Cancer proliferation gene discovery through functional genomics.
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.
Schlabach
Michael R
MR
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.
Luo
Ji
J
Solimini
Nicole L
NL
Hu
Guang
G
Xu
Qikai
Q
Li
Mamie Z
MZ
Zhao
Zhenming
Z
Smogorzewska
Agata
A
Sowa
Mathew E
ME
Ang
Xiaolu L
XL
Westbrook
Thomas F
TF
Liang
Anthony C
AC
Chang
Kenneth
K
Hackett
Jennifer A
JA
Harper
J Wade
JW
Hannon
Gregory J
GJ
Elledge
Stephen J
SJ
D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D002460:Cell Line; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D002470:Cell Survival / Q000235:genetics; D003110:Colonic Neoplasms / Q000235:genetics* / Q000473:pathology; D015723:Gene Library; D052138:Genes, Neoplasm; D005822:Genetic Vectors; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D035683:MicroRNAs; D020411:Oligonucleotide Array Sequence Analysis; D034741:RNA, Small Interfering; D012190:Retroviridae / Q000235:genetics
D035683:MicroRNAs; D034741:RNA, Small Interfering