Single-cell RNA sequencing unveils tumor heterogeneity and immune microenvironment of acral melanoma

Abstract

Background Acral melanom (AM) is a subtype of melanoma with high prevalence in East Asians. AM is characterized by greater aggressiveness and lower survival rates. However, there are still fewer studies on immune mechanisms of AM especially subnodal melanoma (SM) versus non-subnodal melanoma (NSM). In order to explore tumor heterogeneity and immune microenvironment in different subtypes of AM, we applied single-cell RNA sequencing to 24,789 single cells isolated from the SM and plantar melanoma (PM) patients. Methods The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes. Differentially expressed genes (CNVs) was used to differentiate malignant melanocytes. Differentially expressed genes (DEGs) were identified using the FindMarkers function(test.use = presto) in Seurat. RcisTarget package was identified transcription factor (TF). Gene set variation analysis (GSVA) package was used to assign pathway activity estimates to individual cells. The CellChat package was conducted to analyze the cell-cell interaction. We determined the developmental pseudotime with the Monocle2 package. Finally, we verified gene expression by immunofluorescence. Results Aspects of tumor heterogeneity, melanocytes from PM and SM had significant differences in gene expression, CNV and pathways in which tumor-associated such as NF-kb and Wnt were involved. Regarding the immune microenvironment, PM contained more fibroblasts and T/NK cells. The EPHA3-EFNA1 axis was expressed only in cancer-associated fibroblast (CAF) and melanocytes of PM, and the TIGIT-NECTIN2 axis was expressed in both AM subtypes of T/NK cells and melanocytes. Conclusions Altogether, our study helps to elucidate the tumor heterogeneity in AM subpopulations and provides potential therapeutic targets for clinical research.