The confused cell identity is associated with aggressiveness in esophageal squamous cell carcinoma [bulkRNA-Seq]

Seven tumor samples and one distal normal sample from five pathologically confirmed ESCC patients were analyzed with 10X Genomics scRNA-seq. To better represent the squamous epithelial cells, we optimized the dissociation protocol. Total 44,206 cells were obtained, including 16,657 normal and malignant squamous epithelial cells. The squamous epithelial cells, glandular epithelial cells, immune cells, endothelial cells and other tumor microenvironmental cells were clearly separated and identified with classic markers.Seven tumor samples and one distal normal sample from five pathologically confirmed ESCC patients were analyzed with 10X Genomics scRNA-seq. To better represent the squamous epithelial cells, we optimized the dissociation protocol. Total 44,206 cells were obtained, including 16,657 normal and malignant squamous epithelial cells. The squamous epithelial cells, glandular epithelial cells, immune cells, endothelial cells and other tumor microenvironmental cells were clearly separated and identified with classic markers. The cell identity of malignant cells and how they acquire it are fundamental for our understanding of cancer. Here, we report that esophageal squamous cell carcinoma (ESCC) cells display molecular features similar but distinct to all three types of normal esophageal epithelial cells, which we term as confused cell identity (CCI). CCI is an independent prognostic marker associated with poor prognosis in ESCC. Further, we identify tripomyosin 4 (TPM4) as a critical CCI gene that promotes the aggressiveness of ESCC in vitro and in vivo. And TPM4 creates CCI through activating the JAK/STAT-SOX2 pathway. Thus, our study suggests a precedent unrecognized feature of ESCC cells, which might be of value for clinic prognosis and potential interference.