Table7_Construction of EMT related prognostic signature for kidney renal clear cell carcinoma, through integrating bulk and single-cell gene expression profiles.xlsx

Introduction: Kidney renal clear cell carcinoma (KIRC), as a main type of malignant kidney cancers, has a poor prognosis. Epithelial-mesenchymal transformation (EMT) exerts indispensable role in tumor progression and metastasis, including in KIRC. This study aimed to mine more EMT related details and build prognostic signature for KIRC.
Methods: The KIRC scRNA-seq data and bulk data were downloaded from GEO and TCGA databases, respectively. The cell composition in KIRC was calculated using CIBERSORT. Univariate Cox regression analysis and LASSO Cox regression analysis were combined to determine the prognostic genes. Gene set variation analysis and cell-cell communication analysis were conducted to obtain more functional information. Additionally, functional analyses were conducted to determine the biological roles of si-LGALS1 in vitro.
Results: We totally identified 2,249 significant differentially expressed genes (DEGs) in KIRC samples, meanwhile a significant distinct expression pattern was found in KIRC, involving Epithelial Mesenchymal Transition pathway. Among all cell types, significantly higher proportion of epithelial cells were observed in KIRC, and 289 DEGs were identified in epithelial cells. After cross analysis of all DEGs and 970 EMT related genes, SPARC, TMSB10, LGALS1, and VEGFA were optimal to build prognostic model. Our EMT related showed good predictive performance in KIRC. Remarkably, si-LGALS1 could inhibit migration and invasion ability of KIRC cells, which might be involved in suppressing EMT process.
Conclusion: A novel powerful EMT related prognostic signature was built for KIRC patients, based on SPARC, TMSB10, LGALS1, and VEGFA. Of which, si-LGALS1 could inhibit migration and invasion ability of KIRC cells, which might be involved in suppressing EMT process.

引言：肾透明细胞癌（Kidney renal clear cell carcinoma, KIRC）作为肾脏恶性肿瘤的主要类型，预后较差。上皮间质转化（Epithelial-mesenchymal transformation, EMT）在肿瘤进展与转移过程中发挥不可或缺的作用，肾透明细胞癌亦不例外。本研究旨在挖掘更多与上皮间质转化相关的细节信息，并为肾透明细胞癌构建预后特征。
方法：本研究分别从GEO数据库与TCGA数据库下载肾透明细胞癌的单细胞RNA测序（scRNA-seq）数据与批量转录组数据。采用CIBERSORT算法计算肾透明细胞癌样本的细胞组成比例。结合单变量Cox回归分析与套索LASSO Cox回归分析筛选预后相关基因。通过基因集变异分析与细胞间通讯分析获取更多功能层面的信息。此外，本研究开展体外实验，探究靶向LGALS1的小干扰RNA（si-LGALS1）的生物学功能。
结果：本研究共在肾透明细胞癌样本中筛选得到2249个显著差异表达基因（differentially expressed genes, DEGs），同时发现肾透明细胞癌存在显著的独特表达模式，且该模式与上皮间质转化通路密切相关。在所有细胞类型中，肾透明细胞癌样本内上皮细胞的占比显著升高，且在上皮细胞中筛选得到289个差异表达基因。将全部差异表达基因与970个上皮间质转化相关基因进行交叉分析后，最终筛选出SPARC、TMSB10、LGALS1及VEGFA用于构建预后模型。本研究构建的上皮间质转化相关特征在肾透明细胞癌中表现出良好的预测性能。值得注意的是，si-LGALS1可抑制肾透明细胞癌细胞的迁移与侵袭能力，其作用机制可能与抑制上皮间质转化过程相关。
结论：本研究基于SPARC、TMSB10、LGALS1及VEGFA四个基因，为肾透明细胞癌患者构建了一种全新且高效的上皮间质转化相关预后特征。其中，si-LGALS1可抑制肾透明细胞癌细胞的迁移与侵袭能力，该效应可能通过抑制上皮间质转化过程实现。