Intratumoral Heterogeneity in Ngfr+ Melanoma Subpopulations Shapes Immune Evasion and Immunotherapy Resistance

Human melanomas dedifferentiate into a neural crest-like cell state when exposed to T cell cytokines or MAPK pathway inhibitors. This transformation is associated with cellular heterogeneity and the emergence of small, therapy-resistant melanoma populations characterized by elevated nerve growth factor receptor (NGFR) expression. However, the extent of this heterogeneity and its impact on immunotherapy response remain unclear. By dissecting intratumor heterogeneity in patient melanomas, we show here that even within NGFR ⁺ tumor subpopulations, remarkable phenotypic and functional diversity exists. Combined single-cell RNA sequencing (scRNA-seq) of NGFR ⁺ fractions and spatial transcriptomics uncovered pronounced diversity among single-cell clusters, characterized by patient-specific gene regulatory networks (GRNs) and distinct spatial organization. Furthermore, we identify an NGFR ⁺ subpopulation marked by co-expression of Platelet-Derived Growth Factor Receptor (PDGFR), which is associated with increased resistance to the T cell cytokines IFNg and TNF. Clinically corroborating these findings, we observed that NGFR ⁺ /PDGFR ⁺ mesenchymal-like cells are enriched in melanomas infiltrated with active T cells yet failing to respond to immune checkpoint blockade treatment. Our results highlight extreme heterogeneity within human melanoma, which is spatially organized and regulated by patient-specific GRNs, and harboring a distinct subfraction linked to immunotherapy resistance.