A pan-cancer analysis of PBAF complex mutations and their association with immunotherapy response

Nat Commun. 2020 Aug 20;11(1):4168. doi: 10.1038/s41467-020-17965-0.


There is conflicting data regarding the role of PBAF complex mutations and response to immune checkpoint blockade (ICB) therapy in clear cell renal cell carcinoma (ccRCC) and other solid tumors. We assess the prevalence of PBAF complex mutations from two large cohorts including the pan-cancer TCGA project (n = 10,359) and the MSK-IMPACT pan-cancer immunotherapy cohort (n = 3700). Across both cohorts, PBAF complex mutations, predominantly PBRM1 mutations, are most common in ccRCC. In multivariate models of ccRCC patients treated with ICB (n = 189), loss-of-function (LOF) mutations in PBRM1 are not associated with overall survival (OS) (HR = 1.24, p = 0.47) or time to treatment failure (HR = 0.85, p = 0.44). In a series of 11 solid tumors (n = 2936), LOF mutations are not associated with improved OS in a stratified multivariate model (HR = 0.9, p = 0.7). In a current series of solid tumors treated with ICB, we are unable to demonstrate favorable response to ICB in patients with PBAF complex mutations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Carcinoma, Renal Cell / genetics
  • Carcinoma, Renal Cell / pathology
  • Carcinoma, Renal Cell / therapy*
  • Chromosomal Proteins, Non-Histone / genetics*
  • Cohort Studies
  • DNA-Binding Proteins / genetics*
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Immunotherapy / methods*
  • Kaplan-Meier Estimate
  • Kidney Neoplasms / genetics
  • Kidney Neoplasms / pathology
  • Kidney Neoplasms / therapy*
  • Middle Aged
  • Mutation*
  • Transcription Factors / genetics*


  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • PBRM1 protein, human
  • SWI-SNF-B chromatin-remodeling complex
  • Transcription Factors