Neoantigenic properties of TP53 variants influence cancer risk in individuals with Li-Fraumeni syndrome

Abstract

International audienceBackground Li-Fraumeni Syndrome (LFS) is a heterogenous cancer predisposition condition caused by pathogenic TP53 variants, characterised by a lifelong high risk of a broad spectrum of cancers. Certain pathogenic TP53 variants have been shown be immunogenic in a somatic context. Whether neoantigenicity contributes to LFS heterogeneity is unknown. In this study we analysed the correlations between predicted neoantigenic properties of pathogenic TP53 missense variants and LFS phenotypes. MethodsMHC-I presentation scores were generated for the set of nonameric neo-peptides surrounding each TP53 missense variant against 145 different HLA-I using NetMHCpan 4.1 and the Allele Frequency Net Database. A predicted neoantigenic score (PNS) was calculated for each variant. Association study was performed between PNS, LFS presentation and individual HLA-I genotyping, in individuals carrying TP53 germline pathogenic variants using data from mutation databases and clinical registries. Genotype-phenotype data were leveraged from the public TP53 database (germline dataset, n = 3446; https://tp53.isb-cgc.org/) and two independent LFS clinical registries (n = 339). Individual correlations between HLA-I genotyping, TP53 missense variants and phenotypes were investigated in a group of 173 subjects with LFS. Findings Among individuals with frequent TP53 pathogenic variants, PNS was strongly correlated with median age at first cancer (range 18-43 years, R = 0.69, p = 0.0132). Compared to individuals with low PNS (<1) variants, those with high PNS (<1) variants showed delayed median age at first diagnosis (34 years vs. 25 years, p = 0.0009), fewer sarcomas (osteosarcoma [RR 0.29, p = 0.02]; soft-tissue [RR 0.41, p = 0.02]), and more cancer types typically not associated with LFS spectrum [RR 1.61, p = 0.02]. Interpretation MHC-I neoantigenic properties of TP53 variants are associated with differences in cancer risk and spectrum in individuals with pathogenic TP53 variants, suggesting that individual variant-specific immune response could contribute to the heterogenous presentation of LFS