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Science 319 (5863): 617-620

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

Profiling Essential Genes in Human Mammary Cells by Multiplex RNAi Screening

Jose M. Silva,1 Krista Marran,1 Joel S. Parker,3 Javier Silva,1 Michael Golding,1 Michael R. Schlabach,2 Stephen J. Elledge,2 Gregory J. Hannon,1* Kenneth Chang1

Abstract: By virtue of their accumulated genetic alterations, tumor cells may acquire vulnerabilities that create opportunities for therapeutic intervention. We have devised a massively parallel strategy for screening short hairpin RNA (shRNA) collections for stable loss-of-function phenotypes. We assayed from 6000 to 20,000 shRNAs simultaneously to identify genes important for the proliferation and survival of five cell lines derived from human mammary tissue. Lethal shRNAs common to these cell lines targeted many known cell-cycle regulatory networks. Cell line–specific sensitivities to suppression of protein complexes and biological pathways also emerged, and these could be validated by RNA interference (RNAi) and pharmacologically. These studies establish a practical platform for genome-scale screening of complex phenotypes in mammalian cells and demonstrate that RNAi can be used to expose genotype-specific sensitivities.

1 Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
2 Department of Genetics, Center for Genetics and Genomics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
3 Expression Analysis, Inc., 4324 South Alston Avenue, Durham, NC 27713, USA.

* To whom correspondence should be addressed. E-mail: hannon{at}

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