Exploration of the heterogeneity and interaction of epithelial cells and NK/T-cells in Laryngeal Squamous Cell Carcinoma based on single-cell RNA sequencing data

Abstract Objectives We aimed to explore the heterogeneity and differentiation trajectories of epithelial cells and NK/T-cells in Laryngeal Squamous Cell Carcinoma (LSCC). Methods We downloaded the GSE150321 data set containing LSCC01 and LSCC02 samples single cell RNA data from Gene Expression Omnibus. The UMAP analysis was performed to identify the cell subpopulations and cell locations of subpopulations. Seurat package was used to analyze the differential expression of genes. The function of differential expression genes was analyzed using DAVID database. The monocle2 package was used to analyze differentiation trajectories. We used the CellChat package to observe the signaling pathways and ligand-receptor pairs for epithelial cells and NK/T-cells. Results All the LSCC cells were divided into 16 subpopulation that included 7 epithelial cell subsets, 3 T-cell subsets. The function analysis indicated that epithelial cells and NK/T-cells mainly participated in different process, such as cell cycle, immune response, and cell migration. Then, the results of differentiation trajectory indicated that the ability of migration, and the activation of the immune system increases, while the ability of apoptosis, and glucose metabolic process decreases as pseudotime. Migration-related epithelial cells act on all T-cells via the CNTN2-CNTN2 ligand-receptor pair, which suggested that CNTN2 might be an important biomarker for regulating migration of epithelial cells. Conclusions Our study characterized the heterogeneity of LSCC, which provided novel insights into LSCC and identified a new mechanism and target for clinical LSCC threapies. Evidence IV.

摘要 研究目标
本研究旨在探讨喉鳞状细胞癌（Laryngeal Squamous Cell Carcinoma, LSCC）中上皮细胞与NK/T细胞的异质性及分化轨迹。
研究方法
本研究从基因表达综合数据库（Gene Expression Omnibus）下载包含LSCC01与LSCC02样本的单细胞RNA数据集GSE150321。通过UMAP分析鉴定细胞亚群及其亚群分布位置；采用Seurat包开展基因差异表达分析；借助DAVID数据库对差异表达基因进行功能富集分析；使用Monocle2包解析细胞分化轨迹；利用CellChat包探究上皮细胞与NK/T细胞间的信号通路及配体-受体相互作用对。
研究结果
本研究将所有喉鳞状细胞癌细胞划分为16个细胞亚群，其中包含7个上皮细胞亚群与3个T细胞亚群。功能富集分析结果显示，上皮细胞与NK/T细胞主要参与不同的生物学过程，涵盖细胞周期、免疫应答及细胞迁移。细胞分化轨迹分析结果表明，随着拟时间推移，细胞迁移能力与免疫系统激活水平逐步升高，而细胞凋亡及葡萄糖代谢过程相关能力则逐渐下降。迁移相关上皮细胞可通过CNTN2-CNTN2配体-受体对作用于所有T细胞，提示CNTN2或可作为调控上皮细胞迁移的关键生物标志物。
研究结论
本研究阐明了喉鳞状细胞癌的细胞异质性，为喉鳞状细胞癌的研究提供了全新视角，并为临床喉鳞状细胞癌治疗识别了新的作用机制与治疗靶点。本研究证据等级为IV级。