SMARCA2-deficiency confers sensitivity to targeted inhibition of SMARCA4 in esophageal squamous cell carcinoma cell lines

Sci Rep. 2019 Aug 12;9(1):11661. doi: 10.1038/s41598-019-48152-x.

Abstract

SMARCA4/BRG1 and SMARCA2/BRM, the two mutually exclusive catalytic subunits of the BAF complex, display a well-established synthetic lethal relationship in SMARCA4-deficient cancers. Using CRISPR-Cas9 screening, we identify SMARCA4 as a novel dependency in SMARCA2-deficient esophageal squamous cell carcinoma (ESCC) models, reciprocal to the known synthetic lethal interaction. Restoration of SMARCA2 expression alleviates the dependency on SMARCA4, while engineered loss of SMARCA2 renders ESCC models vulnerable to concomitant depletion of SMARCA4. Dependency on SMARCA4 is linked to its ATPase activity, but not to bromodomain function. We highlight the relevance of SMARCA4 as a drug target in esophageal cancer using an engineered ESCC cell model harboring a SMARCA4 allele amenable to targeted proteolysis and identify SMARCA4-dependent cell models with low or absent SMARCA2 expression from additional tumor types. These findings expand the concept of SMARCA2/SMARCA4 paralog dependency and suggest that pharmacological inhibition of SMARCA4 represents a novel therapeutic opportunity for SMARCA2-deficient cancers.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Antineoplastic Agents / pharmacology
  • Antineoplastic Agents / therapeutic use
  • CRISPR-Cas Systems / genetics
  • Cell Line, Tumor
  • Cell Survival / genetics
  • DNA Helicases / antagonists & inhibitors*
  • DNA Helicases / genetics
  • Epigenesis, Genetic
  • Esophageal Neoplasms / drug therapy*
  • Esophageal Neoplasms / genetics
  • Esophageal Neoplasms / pathology
  • Esophageal Squamous Cell Carcinoma / drug therapy*
  • Esophageal Squamous Cell Carcinoma / genetics
  • Esophageal Squamous Cell Carcinoma / pathology
  • Gene Editing
  • Gene Expression Regulation, Neoplastic / drug effects
  • Gene Knockdown Techniques
  • Gene Knockout Techniques
  • Humans
  • Loss of Function Mutation
  • Molecular Targeted Therapy / methods
  • Nuclear Proteins / antagonists & inhibitors*
  • Nuclear Proteins / genetics
  • RNA, Guide / genetics
  • RNA, Small Interfering / metabolism
  • Synthetic Lethal Mutations
  • Transcription Factors / antagonists & inhibitors*
  • Transcription Factors / deficiency
  • Transcription Factors / genetics*

Substances

  • Antineoplastic Agents
  • Nuclear Proteins
  • RNA, Guide
  • RNA, Small Interfering
  • SMARCA2 protein, human
  • Transcription Factors
  • SMARCA4 protein, human
  • DNA Helicases