Endothelial cell heterogeneity and immune-metabolic crosstalk in scleroderma: insights from single-cell RNA sequencing

Aim: Scleroderma is a connective tissue disease characterized by vascular injury, immune dysfunction, and fibrosis. Studies have shown that vascular endothelial cells (ECs) play a significant role in the progression of the disease, but their specific mechanisms in regulating the immune microenvironment of scleroderma remain unclear. This study aims to investigate the mechanisms by which vascular endothelial cells regulate the immune microenvironment in scleroderma. Methods: Two public single-cell RNA sequencing (scRNA-seq) datasets (GSE264508 and GSE138669) from the Gene Expression Omnibus (GEO) database were analyzed, including skin samples from localized and systemic scleroderma patients. Seurat was used for data processing and clustering, CellChat for cell communication analysis, Monocle2 for pseudotime analysis, scMetabolism for metabolic profiling, and TwoSampleMR to identify potential causal genes based on expression quantitative trait loci (eQTL) data. Results: We identified distinct EC subtypes and found enhanced communication between ECs and myeloid cells in scleroderma, indicating an active role in immune regulation. ECs remodeled the immune microenvironment via multiple ligand-receptor pairs. Increased oxidative phosphorylation in early-stage ECs was linked to immune activation. Pseudotime analysis revealed dynamic differentiation, and Mendelian randomization identified COX4I1 as a potential pathogenic and therapeutic target. Conclusion: This study provides a comprehensive single-cell atlas of ECs in scleroderma, highlighting their immunometabolic plasticity and crosstalk with immune cells. The findings suggest that ECs are active participants in the early pathogenesis of skin fibrosis and support COX4I1 as a potential therapeutic target.