Ancient genes establish stress-induced mutation as a hallmark of cancer

PLoS One. 2017 Apr 25;12(4):e0176258. doi: 10.1371/journal.pone.0176258. eCollection 2017.

Abstract

Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes. In order to investigate these hypotheses we estimated the evolutionary ages of all human genes and then studied the probability of mutation and their biological function in relation to their age and genomic location for both normal germline and cancer contexts. We observed that under a model of uniform random mutation across the genome, controlled for gene size, genes less than 500 MY were more frequently mutated in both cases. Paradoxically, causal genes, defined in the COSMIC Cancer Gene Census, were depleted in this age group. When we used functional enrichment analysis to explain this unexpected result we discovered that COSMIC genes with recessive disease phenotypes were enriched for DNA repair and cell cycle control. The non-mutated genes in these pathways are orthologous to those underlying stress-induced mutation in bacteria, which results in the clustering of single nucleotide variations. COSMIC genes were less common in regions where the probability of observing mutational clusters is high, although they are approximately 2-fold more likely to harbor mutational clusters compared to other human genes. Our results suggest this ancient mutational response to stress that evolved among prokaryotes was co-opted to maintain diversity in the germline and immune system, while the original phenotype is restored in cancer. Reversion to a stress-induced mutational response is a hallmark of cancer that allows for effectively searching "protected" genome space where genes causally implicated in cancer are located and underlies the high adaptive potential and concomitant therapeutic resistance that is characteristic of cancer.

MeSH terms

  • Animals
  • Cell Cycle / genetics
  • DNA Repair / genetics
  • Databases, Genetic
  • Humans
  • Mutation*
  • Neoplasms / genetics*
  • Oncogenes*
  • Phenotype
  • Phylogeny

Grants and funding

This work was supported by NIH grant U54CA143862 (https://projectreporter.nih.gov) and NantOmics, LLC. The NIH had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. NantOmics provided support in the form of salaries for authors KJB and LC, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the 'author contributions' section. Data used in this study from the International Cancer Genomics Consortium (ICGC) was generated with the support of the following: Institut National de la Santé et de la Recherche Medicale (Inserm) within the framework of the ICGC, Federal Ministry of Education and Research (BMBF), National Health and Medical Research Council (NHMRC), Queensland State Government, University of Queensland, Institute for Molecular Bioscience, The Cancer Council NSW, Garvan Institute of Medical Research, Cancer Institute NSW, Italian Ministry of Education, University, and Research, University of Verona, German Cancer Aid (DKH), Ontario Institute for Cancer Research, Prostate Cancer Canada, Pio XII Foundation - Barretos Cancer Hospital, and René Rachou Research Center (FIOCRUZ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Data from the 1000 Genomes Project is maintained and supported by the International Genome Sample Resource (IGSR), funded by the Wellcome Trust grant number WT104947/Z/14/Z. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.