shRNA RNAi Screen

Overview

Short hairpin RNA (shRNA) RNAi screening is a pooled or arrayed loss-of-function genetic screen that uses RNA interference to knock down gene expression and assess the proliferative or viability impact of each knockdown across a panel of cell lines. Results identify gene dependencies specific to tumor subtypes or genotypes.

Used by

  • Used to functionally validate copy-number dependencies in dedifferentiated liposarcoma (DDLS): 385 genes screened with 2,007 shRNAs (median 5 shRNAs per gene) in three DDLS cell lines (LPS141, DDLS8817, FU-DDLS-1); 99 genes with significant anti-proliferative effects in ≥1 line confirmed PMID:20601955.
  • siRNA screen of 8 DDR genes (BRCA1, BRCA2, CHEK1, CHEK2, SOD1, PARP1, ATM, CDK2) in FBXO7-knockout colonic epithelial cells identified CHEK1 as a synthetic lethal interactor of FBXO7 loss PMID:36334560
  • siRNA knockdown of individual Fanconi anemia pathway genes (FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, BRIP1, PALB2, SLX4, BRCA1, BRCA2) reduced proliferation in LNCaP, 22Rv1, VCaP, and PC3 prostate cancer cell lines and increased gamma-H2AX following carboplatin exposure. PMID:26928463
  • shRNA knockdown of TRMT10A, USP10, BRCA1, PARP1 and ATM used to functionally dissect the TRMT10A-BRCA1 HR axis in LNCaP, C4-2, 22Rv1, DU145, and PC-3 prostate cancer cell lines PMID:28068672.
  • Employed shRNA/RNAi screen to identify essential genes in cancer cell lines PMID:28196596

Notes

  • CDK4 was the most overexpressed amplified hit; sustained CDK4 shRNA knockdown (>10 days) inhibited proliferation in LPS141 and DDLS8817 PMID:20601955.
  • MDM2 knockdown required sustained depletion (>1 week) to impair proliferation; YEATS4 knockdown phenocopied the MDM2 screen result in DDLS PMID:20601955.
  • Only 1 of 58 overlapping genes (PSMB4) was a common essential in a 12-cell-line pan-cancer reference screen, supporting DDLS-specific dependencies PMID:20601955.

Sources

This page was processed by crosslinker on 2026-05-06. - PMID:36334560

This page was processed by crosslinker on 2026-05-06. - PMID:26928463

This page was processed by entity-page-writer on 2026-05-15. - PMID:28068672

This page was processed by wiki-cli on 2026-05-14. - PMID:28196596

This page was processed by wiki-cli on 2026-05-14.