Identification of a Novel Immune-Related Prognostic Biomarker and Small-Molecule Drugs in Clear Cell Renal Cell Carcinoma (ccRCC) by a Merged Microarray-Acquired Dataset and TCGA Database

Guan-Fa Xiao; Xin Yan; Zhao Chen; Ren-Jie Zhang; Tong-Zu Liu; Wan-Li Hu

doi:10.3389/fgene.2020.00810

Identification of a Novel Immune-Related Prognostic Biomarker and Small-Molecule Drugs in Clear Cell Renal Cell Carcinoma (ccRCC) by a Merged Microarray-Acquired Dataset and TCGA Database

Front Genet. 2020 Aug 18:11:810. doi: 10.3389/fgene.2020.00810. eCollection 2020.

Authors

Guan-Fa Xiao^{1

2}, Xin Yan¹, Zhao Chen¹, Ren-Jie Zhang¹, Tong-Zu Liu¹, Wan-Li Hu¹

Affiliations

¹ Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.
² Department of Pediatric surgery, Ganzhou Maternal and Child Health Hospital, Ganzhou, China.

Abstract

Clear cell renal cell carcinoma (ccRCC) is one of the most common histological subtypes of renal cancer, with a poor prognosis. Our study aimed to identify a biomarker that is significantly associated with ccRCC prognosis and novel immunotherapeutic targets, as well as some novel molecular drugs for ccRCC. Based on the overlap of The Cancer Genome Atlas (TCGA)-Kidney Renal Clear Cell Carcinoma (KIRC) data and the ImmPort database, we obtained 1,292 immune-related genes (IRGs) and constructed a weighed co-expression network based on the IRGs. A total of 39 hub genes were screened out in three modules. CTLA4, which had the highest connectivity degree among the screened genes in a protein-protein interaction network (degree = 24), was selected. Internal validation based on the GEPIA database revealed that patients with a higher expression of CTLA4 had a significantly shorter overall survival time and disease-free survival time. Expression of CTLA4 was also closely correlated with local recurrence, pathologic stage, and immune infiltration level. External validation based on the Oncomine database and merged microarray-acquired dataset validated the mRNA expression level of hub genes. Gene-set enrichment analysis revealed that six KEGG signaling pathways, which were significantly associated with CTLA4, were enriched on immune-related pathways. Further analysis according to the TIMER database demonstrated that CTLA4 expression was positively related to dendritic cells (cor = 0.446, P = 1.32E-23) and negatively associated with tumor purity (cor = -0.267, P = 5.51E-09). Finally, we screened out 293 differentially expressed genes by integrating six datasets from the GEO database. The Connectivity Map (CMap) analysis revealed the strong potential of three small molecule drugs (monensin, quercetin, and fenbufen) for ccRCC treatment. In conclusion, CTLA4 was identified and validated in prognosis of ccRCC. CTLA4 may be a new prognostic biomarker and immunotherapeutic target for ccRCC. Monensin, quercetin, and fenbufen may be novel choices for ccRCC treatment.

Keywords: CTLA4; clear cell renal cell carcinoma; immune infiltration; immune-related prognostic biomarkers; small molecule drugs.