Identification of PTPRR and JAG1 as key genes in castration-resistant prostate cancer by integrated bioinformatics methods<sup></sup>.

Ji-li Wang; Yan Wang; Guo-ping Ren

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Identification of PTPRR and JAG1 as key genes in castration-resistant prostate cancer by integrated bioinformatics methods.

Author: Ji-Li WANG ¹ ; Yan WANG ¹ ; Guo-Ping REN ¹
Author Information

1. Department of Pathology, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
Publication Type:Journal Article
Keywords: Bioinformatics; Protein tyrosine phosphatase receptor-type R (PTPRR); Jagged1 (JAG1); Differentially expressed genes (DEGs); Castration-resistant prostate cancer (CRPC); Functional enrichment
MeSH: Computational Biology/methods*; Gene Ontology; Humans; Jagged-1 Protein/genetics*; Male; Prognosis; Prostatic Neoplasms, Castration-Resistant/mortality*; Protein Interaction Maps; Receptor-Like Protein Tyrosine Phosphatases, Class 7/genetics*
From: Journal of Zhejiang University. Science. B 2020;21(3):246-255
CountryChina
Language:English
Abstract: To identify novel genes in castration-resistant prostate cancer (CRPC), we downloaded three microarray datasets containing CRPC and primary prostate cancer in Gene Expression Omnibus (GEO). R packages affy and limma were performed to identify differentially expressed genes (DEGs) between primary prostate cancer and CRPC. After that, we performed functional enrichment analysis including gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway. In addition, protein-protein interaction (PPI) analysis was used to search for hub genes. Finally, to validate the significance of these genes, we performed survival analysis. As a result, we identified 53 upregulated genes and 58 downregulated genes that changed in at least two datasets. Functional enrichment analysis showed significant changes in the positive regulation of osteoblast differentiation pathway and aldosterone-regulated sodium reabsorption pathway. PPI network identified hub genes like cortactin-binding protein 2 (CTTNBP2), Rho family guanosine triphosphatase (GTPase) 3 (RND3), protein tyrosine phosphatase receptor-type R (PTPRR), Jagged1 (JAG1), and lumican (LUM). Based on PPI network analysis and functional enrichment analysis, we identified two genes (PTPRR and JAG1) as key genes. Further survival analysis indicated a relationship between high expression of the two genes and poor prognosis of prostate cancer. In conclusion, PTPRR and JAG1 are key genes in the CRPC, which may serve as promising biomarkers of diagnosis and prognosis of CRPC.