Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer

PLoS Genet. 2020 Feb 3;16(2):e1008572. doi: 10.1371/journal.pgen.1008572. eCollection 2020 Feb.

Abstract

Cancer genomes with mutations in the exonuclease domain of Polymerase Epsilon (POLE) present with an extraordinarily high somatic mutation burden. In vitro studies have shown that distinct POLE mutants exhibit different polymerase activity. Yet, genome-wide mutation patterns and driver mutation formation arising from different POLE mutants remains unclear. Here, we curated somatic mutation calls from 7,345 colorectal cancer samples from published studies and publicly available databases. These include 44 POLE mutant samples including 9 with whole genome sequencing data available. The POLE mutant samples were categorized based on the specific POLE mutation present. Mutation spectrum, associations of somatic mutations with epigenomics features and co-occurrence with specific driver mutations were examined across different POLE mutants. We found that different POLE mutants exhibit distinct mutation spectrum with significantly higher relative frequency of C>T mutations in POLE V411L mutants. Our analysis showed that this increase frequency in C>T mutations is not dependent on DNA methylation and not associated with other genomic features and is thus specifically due to DNA sequence context alone. Notably, we found strong association of the TP53 R213* mutation specifically with POLE P286R mutants. This truncation mutation occurs within the TT[C>T]GA context. For C>T mutations, this sequence context is significantly more likely to be mutated in POLE P286R mutants compared with other POLE exonuclease domain mutants. This study refines our understanding of DNA polymerase fidelity and underscores genome-wide mutation spectrum and specific cancer driver mutation formation observed in POLE mutant cancers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carcinogenesis / genetics*
  • Colorectal Neoplasms / genetics*
  • CpG Islands / genetics
  • Cytosine / metabolism
  • DNA Methylation / genetics
  • DNA Mutational Analysis / statistics & numerical data
  • DNA Polymerase II / genetics
  • DNA Polymerase II / metabolism*
  • Databases, Genetic / statistics & numerical data
  • Datasets as Topic
  • Epigenesis, Genetic
  • Humans
  • Mutation
  • Poly-ADP-Ribose Binding Proteins / genetics
  • Poly-ADP-Ribose Binding Proteins / metabolism*
  • Protein Domains / genetics*
  • Tumor Suppressor Protein p53 / genetics*
  • Whole Genome Sequencing / statistics & numerical data

Substances

  • Poly-ADP-Ribose Binding Proteins
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • Cytosine
  • DNA Polymerase II
  • POLE protein, human

Grants and funding

This project is supported by a Project Grant from the National Health and Medical Research Council (NHMRC), Australia (APP1119932) to J.W.H.W. R.C.P. is supported by an NHMRC Early Career Fellowship (APP1138536). R.K. is supported by the Juhani Aho Foundation for Medical Research, the Ida Montin Foundation and the Instrumentarium Science Foundation. R.K. and L.A.A. are supported by the Academy of Finland (Finnish Center of Excellence Program 2018-2025, 312041). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.