Profiling transcriptional heterogeneity of epithelium, fibroblasts and immune cells in esophageal squamous cell carcinoma by single-cell RNA sequencing

We generated single-cell RNA sequencing (scRNA-seq) of 25,796 immune and 8,197 non-immune cells from three primary tumor and paired normal samples in ESCC patients. The results revealed that transcriptional signatures of malignant epithelium could be effectively distinguished from that of non-malignant epithelium by scRNA-seq data. The infiltration of myofibroblasts, one subtype of fibroblasts, might play important roles in the progression of ESCC. Diverse cell subtypes of T cells and myeloid cells were identified, including tumor-enriched HAVCR2+ CD4+ T cells with significantly exhausted signature. We also found that epithelium and myeloid cells had more frequent cell-cell communication compared with epithelium and T cells. Taken together, this study provided in-depth insights into the cellular heterogeneity of TME in ESCC and highlighted potential therapeutic targets including for immunotherapy. Single-cell RNA sequencing was performed from three treatment-naïve ESCC samples and three paired adjacent tissues by using 10x Genomics platform.