Fundamental immune-oncogenicity trade-offs define driver mutation fitness.

TitleFundamental immune-oncogenicity trade-offs define driver mutation fitness.
Publication TypeJournal Article
Year of Publication2022
AuthorsHoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KCésar, Bajorin DF, Bandlamudi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, Wu M, Zamarin D, Campitelli LF, Osborne EJ, Klinger M, Robins HS, Khincha PP, Savage SA, Balachandran VP, Wolchok JD, Hellmann MD, Merghoub T, Levine AJ, Łuksza M, Greenbaum BD
JournalNature
Volume606
Issue7912
Pagination172-179
Date Published2022 Jun
ISSN1476-4687
KeywordsCarcinogenesis, Datasets as Topic, Evolution, Molecular, Genes, p53, Genetic Fitness, Genomics, Healthy Volunteers, Humans, Immunotherapy, Lung Neoplasms, Mutation, Mutation, Missense, Reproducibility of Results
Abstract

Missense driver mutations in cancer are concentrated in a few hotspots1. Various mechanisms have been proposed to explain this skew, including biased mutational processes2, phenotypic differences3-6 and immunoediting of neoantigens7,8; however, to our knowledge, no existing model weighs the relative contribution of these features to tumour evolution. We propose a unified theoretical 'free fitness' framework that parsimoniously integrates multimodal genomic, epigenetic, transcriptomic and proteomic data into a biophysical model of the rate-limiting processes underlying the fitness advantage conferred on cancer cells by driver gene mutations. Focusing on TP53, the most mutated gene in cancer1, we present an inference of mutant p53 concentration and demonstrate that TP53 hotspot mutations optimally solve an evolutionary trade-off between oncogenic potential and neoantigen immunogenicity. Our model anticipates patient survival in The Cancer Genome Atlas and patients with lung cancer treated with immunotherapy as well as the age of tumour onset in germline carriers of TP53 variants. The predicted differential immunogenicity between hotspot mutations was validated experimentally in patients with cancer and in a unique large dataset of healthy individuals. Our data indicate that immune selective pressure on TP53 mutations has a smaller role in non-cancerous lesions than in tumours, suggesting that targeted immunotherapy may offer an early prophylactic opportunity for the former. Determining the relative contribution of immunogenicity and oncogenic function to the selective advantage of hotspot mutations thus has important implications for both precision immunotherapies and our understanding of tumour evolution.

DOI10.1038/s41586-022-04696-z
Alternate JournalNature
PubMed ID35545680
PubMed Central IDPMC9159948
Grant ListR01 CA240924 / CA / NCI NIH HHS / United States
R01 AI081848 / AI / NIAID NIH HHS / United States
R01 CA227534 / CA / NCI NIH HHS / United States
P30 CA008748 / CA / NCI NIH HHS / United States
P50 CA221745 / CA / NCI NIH HHS / United States
U01 CA228963 / CA / NCI NIH HHS / United States
K12 CA184746 / CA / NCI NIH HHS / United States
P01 CA087497 / CA / NCI NIH HHS / United States
U01 CA224175 / CA / NCI NIH HHS / United States