Highly parallel identification of essential genes in cancer cells.
More complete knowledge of the molecular mechanisms underlying cancer will improve prevention, diagnosis and treatment. Efforts such as The Cancer Genome Atlas are systematically characterizing the structural basis of cancer, by identifying the genomic mutations associated with each cancer type. A powerful complementary approach is to systematically characterize the functional basis of cancer, by identifying the genes essential for growth and related phenotypes in different cancer cells. Such information would be particularly valuable for identifying potential drug targets. Here, we report the development of an efficient, robust approach to perform genome-scale pooled shRNA screens for both positive and negative selection and its application to systematically identify cell essential genes in 12 cancer cell lines. By integrating these functional data with comprehensive genetic analyses of primary human tumors, we identified known and putative oncogenes such as EGFR, KRAS, MYC, BCR-ABL, MYB, CRKL, and CDK4 that are essential for cancer cell proliferation and also altered in human cancers. We further used this approach to identify genes involved in the response of cancer cells to tumoricidal agents and found 4 genes required for the response of CML cells to imatinib treatment: PTPN1, NF1, SMARCB1, and SMARCE1, and 5 regulators of the response to FAS activation, FAS, FADD, CASP8, ARID1A and CBX1. Broad application of this highly parallel genetic screening strategy will not only facilitate the rapid identification of genes that drive the malignant state and its response to therapeutics but will also enable the discovery of genes that participate in any biological process.
Luo
Biao
B
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
Cheung
Hiu Wing
HW
Subramanian
Aravind
A
Sharifnia
Tanaz
T
Okamoto
Michael
M
Yang
Xiaoping
X
Hinkle
Greg
G
Boehm
Jesse S
JS
Beroukhim
Rameen
R
Weir
Barbara A
BA
Mermel
Craig
C
Barbie
David A
DA
Awad
Tarif
T
Zhou
Xiaochuan
X
Nguyen
Tuyen
T
Piqani
Bruno
B
Li
Cheng
C
Golub
Todd R
TR
Meyerson
Matthew
M
Hacohen
Nir
N
Hahn
William C
WC
Lander
Eric S
ES
Sabatini
David M
DM
Root
David E
DE
D000970:Antineoplastic Agents / Q000493:pharmacokinetics; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D000090266:Chromobox Protein Homolog 5; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D009369:Neoplasms / Q000473:pathology*; D009857:Oncogenes / Q000235:genetics / Q000502:physiology*; D010597:Pharmacogenetics; D034741:RNA, Small Interfering; D014407:Tumor Cells, Cultured; D019014:fas Receptor / Q000378:metabolism
D000970:Antineoplastic Agents; C000715593:CBX1 protein, human; D047908:Intracellular Signaling Peptides and Proteins; D034741:RNA, Small Interfering; D019014:fas Receptor; D000090266:Chromobox Protein Homolog 5