular vulnerabilities in human multiple myeloma cells by RNA interference lethality screening of the druggable genome. Cancer Res 72(3):757–768
12. Tiedemann RE, Zhu YX et al (2010) Kinomewide RNAi studies in human multiple myeloma identify vulnerable kinase targets, including a lymphoid-restricted kinase, GRK 6. Blood 115(8):1594–1604
13. Scholl C, Frohling S et al (2009) Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells. Cell 137(5):821–834
14. Turner NC, Lord CJ et al (2008) A synthetic lethal siRNA screen identifying genes mediating sensitivity to a PARP inhibitor. EMBO J 27(9):1368–1377
15. Whitehurst AW, Bodemann BO et al (2007) Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Nature 446(7137):815–819
16. Harradine KA, Kassner M et al (2011) Functional genomics reveals diverse cellular processes that modulate tumor cell response to oxaliplatin. Mol Cancer Res 9(2):173–182
17. Zhu YX, Tiedemann R et al (2011) RNAi screen of the druggable genome identifies modulators of proteasome inhibitor sensitivity in myeloma including CDK 5. Blood 117(14):3847–3857
18. Zhu YX, Yin H et al (2015) RNA interference screening identifies lenalidomide sensitizers in multiple myeloma, including RSK 2. Blood 125(3):483–491
19. Xie L, Kassner M et al (2012) Kinome-wide siRNA screening identifies molecular targets mediating the sensitivity of pancreatic cancer cells to Aurora kinase inhibitors. Biochem Pharmacol 83(4):452–461
20. Falkenberg KJ, Gould CM et al (2014) Genome-wide functional genomic and transcriptomic analyses for genes regulating sensitivity to vorinostat. Sci Data 1:140017
21. MacKeigan JP, Murphy LO et al (2005) Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance. Nat Cell Biol 7(6):591–600
22. Bartz SR, Zhang Z et al (2006) Small interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions. Mol Cell Biol 26(24):9377–9386
23. Giroux V, Iovanna J et al (2006) Probing the human kinome for kinases involved in pancreatic cancer cell survival and gemcitabine resistance. FASEB J 20(12):1982–1991
24. Iorns E, Lord CJ et al (2009) Parallel RNAi and compound screens identify the PDK1 pathway as a target for tamoxifen sensitization. Biochem J 417(1):361–370
25. Lord CJ, McDonald S et al (2008) A highthroughput RNA interference screen for DNA repair determinants of PARP inhibitor sensitivity. DNA Repair (Amst) 7(12):2010–2019
26. Morgan-Lappe S, Woods KW et al (2006) RNAi-based screening of the human kinome identifies Akt-cooperating kinases: a new approach to designing efficacious multitargeted kinase inhibitors. Oncogene 25(9):1340–1348
27. Bogenberger JM, Kornblau SM et al (2014) BCL-2 family proteins as 5-Azacytidine-sensitizing targets and determinants of response in myeloid malignancies. Leukemia 28(8):1657–1665
28. Tibes R, Bogenberger JM et al (2012) RNAi screening of the kinome with cytarabine in leukemias. Blood 119(12):2863–2872
29. Yin H, Kiefer J, Kassner M, Tang N, Mousses S (2010) The application of high-throughput RNAi in pancreatic cancer target discovery and drug development. In: Han H, Grippo P (eds) Drug discovery in pancreatic cancer. Springer Science + Business Media, LLC, New York, pp 153–170