Spatial Transcriptomic and Proteomic Analysis Identifies Novel Immune-Associated Biomarkers of Anti-PD1 Response in Metastatic Melanoma.

Resistance to anti-PD1 therapy remains a major challenge in metastatic melanoma, despite long-term benefit in some patients. Since a functional dendritic cell (DC)-CD8+ T cell axis is essential for anti-PD1 response, biomarkers associated with this axis may help characterize underexplored immune states linked to resistance. Here, we further characterized poor survival predictor (PSP) biomarkers previously negatively correlated with DC-CD8+ T cell axis in melanoma, evaluating their associations with anti-PD1 response, immune infiltration, and transcriptional and proteomic signatures. Pre-treatment transcriptomic data were analysed using CIBERSORTx and Reactome, while NanoString GeoMx spatial transcriptomic and proteomic data were used to resolve biomarker-associated features across tumour and immune compartments. We identified 28 PSP biomarkers significantly increased in non-responsive patients with strong correlations with one another, suggesting coordinated transcriptional patterns within a tumour microenvironment unfavourable to therapeutic response and survival. These biomarkers were associated with immunosuppressive cell types, decreased cytotoxicity, and pathways related to transcription, translation, epigenetic regulation, and signal transduction. Spatially, PSP biomarkers were expressed in both tumour and immune compartments, but survival associations were compartment- and site-specific. Among them, FAM57A, GSTA4 and KCTD1 were associated with poor survival when highly expressed in the CD45+ immune compartment of lymph node metastases. Their expression was associated with transcriptomic signatures of reduced immune activation, altered antigen presentation, and epigenetic regulation, and increased proteomic PI3K-AKT-mTORC1/MAPK signalling, especially upon co-expression. Together, these results identify FAM57A, GSTA4 and KCTD1 as emerging immune-associated biomarkers linked to established resistance-associated immune states and poor prognosis in metastatic melanoma.