The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic

Nat Genet. 2019 Mar;51(3):506-516. doi: 10.1038/s41588-018-0331-5. Epub 2019 Feb 4.

Abstract

Esophageal adenocarcinoma (EAC) is a poor-prognosis cancer type with rapidly rising incidence. Understanding of the genetic events driving EAC development is limited, and there are few molecular biomarkers for prognostication or therapeutics. Using a cohort of 551 genomically characterized EACs with matched RNA sequencing data, we discovered 77 EAC driver genes and 21 noncoding driver elements. We identified a mean of 4.4 driver events per tumor, which were derived more commonly from mutations than copy number alterations, and compared the prevelence of these mutations to the exome-wide mutational excess calculated using non-synonymous to synonymous mutation ratios (dN/dS). We observed mutual exclusivity or co-occurrence of events within and between several dysregulated EAC pathways, a result suggestive of strong functional relationships. Indicators of poor prognosis (SMAD4 and GATA4) were verified in independent cohorts with significant predictive value. Over 50% of EACs contained sensitizing events for CDK4 and CDK6 inhibitors, which were highly correlated with clinically relevant sensitivity in a panel of EAC cell lines and organoids.

Publication types

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

MeSH terms

  • Adenocarcinoma / genetics*
  • Biomarkers, Tumor / genetics*
  • Cohort Studies
  • DNA Copy Number Variations / genetics
  • Esophageal Neoplasms / genetics*
  • Exome / genetics
  • Female
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Neoplastic / genetics
  • Genomics / methods
  • Humans
  • Male
  • Mutation / genetics

Substances

  • Biomarkers, Tumor

Supplementary concepts

  • Adenocarcinoma Of Esophagus