Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes

Brian D. Lehmann, Antonio Colaprico, Tiago C. Silva, Jianjiao Chen, Hanbing An, Yuguang Ban, Hanchen Huang, Lily Wang, Jamaal L. James, Justin M. Balko, Paula I. Gonzalez-Ericsson, Melinda E. Sanders, Bing Zhang, Jennifer A. Pietenpol, X. Steven Chen

Research output: Contribution to journalArticlepeer-review


Triple-negative breast cancer (TNBC) is a collection of biologically diverse cancers characterized by distinct transcriptional patterns, biology, and immune composition. TNBCs subtypes include two basal-like (BL1, BL2), a mesenchymal (M) and a luminal androgen receptor (LAR) subtype. Through a comprehensive analysis of mutation, copy number, transcriptomic, epigenetic, proteomic, and phospho-proteomic patterns we describe the genomic landscape of TNBC subtypes. Mesenchymal subtype tumors display high mutation loads, genomic instability, absence of immune cells, low PD-L1 expression, decreased global DNA methylation, and transcriptional repression of antigen presentation genes. We demonstrate that major histocompatibility complex I (MHC-I) is transcriptionally suppressed by H3K27me3 modifications by the polycomb repressor complex 2 (PRC2). Pharmacological inhibition of PRC2 subunits EZH2 or EED restores MHC-I expression and enhances chemotherapy efficacy in murine tumor models, providing a rationale for using PRC2 inhibitors in PD-L1 negative mesenchymal tumors. Subtype-specific differences in immune cell composition and differential genetic/pharmacological vulnerabilities suggest additional treatment strategies for TNBC.

Original languageEnglish (US)
Article number6276
JournalNature communications
Issue number1
StatePublished - Dec 2021

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)


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