Mast cell phenotypic remodeling toward a PD-1-positive, Chymase-negative phenotype is associated with metastatic melanoma and poor survival

Mast cells (MCs) display phenotypic heterogeneity across tissues and disease contexts, yet their relevance in melanoma remains unclear. Here, we investigated MC phenotypic programs associated with melanoma progression using high-dimensional phenotyping of MCs co-cultured with melanoma spheroids, trajectory inference, and transcriptomic analyzes. Human melanoma tissues showed differences in MC phenotypic composition despite comparable abundance between outcome groups, with metastatic melanomas enriched for Tryptase⁺ Chymase- MCs. Melanoma exposure induced MC phenotypic remodeling, characterized by loss of lineage- and effector-associated features and increased PD-1 expression, with more pronounced changes following metastatic melanoma co-culture. Trajectory analysis was consistent with a continuum toward a PD-1⁺ Chymase- phenotype, which was detected in melanoma tissues and enriched within intratumoral regions of metastatic melanomas. Experimentally defined protein changes were used to derive two MC-associated transcriptomic signatures with opposing clinical associations, reflecting lineage- and effector-enriched versus melanoma-remodeled programs. The MC-LE signature was associated with favorable survival and interferon-responsive pathways, whereas the MC-MR signature was associated with poorer survival and tumor-associated pathways. These transcriptomic associations extended beyond melanoma across multiple TCGA cancer cohorts, and independent analysis of MCs from healthy skin, basal cell carcinoma, and melanoma showed corresponding differences in MC-LE-related features. Together, these findings support distinct mast cell phenotypic programs associated with melanoma progression and identify a PD-1⁺ Chymase- MC phenotype enriched in metastatic disease and linked to transcriptomic features of poor survival.