Extended T cell epitope landscape in Merkel cell polyomavirus large T and small T oncoproteins identified uniquely in cancer patients

Merkel Cell carcinoma (MCC) is a rare, aggressive human skin cancer with poor prognosis for advanced disease (Harms et al. 2016). The oncovirus Merkel cell polyomavirus (MCPyV) is associated with at least 80% of MCC cases (Feng et al. 2008) with persistent expression of the viral T antigens (T-Ag; large T antigen (LTA) and small T antigen (STA)) driving oncogenesis (Shuda et al. 2008). Immune surveillance is critical for tumor control. Highlighted by associations between survival and intratumoral levels of CD3⁺ and CD8⁺ lymphocytes (Paulson et al. 2014; Sihto and Joensuu 2012), and T-Ag-specific T-cells (Miller et al. 2017). As well as the high efficacy of checkpoint inhibitors (D’Angelo et al. 2018; Nghiem et al. 2016; Topalian et al. 2020). Nevertheless, for half of the patients, this treatment strategy is insufficient. Instead, T-cell-based therapies, such as cell therapies or vaccines, could be attractive, but require identification of CD8⁺ T-cell epitopes within T-Ag that serve as targets for tumor cell elimination. Several T-Ag-derived epitopes have been identified for a limited number of HLA haplotypes (Iyer et al. 2011; Jing et al. 2020; Lyngaa et al. 2014; Samimi et al. 2019), which reduces such applications to patients with the given HLA haplotypes. In addition, limited evidence is available for natural processing and MHC class I presentation of T-Ag-derived epitopes on MCC tumors, which is essential for T-cell-mediated tumor cell elimination. We, therefore, aimed to expand the repertoire of T-Ag-derived epitopes by creating a library of 146 potential CD8⁺ T-cell epitopes derived from STA, truncated LTA, including their shared common T antigen (CT) region, and viral capsid protein 1 (VP1) (Figure S1a, and Table S1). The majority of peptides were restricted to the newly evaluated HLA haplotypes, HLA-A*24:02, -B*08:01, -B*35:01, and -B*44:02 (Figure 1a), selected through in-silico predictions of HLA binding. T-cell epitopes restricted to HLA-A*01:01, -A*02:01, -A*03:01, -A*11:01, and -B*07:02 were previously described by Lyngaa et al. Additional HLA-matched control epitopes from common non-oncogenic viruses were included as positive controls for the T-cell detection process.