Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling

Nat Commun. 2021 Apr 14;12(1):2242. doi: 10.1038/s41467-021-22445-0.

Abstract

Breast cancer is a heterogeneous disease, affecting over 3.5 million women worldwide, yet the functional role of cis-regulatory elements including super-enhancers in different breast cancer subtypes remains poorly characterized. Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a poor prognosis. Here we apply integrated epigenomic and transcriptomic profiling to uncover super-enhancer heterogeneity between breast cancer subtypes, and provide clinically relevant biological insights towards TNBC. Using CRISPR/Cas9-mediated gene editing, we identify genes that are specifically regulated by TNBC-specific super-enhancers, including FOXC1 and MET, thereby unveiling a mechanism for specific overexpression of the key oncogenes in TNBC. We also identify ANLN as a TNBC-specific gene regulated by super-enhancer. Our studies reveal a TNBC-specific epigenomic landscape, contributing to the dysregulated oncogene expression in breast tumorigenesis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line, Tumor
  • Enhancer Elements, Genetic
  • Female
  • Forkhead Transcription Factors / genetics
  • Gene Editing
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Mice
  • Mice, Nude
  • Microfilament Proteins / genetics
  • Proto-Oncogene Proteins c-met / genetics
  • Triple Negative Breast Neoplasms / genetics*

Substances

  • ANLN protein, human
  • FOXC1 protein, human
  • Forkhead Transcription Factors
  • Microfilament Proteins
  • MET protein, human
  • Proto-Oncogene Proteins c-met