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 spatially modulates immune responses within the tumor microenvironment and how such are linked to patient outcomes remains unknown. We interrogated the cellular and transcriptional landscapes of 60 MCC-patients using a combination of multiplex proteomics, in-situ RNA-hybridization, and spatially oriented transcriptomics. We identified a spatial co-enrichment of activated CD8 ⁺ T-cells and CXCL9 ⁺ PD-L1 ⁺ macrophages at the invasive front of virus-positive MCC. This spatial immune response pattern was conserved in another virus-positive tumor, HPV ⁺ head-and-neck cancer. Importantly, we show that virus-negativity correlated with high risk of metastasis through low CD8 ⁺ T-cell infiltration and the enrichment of cancer-associated-fibroblasts at the tumor boundary. By contrast, responses to immune-checkpoint blockade (ICB) were independent of viral-status but correlated with the presence of a B-cell-enriched spatial contexts. Our work is the first to reveal distinct immune-response patterns between virus-positive and virus-negative MCC and their impact on metastasis and ICB-response.