Roadmap of MCPyV T-antigens for off-the-shelf therapeutic MCC vaccine development 2309574

Introduction Merkel cell carcinoma (MCC) is a rare but extremely aggressive neuroendocrine skin cancer with a two-year mortality approaching 20% in patients with distant metastasis, representing a significant unmet clinical need. More than 80% of MCC cases are driven by Merkel cell polyomavirus (MCPyV), whose antigens are foreign to the immune system, highly immunogenic, and correlate with survival and response to immunotherapy. The uniform expression of its oncoprotein makes a virus-positive MCC (VP-MCC) an ideal target for antigen-specific immunotherapies. Methods We systematically defined MCPyV-derived epitopes presented by HLA-I molecules to identify suitable targets for development of a universal off-the-shelf vaccine. An integrated discovery pipeline was developed combining HLA-I pull-downs and LC—MS/MS-based detection using a panel of 95 monoallelic HLA lines, in silico antigen prediction, and literature curation. Immunogenicity of candidates was evaluated using VP-MCC patients and HLA-matched healthy PBMCs, with ELISpot assays as the primary readout. To enable functional validation, the MCPyV immunopeptidome was expanded to a dozen patient-derived VP-MCC cell lines, providing a platform to examine T cell targeting. Results This approach enabled the identification of MCPyV-derived epitopes presented across diverse HLA-I alleles, including conserved and promiscuous peptides with measurable T cell reactivity in both patients and healthy donors. Expansion of the MCPyV immunopeptidome across patient-derived MCC models supported downstream functional evaluation of antigen-specific T cell responses in physiologically relevant tumor contexts. Conclusion Our findings define a roadmap for MCPyV antigen selection and support the feasibility of developing an off-the-shelf therapeutic vaccine for VP-MCC. More broadly, this systematic framework for epitope discovery and validation may be broadly applicable to immunotherapy development in other virally driven cancers.