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Science 319 (5863): 620-624

Copyright © 2008 by the American Association for the Advancement of Science

Cancer Proliferation Gene Discovery Through Functional Genomics

Michael R. Schlabach,1* Ji Luo,1* Nicole L. Solimini,1* Guang Hu,1* Qikai Xu,1 Mamie Z. Li,1 Zhenming Zhao,1 Agata Smogorzewska,1,2 Mathew E. Sowa,3 Xiaolu L. Ang,3 Thomas F. Westbrook,1 Anthony C. Liang,1 Kenneth Chang,4 Jennifer A. Hackett,1 J. Wade Harper,3 Gregory J. Hannon,4 Stephen J. Elledge1{dagger}

Abstract: Retroviral short hairpin RNA (shRNA)–mediated genetic screens in mammalian cells are powerful tools for discovering loss-of-function phenotypes. We describe a highly parallel multiplex methodology for screening large pools of shRNAs using half-hairpin barcodes for microarray deconvolution. We carried out dropout screens for shRNAs that affect cell proliferation and viability in cancer cells and normal cells. We identified many shRNAs to be antiproliferative that target core cellular processes, such as the cell cycle and protein translation, in all cells examined. Moreover, we identified genes that are selectively required for proliferation and survival in different cell lines. Our platform enables rapid and cost-effective genome-wide screens to identify cancer proliferation and survival genes for target discovery. Such efforts are complementary to the Cancer Genome Atlas and provide an alternative functional view of cancer cells.

1 Howard Hughes Medical Institute and Department of Genetics, Center for Genetics and Genomics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
2 Department of Pathology, Massachusetts General Hospital (MGH), Boston, MA 02114, USA.
3 Department of Pathology, Harvard Medical School, Boston, MA 02115, USA.
4 Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: selledge{at}genetics.med.harvard.edu

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   Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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