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Dr. Gregory Hoffman’s group from Novartis recently used a custom library from Cellecta that identified BRM/SMARCA2 as a critical target in BRG1-deficient cancers (PMID: 24520176). The shRNA library consisted of 6500 shRNAs (380 genes with 17 shRNAs per gene) involved in epigenetic regulation. These genes represented primarily druggable targets involved in covalent modification of histones and proteins with reader domains recognizing histone marks. This barcoded custom library was screened against 58 cancer cell lines representing various diverse genetic backgrounds.

The SWI/SNF complex is a nucleosome remodeling complex that destabilizes histone-DNA interactions and also acts as a tumor suppressor. An estimated 20% of all cancers are affected by mutations in genes in the SWI/SNF complex. Both BGI/SMARCA4 and BRM/SMARCA2 are catalytic proteins in the SWI/SNF complex. Here they found that BRM/SMARCA2 depletion caused cell cycle arrest, induction of senescence and increased levels of H3K9me3, which is typically expressed in constitutively repressed genes. They further provide insight into the mechanism of BRG1/BRM synthetic lethality in vivo using inducible shRNA constructs to BRM in BRG1-mutant tumors.

Many mutations in the SWI/SNF complex are inactivating, which makes studying these mutations a challenge. This study provides an excellent example of how a customized shRNA library can be used to provide mechanistic insight into epigenetic changes involved in cancer.