DF/HCC Program Affiliation

Cancer Genetics

Research Abstract

The purpose of the Drosophila RNAi Screening Center (DRSC) established at Harvard Medical School is to provide the community with a unique infrastructure and expertise for high-throughput RNA interference screens (RNAi HTS) in Drosophila cell lines using a genome-wide collection of double stranded RNAs (dsRNAs). Over the last 3 years, 65 genome-wide screens have been completed by groups affiliated with institutions from all over the world, and 17 have already resulted in publication (http://flyrnai.org). The vast experience gained during these first years has been instrumental in shaping our view on how to build upon our initial goals and expand the scope and technology of RNAi HTS in Drosophila. To face those new challenges and develop the DRSC into an integrated center for technology transfer in functional genomics, our goals are: (1) To address the off-target effects observed with long dsRNAs through a re-design of our library and the ability to offer two or more dsRNAs to confirm the specificity of RNAi phenotypes. (2) To implement a number of key improvements to expand the range of functional screens available at the DRSC. We plan to offer sub-collections of dsRNAs against a variety of large gene families such as transcription factors or cytoskeletal proteins for more focused screens, and add miRNA and cDNA constructs over-expression libraries for gain of function studies in Drosophila cell-based assays. (3) To meet the growing demand on performing more sophisticated screens with greater biological relevance, we have added the ability to perform RNAi HTS in primary Drosophila cell cultures and have acquired an ultra high-throughput confocal, imaging platform that will be ideal for high content imaging screens. (4) To address the need of screeners to handle vast amount of data and the challenge to analyze them, we plan to add functionality to our database and develop powerful computational approaches for data analysis and data mining. Lastly, we are engaged in a collaborative effort with the Perrimon lab to generate a large collection of optimized short hairpin RNA transgenic flies for rapid in vivo validation.

Publications

• Mathey-Prevot B, Perrimon N.Do-it-yourself RNAi made easy?.Nat Methods 2007 Apr;4(4):308-9.
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• Mathey-Prevot B, Perrimon N.Drosophila genome-wide RNAi screens: are they delivering the promise?.Cold Spring Harb Symp Quant Biol 2006;71:141-8.
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• Perrimon N, Mathey-Prevot B.Applications of high-throughput RNA interference screens to problems in cell and developmental biology.Genetics 2007 Jan;175(1):7-16.
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• Perrimon N, Friedman A, Mathey-Prevot B, Eggert US.Drug-target identification in Drosophila cells: combining high-throughout RNAi and small-molecule screens.Drug Discov Today 2007 Jan;12(1-2):28-33.
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• 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-Prévôt B, Root DE, Sabatini DM, Taipale J, Perrimon N, Bernards R.Minimizing th
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• Kulkarni MM, Booker M, Silver SJ, Friedman A, Hong P, Perrimon N, Mathey-Prevot B.Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays.Nat Methods 2006 Oct;3(10):833-8.
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• Flockhart I, Booker M, Kiger A, Boutros M, Armknecht S, Ramadan N, Richardson K, Xu A, Perrimon N, Mathey-Prevot B.FlyRNAi: the Drosophila RNAi screening center database.Nucleic Acids Res 2006 Jan 1;34(Database issue):D489-94.
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• Callus BA, Mathey-Prevot B.Interleukin-3-induced activation of the JAK/STAT pathway is prolonged by proteasome inhibitors.Blood 1998 May 1;91(9):3182-92.
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