Profiling essential genes in human mammary cells by multiplex RNAi screening.
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.
Silva
Jose M
JM
Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
Marran
Krista
K
Parker
Joel S
JS
Silva
Javier
J
Golding
Michael
M
Schlabach
Michael R
MR
Elledge
Stephen J
SJ
Hannon
Gregory J
GJ
Chang
Kenneth
K
D001940:Breast / Q000166:cytology* / Q000378:metabolism*; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D002460:Cell Line; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D002470:Cell Survival; D020869:Gene Expression Profiling; D020043:Genes, Essential; D023281:Genomics; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D034622:RNA Interference; D034741:RNA, Small Interfering
D034741:RNA, Small Interfering