Spatially organized inflammatory myeloid-CD8+ T cell aggregates linked to Merkel-cell Polyomavirus driven Reorganization of the Tumor Microenvironment

Merkel cell carcinoma (MCC) is an aggressive skin cancer with high propensity for metastasis, caused by Merkel cell polyomavirus (MCPyV), or chronic UV-light-exposure. How MCPyV modulates immune responses within the tumor microenvironment and how such are linked to patient outcomes remain unknown partly due to technical barriers to understanding the spatial organization of the tumor microenvironment at single-cell resolution. We interrogated the cellular and transcriptional landscapes of 60 MCC-patients using Co-detection-by-indexing (CODEX) and targeted bulk RNA sequencing. Notably, we identified an enrichment of dysfunctional T cells spatially associating with CXCL9+ myeloid cells at the tumor invasive front as key feature of virus-positive MCC. While MCPyV-positivity and CD8+ T cell infiltration correlated with metastasis-free-survival, responses to immune checkpoint blockade were high regardless of virus-status. Instead, we found an enrichment of central memory T cells within tertiary-lymphoid-structures that associated with response to immune-checkpoint blockade. These findings highlight fundamental differences in the organization of the native tumor microenvironment of virus-positive MCC, that are linked to differential survival outcomes and could be used for personalized treatment strategies. Overall design: We laser capture microdissected circular tissue regions of 0.5 mm in diameter of FFPE merkel cell carcinoma samples and performed sequencing