Olivier Manches

STRUCTURED Importance: Li-Fraumeni Syndrome (LFS) is an heterogenous cancer predisposition caused by pathogenic TP53 variants, characterized by a lifelong high risk of a broad spectrum of cancers. At least certain pathogenic TP53 variants have been shown be immunogenic in a somatic context. Whether neoantigenicity contributes to the heterogeneity of LFS is unknown. Objective: To analyze the correlations between predicted neoantigenic properties of pathogenic TP53 missense variants and LFS patterns. Design: Association study between predicted MHC-I presentation scores for TP53 hotspot variants, LFS presentation and individual HLA-I genotyping in carriers of TP53 germline pathogenic variants using data from mutation databases and clinical registries. Setting: MHC-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. Genotype-phenotype data were leveraged from the public TP53 database (germline dataset, n=3,446; 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. Participants: Individuals with LFS enrolled in LFS-registries in France and Germany were included. Main outcomes and measures: A predicted neoantigenic score (PNS) was calculated for each variant. Correlations with median age at first cancer, and cancer type were analyzed. Results: Among 709 carriers of frequent TP53 pathogenic variants, PNS was strongly correlated with median age at first cancer (range 18-43 years, p=0.01319, R=0.69). Compared to carriers of low PNS (2) variants showed delayed median age at first diagnosis (34 [CI95%, 29-40] vs. 25 years [CI95%, 22-27]), fewer sarcomas (osteosarcoma [RR 0.29, p-adj = 0.02]; soft-tissue [RR 0.41, p-adj = 0.02]), and more cancer types typically not associated with LFS [RR 1.61, p-adj = 0.02]. Conclusion and Relevance: MHC-I neoantigenic properties of TP53 variants modify cancer risk and spectrum in carriers of pathogenic TP53 variants, suggesting that individual variant-specific immune response may contribute to the heterogenous presentation of LFS.

Background: HCC is the most common form of primary liver cancer, and despite recent advances in cancer treatment, it remains associated with poor prognosis and a lack of response to conventional therapies. Immunotherapies have emerged as a promising approach for cancer treatment, especially through the identification of tumor-specific immunogenic epitopes that can trigger a targeted immune response. This study aimed to identify immunogenic epitopes associated with HCC for the development of specific immunotherapies. Methods: We used high-throughput data screening and bioinformatics tools for antigens and epitope selection. The immunogenicity of the selected epitopes was studied after coculture of peripheral blood mononuclear cells obtained from healthy donors or HCC patients with a plasmacytoid dendritic cell line loaded with the selected peptides. Specific CD8⁺ T cell amplification and functionality were determined by labeling with tetramers and by IFN-γ and CD107a expression (flow cytometry and ELISpot). Results: We analyzed the transcriptional gene expression landscape of HCC to screen for a set of 16 ectopically expressed genes in a majority of HCC samples. Epitopes predicted to bind to HLA-A*02:01 with high affinity were further validated for their immunogenicity using the previously described plasmacytoid dendritic cell line in ex vivo CD8⁺ activation assays using patient immune cells. Three out of the 30 tested epitopes, namely FLWGPRALV (MAGE-A3), FMNKFIYEI (AFP), and KMFHTLDEL (LRRC46), elicited a strong T-cell response, in activation assays, degranulation assays, and IFN-γ secretion assays. Conclusions: These results highlight the potential of these peptides to be considered as targets for immunotherapies. The discovery of such immunogenic epitopes should improve immune-based treatments for liver cancer in combination with the current treatment approach.

Supplementary figure 7 shows heat map and dot plots illustrating correlations between CD3E and chemokines levels, detailed migration of CD4 and CD8 lymphocytes driven by cell lines, correlations between CD3E and CD1c and between CCL19/CCL22 and APC specific markers.