Essential gene profiles in breast, pancreatic, and ovarian cancer cells.

Abstract

UNLABELLED Genomic analyses are yielding a host of new information on the multiple genetic abnormalities associated with specific types of cancer. A comprehensive description of cancer-associated genetic abnormalities can improve our ability to classify tumors into clinically relevant subgroups and, on occasion, identify mutant genes that drive the cancer phenotype ("drivers"). More often, though, the functional significance of cancer-associated mutations is difficult to discern. Genome-wide pooled short hairpin RNA (shRNA) screens enable global identification of the genes essential for cancer cell survival and proliferation, providing a "functional genomic" map of human cancer to complement genomic studies. Using a lentiviral shRNA library targeting ~16,000 genes and a newly developed, dynamic scoring approach, we identified essential gene profiles in 72 breast, pancreatic, and ovarian cancer cell lines. Integrating our results with current and future genomic data should facilitate the systematic identification of drivers, unanticipated synthetic lethal relationships, and functional vulnerabilities of these tumor types. SIGNIFICANCE This study presents a resource of genome-scale, pooled shRNA screens for 72 breast, pancreatic, and ovarian cancer cell lines that will serve as a functional complement to genomics data, facilitate construction of essential gene profiles, help uncover synthetic lethal relationships, and identify uncharacterized genetic vulnerabilities in these tumor types. SIGNIFICANCE This study presents a resource of genome-scale, pooled shRNA screens for 72 breast, pancreatic, and ovarian cancer cell lines that will serve as a functional complement to genomics data, facilitate construction of essential gene profiles, help uncover synthetic lethal relationships, and identify uncharacterized genetic vulnerabilities in these tumor types.

DOI: 10.1158/2159-8290.CD-11-0224
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@article{Marcotte2012EssentialGP, title={Essential gene profiles in breast, pancreatic, and ovarian cancer cells.}, author={Richard A. Marcotte and Kevin R. Brown and Fernando Su{\'a}rez and Azin Sayad and Konstantina Karamboulas and Paul M. Krzyzanowski and Fabrice Sircoulomb and Mauricio Medrano and Yaroslav Ya Fedyshyn and Judice L. Y. Koh and Dewald van Dyk and Bodhana Fedyshyn and Marianna Luhova and Glauber C. Brito and Franco J. Vizeacoumar and Frederick S. Vizeacoumar and Alessandro Datti and Dahlia Kasimer and Alla Buzina and Patricia Mero and Christine Misquitta and Jos{\'e}e Normand and Maliha Haider and Troy Ketela and Jeffrey L. Wrana and Robert Rottapel and Benjamin G . Neel and Jason Moffat}, journal={Cancer discovery}, year={2012}, volume={2 2}, pages={172-189} }