Identification of UBE2I as a Novel Biomarker in ccRCC Based on a Large-Scale CRISPR-Cas9 Screening Database and Immunohistochemistry

Feng Li; Li Lai; Zhijie You; Hui Cheng; Guodong Guo; Chenchen Tang; Luyun Xu; Hongxia Liu; Wenting Zhong; Youyu Lin; Qingshui Wang; Yao Lin; Yongbao Wei

doi:10.3389/fmolb.2022.813428

Identification of UBE2I as a Novel Biomarker in ccRCC Based on a Large-Scale CRISPR-Cas9 Screening Database and Immunohistochemistry

Front Mol Biosci. 2022 Feb 8:9:813428. doi: 10.3389/fmolb.2022.813428. eCollection 2022.

Authors

Feng Li^{1

2

3}, Li Lai^{1

4}, Zhijie You^{1

2}, Hui Cheng^{1

2}, Guodong Guo^{1

2}, Chenchen Tang^{1

3}, Luyun Xu⁵, Hongxia Liu⁵, Wenting Zhong⁵, Youyu Lin⁵, Qingshui Wang^{5

6}, Yao Lin^{7

5}, Yongbao Wei^{1

8}

Affiliations

¹ Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China.
² Department of Pathology, Fujian Provincial Hospital, Fuzhou, China.
³ The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
⁴ Central Laboratory, Fujian Provincial Hospital, Fuzhou, China.
⁵ Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.
⁶ Fujian Provincial Key Laboratory of Hepatic Drug Research, Fuzhou, China.
⁷ Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, China.
⁸ Department of Urology, Fujian Provincial Hospital, Fuzhou, China.

Abstract

Background: 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. Methods: 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. Results: 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. Conclusion: 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.

Keywords: CRISPR-cas9 screening; UBE2I; ccRCC; cell cycle; nuclear translocation.