Abstract
High-throughput RNA interference (HT-RNAi) is a powerful tool that can be used to knock down gene expression in order to identify novel genes and pathways involved in many cellular processes. It is a systematic, yet unbiased, approach to identify essential or synthetic lethal genes that promote cell survival in diseased cells as well as genes that confer resistance or sensitivity to drug treatment. This information serves as a foundation for enhancing current treatments for cancer and other diseases by identifying new drug targets, uncovering potential combination therapies, and helping clinicians match patients with the most effective treatment based on genetic information. Here, we describe the method of performing an in vitro HT-RNAi screen using chemically synthesized siRNA.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Agrawal N, Dasaradhi PV et al (2003) RNA interference: biology, mechanism, and applications. Microbiol Mol Biol Rev 67(4):657–685
Boutros M, Ahringer J (2008) The art and design of genetic screens: RNA interference. Nat Rev Genet 9(7):554–566
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
Duxbury MS, Whang EE (2004) RNA interference: a practical approach. J Surg Res 117(2):339–344
Elbashir SM, Harborth J et al (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411(6836):494–498
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
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
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
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
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
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
Tiedemann RE, Zhu YX et al (2010) Kinome-wide RNAi studies in human multiple myeloma identify vulnerable kinase targets, including a lymphoid-restricted kinase, GRK6. Blood 115(8):1594–1604
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
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
Whitehurst AW, Bodemann BO et al (2007) Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Nature 446(7137):815–819
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
Zhu YX, Tiedemann R et al (2011) RNAi screen of the druggable genome identifies modulators of proteasome inhibitor sensitivity in myeloma including CDK5. Blood 117(14):3847–3857
Zhu YX, Yin H et al (2015) RNA interference screening identifies lenalidomide sensitizers in multiple myeloma, including RSK2. Blood 125(3):483–491
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
Falkenberg KJ, Gould CM et al (2014) Genome-wide functional genomic and transcriptomic analyses for genes regulating sensitivity to vorinostat. Sci Data 1:140017
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
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
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
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
Lord CJ, McDonald S et al (2008) A high-throughput RNA interference screen for DNA repair determinants of PARP inhibitor sensitivity. DNA Repair (Amst) 7(12):2010–2019
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
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
Tibes R, Bogenberger JM et al (2012) RNAi screening of the kinome with cytarabine in leukemias. Blood 119(12):2863–2872
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
Acknowledgements
We would like to thank TGen for their support, Mr. Chris Sereduk for editing, and Springer Publishing.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Yin, H., Kassner, M. (2016). In Vitro High-Throughput RNAi Screening to Accelerate the Process of Target Identification and Drug Development. In: Azorsa, D., Arora, S. (eds) High-Throughput RNAi Screening. Methods in Molecular Biology, vol 1470. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6337-9_11
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6337-9_11
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6335-5
Online ISBN: 978-1-4939-6337-9
eBook Packages: Springer Protocols