Low immunogenicity of common cancer hot spot mutations resulting in false immunogenic selection signals

PLoS Genet. 2021 Feb 8;17(2):e1009368. doi: 10.1371/journal.pgen.1009368. eCollection 2021 Feb.

Abstract

Cancer is driven by somatic mutations that result in a cellular fitness advantage. This selective advantage is expected to be counterbalanced by the immune system when these driver mutations simultaneously lead to the generation of neoantigens, novel peptides that are presented at the cancer cell membrane via HLA molecules from the MHC complex. The presentability of these peptides is determined by a patient's MHC genotype and it has been suggested that this results in MHC genotype-specific restrictions of the oncogenic mutational landscape. Here, we generated a set of virtual patients, each with an identical and prototypical MHC genotype, and show that the earlier reported HLA affinity differences between observed and unobserved mutations are unrelated to MHC genotype variation. We demonstrate how these differences are secondary to high frequencies of 13 hot spot driver mutations in 6 different genes. Several oncogenic mechanisms were identified that lower the peptides' HLA affinity, including phospho-mimicking substitutions in BRAF, destabilizing tyrosine mutations in TP53 and glycine-rich mutational contexts in the GTP-binding KRAS domain. In line with our earlier findings, our results emphasize that HLA affinity predictions are easily misinterpreted when studying immunogenic selection processes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Carcinogenesis / genetics*
  • Cell Line, Tumor
  • Gene Frequency
  • Genotype
  • Glycine / genetics
  • Glycine / metabolism
  • HLA Antigens / genetics*
  • HLA Antigens / metabolism
  • Humans
  • Mutation*
  • Neoplasms / genetics*
  • Neoplasms / immunology
  • Neoplasms / metabolism
  • Oncogenes / genetics*
  • Proto-Oncogene Proteins B-raf / genetics
  • Proto-Oncogene Proteins p21(ras) / genetics
  • Tumor Suppressor Protein p53 / genetics

Substances

  • HLA Antigens
  • KRAS protein, human
  • Tumor Suppressor Protein p53
  • BRAF protein, human
  • Proto-Oncogene Proteins B-raf
  • Proto-Oncogene Proteins p21(ras)
  • Glycine

Grants and funding

This work was supported by the Ghent University Special Research Fund Starting Grant (JVdE, BOF.STG.2019.0073.01, https://www.ugent.be/en/research/funding/bof) and Fonds Wetenschappelijk Onderzoek-Vlaanderen (FWO; KM, 3G045620). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.