Identification of microbial-derived HLA-bound peptides in melanoma

Various bacterial species are known to colonize human tumors , proliferate within them and modulate immune function, ultimately affecting patient survival and response to treatment. However, it is not known whether intracellular bacterial antigens are presented by HLA-I and HLA-II molecules of tumor cells, and whether potential tumor-presented bacterial-derived antigens may elicit a tumor infiltrating T-cell immune response. Here, we used 16S rRNA gene sequencing and HLA-peptidomics to unbiasedly identify an intracellular bacterial peptide repertoire presented on HLA-I and HLA-II molecules in melanoma tumors. Our microbial analysis of 17 melanoma metastases, derived from 9 patients, revealed 248 and 38 unique HLA-I and HLA-II peptides, respectively, derived from 41 different classified bacterial species. Recurrent bacterial peptides were identified in different tumors. Our study reveals that intra-tumor intracellular bacteria can be presented by tumor cells and elicit immune-reactivity, thus providing insight into how bacteria influence immune system activation and response to therapy.