Identification of microbial-derived HLA-bound peptides in melanoma

Bacteria were first detected in human tumors more than 100 years ago, but the complex interplay between the microbiome and cancer initiation, progression, and response to therapies is only starting to unravel. While different mechanisms by which bacteria can affect the immune response were reported, the role of bacterial antigen presentation as the mediator of immune recognition and response has remained unclear. Recent investigations, of stool samples collected from cancer patients treated with immune-checkpoint-inhibitors, allowed the identification of bacteria subsets that were more abundant in responding versus nonresponding patients. Fecal microbiota transplantation of feces from patients who showed clinical response to immune-checkpoint-inhibitors, induced similar improved immune response in the recipients, both in pre-clinical mouse models and human patients. These results highlight the fact that immune responses observed in the patients were derived from their microbiome composition, and strengthens the importance of identifying the mechanisms by which specific bacteria influence an anti-tumor response.

In this study, combination of human leucocyte antigen (HLA) peptidomics with 16S rRNA sequencing of 19 melanoma metastasis derived from 9 different patients, lead us to the unbiased identification of hundreds of HLA-I- and tens of HLA-II-bacterial peptides. We were able to validate these results by controlled cell culture work, from the step of bacteria invasion, by co-culturing the bacterial species identified by 16S sequencing with the patient derived melanoma cells, throughout validating the peptide’s presentation by preforming HLA peptidomics on the infected cells. Importantly, we were able to identify common bacterial peptides from different metastases of the same patient as well as from different patients. Some of the common bacterial peptides, as well as others, were able to elicit an immune response by the autologous tumor infiltrating lymphocytes.

By identifying immunogenic microbial-derived antigens presented on tumor HLA molecules, we demonstrate that tumor bacteria may not only shape the immune tumor microenvironment but also directly affect T cell immune-reactivity. Antigen presentation of bacterial antigens provides insights into a new mechanism by which bacteria influence immune system activation and response to immunotherapy. Introducing bacterial derived antigens to the repertoire of tumor associated antigens, potentially extends the variety of targets for cancer immunotherapies.