Li Feng, Lai Li, You Zhijie, Cheng Hui, Guo Guodong, Tang Chenchen, Xu Luyun, Liu Hongxia, Zhong Wenting, Lin Youyu, Wang Qingshui, Lin Yao, Wei Yongbao
Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China.
Department of Pathology, Fujian Provincial Hospital, Fuzhou, China.
Front Mol Biosci. 2022 Feb 8;9:813428. doi: 10.3389/fmolb.2022.813428. eCollection 2022.
The genome-wide CRISPR-cas9 dropout screening has emerged as an outstanding approach for characterization of driver genes of tumor growth. The present study aims to investigate core genes related to clear cell renal cell carcinoma (ccRCC) cell viability by analyzing the CRISPR-cas9 screening database DepMap, which may provide a novel target in ccRCC therapy. Candidate genes related to ccRCC cell viability by CRISPR-cas9 screening from DepMap and genes differentially expressed between ccRCC tissues and normal tissues from TCGA were overlapped. Weighted gene coexpression network analysis, pathway enrichment analysis, and protein-protein interaction network analysis were applied for the overlapped genes. The least absolute shrinkage and selection operator (LASSO) regression was used to construct a signature to predict the overall survival (OS) of ccRCC patients and validated in the International Cancer Genome Consortium (ICGC) and E-MTAB-1980 database. Core protein expression was determined using immunohistochemistry in 40 cases of ccRCC patients. A total of 485 essential genes in the DepMap database were identified and overlapped with differentially expressed genes in the TCGA database, which were enriched in the cell cycle pathway. A total of four genes, including UBE2I, NCAPG, NUP93, and TOP2A, were included in the gene signature based on LASSO regression. The high-risk score of ccRCC patients showed worse OS compared with these low-risk patients in the ICGC and E-MTAB-1980 validation cohort. UBE2I was screened out as a key gene. The immunohistochemistry indicated UBE2I protein was highly expressed in ccRCC tissues, and a high-level nuclear translocation of UBE2I occurs in ccRCC. Based on the area under the curve (AUC) values, nuclear UBE2I had the best diagnostic power (AUC = 1). Meanwhile, the knockdown of UBE2I can inhibit the proliferation of ccRCC cells. UBE2I, identified by CRISPR-cas9 screening, was a core gene-regulating ccRCC cell viability, which accumulated in the nucleus and acted as a potential novel promising diagnostic biomarker for ccRCC patients. Blocking the nuclear translocation of UBE2I may have potential therapeutic value with ccRCC patients.
全基因组CRISPR-cas9敲除筛选已成为一种出色的方法，用于表征肿瘤生长的驱动基因。本研究旨在通过分析CRISPR-cas9筛选数据库DepMap来探究与透明细胞肾细胞癌（ccRCC）细胞活力相关的核心基因，这可能为ccRCC治疗提供新靶点。对通过DepMap的CRISPR-cas9筛选得到的与ccRCC细胞活力相关的候选基因，以及来自TCGA的ccRCC组织和正常组织之间差异表达的基因进行了重叠分析。对重叠基因应用了加权基因共表达网络分析、通路富集分析和蛋白质-蛋白质相互作用网络分析。使用最小绝对收缩和选择算子（LASSO）回归构建一个特征来预测ccRCC患者的总生存期（OS），并在国际癌症基因组联盟（ICGC）和E-MTAB-1980数据库中进行验证。采用免疫组织化学法检测40例ccRCC患者的核心蛋白表达。在DepMap数据库中总共鉴定出485个必需基因，并与TCGA数据库中的差异表达基因重叠，这些基因在细胞周期通路中富集。基于LASSO回归，基因特征中总共包含四个基因，即UBE2I、NCAPG、NUP93和TOP2A。在ICGC和E-MTAB-1980验证队列中，ccRCC患者的高风险评分显示其OS比低风险患者更差。UBE2I被筛选为关键基因。免疫组织化学表明UBE2I蛋白在ccRCC组织中高表达，且在ccRCC中发生高水平的UBE2I核转位。基于曲线下面积（AUC）值，核UBE2I具有最佳诊断效能（AUC = 1）。同时，敲低UBE2I可抑制ccRCC细胞的增殖。通过CRISPR-cas9筛选鉴定出的UBE2I是调节ccRCC细胞活力的核心基因，其在细胞核中积累，可作为ccRCC患者潜在的新型有前景的诊断生物标志物。阻断UBE2I的核转位可能对ccRCC患者具有潜在治疗价值。
