Intrinsic failure of immune activation in NRAS -mutant melanoma reveals a targetable mechanism of checkpoint resistance

Background: Melanoma is frequently driven by MAPK pathway mutations, most prominently BRAF (~50%) and NRAS (20-30%). Unlike BRAF -mutant melanoma, which benefits from effective targeted therapies, NRAS -mutant melanoma responds poorly to MEK inhibition and lacks approved targeted options, contributing to poorer outcomes. This limitation has encouraged immunotherapy-based combinations, yet responses to immune checkpoint blockade (ICB) remain variable. We found that NRAS -mutant melanoma exhibits high immune-gene activity in cancer cells alone but shows suppressed inducibility upon immune stimulation, indicating an intrinsic failure to activate immune programs that may limit ICB responsiveness. Methods: DEG and pathway analyses were performed using DESeq2 and GSEA with TCGA-SKCM (tumor biopsy) and CCLE/DepMap (cell line RNA-seq) datasets. “Shift genes” were defined by comparing relative expression between cell line-intrinsic and tumor datasets, selecting genes with the largest directional changes and significant adjusted p-values (FDR < 0.05, moderated t-tests). Anti-PD-1-resistant cell lines were generated through serial in vivo selection involving repeated implantation and anti-PD-1 treatment of NRAS -mutant melanoma until tumor growth matched untreated controls. Results: RNA expression analysis of NRAS -mutant melanoma cell lines revealed strong intrinsic immune-gene activity; however, this activity was markedly reduced in TCGA tumors, indicating suppressed inducibility in the tumor setting. Among the T cell-inflamed GEP genes-an established immune signature highly expressed in tumors responding to anti-PD-1 therapy-MHC class II-related genes and CCL5 showed the most pronounced reduction (≈1.3-1.4-fold), while most others remained stable. Consistent with these findings, NRAS -mutant murine melanoma cell lines exhibited high basal immune-gene expression but nearly 200-fold weaker induction following Interferon-gamma stimulation-used to evaluate inducible immune-gene responses-compared with wild-type cells. Anti-PD-1-resistant models mirrored this pattern, suggesting that such immune non-responsiveness reflects an inherent characteristic of NRAS -mutant melanoma. Conclusion: The immunotherapy responsiveness of NRAS -mutant melanoma remains uncertain, underscoring the need to define its immune features. Our findings indicate that the immune unresponsiveness in this subtype reflects a fundamental, cell-intrinsic limitation rather than an acquired consequence, suggesting a targetable mechanism to improve ICB outcomes.