Table9_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亚型，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，并构建肾透明细胞癌的预后特征模型。
方法：分别从基因表达综合数据库（Gene Expression Omnibus, GEO）与癌症基因组图谱（The Cancer Genome Atlas, TCGA）下载肾透明细胞癌的单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）数据及批量转录组数据（bulk data）。采用CIBERSORT算法计算肾透明细胞癌样本的细胞组成比例。结合单因素Cox回归分析与最小绝对收缩和选择算子（Least Absolute Shrinkage and Selection Operator, LASSO）Cox回归分析筛选预后相关基因。通过基因集变异分析（Gene Set Variation Analysis, GSVA）与细胞间通讯分析获取更多功能层面的相关信息。此外，本研究还开展了体外实验，以明确靶向LGALS1的小干扰RNA（small interfering 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出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独特的表达模式，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，肾透明细胞癌样本中的上皮细胞比例显著升高，且在上皮细胞中筛选出289个差异表达基因。将所有差异表达基因与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。我们构建的上皮间质转化相关预后特征模型在肾透明细胞癌中表现出良好的预测效能。值得注意的是，靶向LGALS1的小干扰RNA可抑制肾透明细胞癌细胞的迁移与侵袭能力，这一作用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构建了一种新型且高效的上皮间质转化相关肾透明细胞癌预后特征模型。其中，靶向LGALS1的小干扰RNA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有关。