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Identification of UBE2I as a Novel Biomarker in ccRCC Based on a Large-Scale CRISPR-Cas9 Screening Database and
Feng Li1,2,3, Li Lai1,4, Zhijie You1,2
1Shengli Clinical Medical College, Fujian Medical University, 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.
Insights
CRISPR-cas9 screening identified UBE2I as a key gene regulating clear cell renal cell carcinoma (ccRCC) cell viability. High nuclear UBE2I expression in ccRCC indicates poor prognosis and offers a potential therapeutic target.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Genome-wide CRISPR-cas9 dropout screening is a powerful tool for identifying cancer driver genes.
- Clear cell renal cell carcinoma (ccRCC) presents a need for novel therapeutic targets to improve patient outcomes.
Purpose of the Study:
- To identify core genes associated with ccRCC cell viability using CRISPR-cas9 screening data.
- To explore potential therapeutic targets and diagnostic biomarkers for ccRCC.
Main Methods:
- Integrated CRISPR-cas9 screening data (DepMap) with differential gene expression data (TCGA) for ccRCC.
- Applied weighted gene coexpression network analysis, pathway enrichment, and protein-protein interaction network analysis.
- Developed and validated a prognostic gene signature using LASSO regression and immunohistochemistry.
Main Results:
- Identified 485 essential genes enriched in the cell cycle pathway, overlapping between DepMap and TCGA datasets.
- A four-gene signature (UBE2I, NCAPG, NUP93, TOP2A) predicted overall survival in ccRCC patients.
- UBE2I was identified as a key gene, highly expressed and translocated to the nucleus in ccRCC tissues, correlating with poor prognosis and inhibited proliferation upon knockdown.
Conclusions:
- UBE2I is a critical gene regulating ccRCC cell viability, acting as a potential diagnostic biomarker due to its nuclear accumulation.
- Targeting UBE2I nuclear translocation presents a promising therapeutic strategy for ccRCC treatment.
