Genomic profiling reveals high frequency of DNA repair genetic aberrations in gallbladder cancer

Sci Rep. 2020 Dec 16;10(1):22087. doi: 10.1038/s41598-020-77939-6.

Abstract

DNA repair gene aberrations (GAs) occur in several cancers, may be prognostic and are actionable. We investigated the frequency of DNA repair GAs in gallbladder cancer (GBC), association with tumor mutational burden (TMB), microsatellite instability (MSI), programmed cell death protein 1 (PD-1), and its ligand (PD-L1) expression. Comprehensive genomic profiling (CGP) of 760 GBC was performed. We investigated GAs in 19 DNA repair genes including direct DNA repair genes (ATM, ATR, BRCA1, BRCA2, FANCA, FANCD2, MLH1, MSH2, MSH6, PALB2, POLD1, POLE, PRKDC, and RAD50) and caretaker genes (BAP1, CDK12, MLL3, TP53, and BLM) and classified patients into 3 groups based on TMB level: low (< 5.5 mutations/Mb), intermediate (5.5-19.5 mutations/Mb), and high (≥ 19.5 mutations/Mb). We assessed MSI status and PD-1 & PD-L1 expression. 658 (86.6%) had at least 1 actionable GA. Direct DNA repair gene GAs were identified in 109 patients (14.2%), while 476 (62.6%) had GAs in caretaker genes. Both direct and caretaker DNA repair GAs were significantly associated with high TMB (P = 0.0005 and 0.0001, respectively). Tumor PD-L1 expression was positive in 119 (15.6%), with 17 (2.2%) being moderate or high. DNA repair GAs are relatively frequent in GBC and associated with coexisting actionable mutations and a high TMB.

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • B7-H1 Antigen / genetics*
  • Biomarkers, Tumor / genetics
  • DNA Repair / genetics*
  • Female
  • Gallbladder Neoplasms / epidemiology
  • Gallbladder Neoplasms / genetics*
  • Gallbladder Neoplasms / pathology
  • Gene Expression Regulation, Neoplastic
  • Genome, Human / genetics
  • Genomics
  • Humans
  • Male
  • Microsatellite Instability
  • Middle Aged
  • Mutation / genetics
  • Neoplasm Proteins / genetics
  • Programmed Cell Death 1 Receptor / genetics*
  • Tumor Suppressor Proteins / genetics

Substances

  • B7-H1 Antigen
  • Biomarkers, Tumor
  • Neoplasm Proteins
  • Programmed Cell Death 1 Receptor
  • Tumor Suppressor Proteins