Spatial compartmentalization of melanoma cell states reveals CAF-associated tumor cells with enhanced proliferative capacity

Abstract

Background Cancer-associated fibroblasts (CAFs) are key components of the melanoma tumor microenvironment and have been implicated in immune evasion and therapy resistance. However, the spatial relationships between CAFs, extracellular matrix (ECM) remodeling, and immune exclusion remain incompletely characterized. Methods We integrated single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics from primary melanoma samples (892 regions of interest) to investigate the landscape of CAF-immune interactions. CAF scores were calculated based on five fibroblast-associated genes. Differential expression analysis, Spearman correlation, and cell state subclustering were performed to characterize the spatial organization of the tumor microenvironment. Findings were examined using TCGA bulk RNA-seq data and drug sensitivity was assessed using the GDSC database. Results CAF-high regions exhibited significantly lower immune scores compared to CAF-low regions (ρ = −0.442, p < 0.001), with enrichment of ECM-related genes (COL1A1, COL1A2, DCN, FBLN1) and downregulation of immune genes (PTPRC, CD4, CD8A). Spatial co-expression of FN1 and its integrin receptor subunit ITGB1 was observed (ρ = 0.100, p = 0.003), supporting a potential role for ECM-receptor signaling in immune exclusion. Six distinct melanoma cell states were identified, with CAF-associated tumor states (State 4) exhibiting significantly higher proliferative capacity than immune-associated states (State 5) (p = 0.007). The CAF signature correlated with cisplatin sensitivity (ρ = −0.627, p < 0.001) and trametinib resistance (ρ = 0.354, p = 0.009). Conclusions This study provides a spatial atlas of CAF-immune interactions in melanoma. CAF abundance is negatively correlated with immune infiltration at the spatial level, with ECM remodeling and FN1-ITGB1 signaling potentially mediating this immune exclusion. The CAF signature showed correlations with drug sensitivity in cell line models, warranting further investigation in CAF-containing systems.