Bioinformatics Study Identified EGF as a Crucial Gene in Papillary Renal Cell Cancer

Due to a lack of knowledge of the disease process, papillary renal cell carcinoma (PRCC) has a dismal outlook. This research was aimed at uncovering the possible biomarkers and the underlying principles in PRCC using a bioinformatics method.

We searched the Gene Expression Omnibus (GEO) datasets to obtain the GSE11151 and GSE15641 gene expression profiles of PRCC. We used the R package limma to identify the differentially expressed genes (DEGs). The online tool DAVID and ClusterProfiler package in R software were used to analyze Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway dominance, respectively. The STRING database was utilized to construct the PPI network of DEGs. Using the Cytoscape technology, a protein-protein interaction (PPI) network that associated with DEGs was created, and the hub genes were identified using the Cytoscape plug-in CytoHubba. The hub genes were subjected to a Kaplan-Meier analysis to identify their correlations with survival rates.

From the selected datasets, a total of 240 common DEGs were identified in the PRCC, including 50 upregulated genes and 190 downregulated regulated genes. Renal growth, external exosome, binding of heparin, and metabolic processes were all substantially associated with DEGs. The CytoHubba plug-in-based analysis identified the 10 hub genes (ALB, KNG1, C3, CXCL12, EGF, TIMP1, VCAN, PLG, LAMC1, and CASR) from the original PPI network. The higher expression group of EGF was associated with poor outcome in patients with PRCC.

We revealed important genes and proposed biological pathways that may be implicated in the formation of PRCC. EGF might be a predictive biomarker for PRCC and therefore should be investigated as a novel treatment strategy.