Integrative single-cell analysis uncovers distinct tumour microenvironment ecotypes and immune evasion across skin cancers

Abstract

Background: Skin cancers, including basal cell carcinoma (BCC), squamous cell carcinoma (SCC), cutaneous melanoma (CM) and acral melanoma (AM), exhibit profound heterogeneity in clinical behaviour and therapeutic response. However, how tumour-immune ecosystems are remodelled across skin cancer types and disease stages, and how these changes influence immune escape and treatment resistance, remain poorly understood.

Methods: Here, we integrate single-cell transcriptomics data from 102 skin cancer samples (including adjacent normal skin, early-stage and advanced-stage tumours), with bulk RNA-seq prognosis cohorts, immunofluorescence staining and in vitro assays to define clinically relevant immune remodelling patterns.

Results: Our analyses identify a malignant NARS2⁺NDUFC2⁺ melanoma cell subpopulation, characterised by reduced MHC-I expression, enriched in advanced-stage tumours and associated with worse survival and immunotherapy response. CRISPR screening further showed that NARS2 and NDUFC2 are necessary for the proliferation of melanoma cells, highlighting these genes as potential therapeutic targets. Tumour-associated macrophages (TAMs) originate from both FCN1⁺ monocytes and FOLR2⁺ tissue-resident macrophages, displaying two polarisation states with distinct prognostic associations. Specifically, pro-inflammatory CXCL9⁺CXCL10⁺ TAMs are enriched in SCC, while tissue-remodelling SPP1⁺ TAMs are predominant in melanoma. Immunofluorescence staining confirmed that SPP1⁺ macrophage accumulation correlates with advanced stage, metastasis and poor prognosis in the melanoma cohort. Immune ecotype analysis reveals a transition from ‘T-cell-dominant’ ecotypes to ‘desert’ ecotypes as disease advances in BCC, CM and AM. Cell‒cell communication analysis shows that ‘T-cell-dominant’ ecotypes have higher MHC-I signalling pathways in tumour cells, whereas ‘Desert’ ecotypes have higher SPP1⁺ macrophage signalling, underlining the role of SPP1 on immune remodelling. Functional assays confirm that melanoma cells could drive M2 polarisation and SPP1 upregulation in macrophages. Knocking down or overexpressing SPP1 correspondingly alters M2 gene expression in macrophages.

Conclusions: This study establishes a pan-skin cancer immune remodelling framework, providing a foundation for biomarker discovery and the development of new immunotherapy strategies.

Keywords

immunotherapy / melanoma / skin cancer / tumour microenvironment / tumour progression

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2026 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.