Bioinformatics analysis and identification of genes and pathways involved in patients with Wilms tumor

Abstract

Background: Wilms tumor is the most common childhood kidney malignant tumor. However, the genes and signaling pathways associated with the disease remain incompletely understood.Methods: GSE66405, GSE73209, and GSE11151 were collected from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were detected using R software. A proteinprotein interaction (PPI) network was constructed using the STRING database, and the clustering modules and hub genes were analyzed with the Cytoscape software. Genes functional enrichment analyses were performed using the package "clusterProfiler" in R software, and the gene set enrichment analysis (GSEA) analysis was performed using GSEA v4.1.0 software.Results: Respectively, 3,092, 620, and 3,567 DEGs were screened in GSE66405, GSE73209, and GSE11151, with a total of 474 common DEGs detected in three expression profiles. For the common DEGs, the top 30 significant results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were presented. Furthermore, five modules were found as the most related modules to Wilms tumor. GO term and KEGG pathway enrichment analyses of the genes in all the modules identified 10 GO terms and 5 KEGG pathways as significantly enriched. The top 10 hub DEGs of the PPI network were ALB, CDH1, EGF, AQP2, REN, SLC2A2, SPP1, UMOD, NPHS2, and FOXM1, with ALB identified as the highest degree. GSEA results showed 11 pathways were correlated with ALB expression in GSE66405 and 10 pathways were related to the expression of the ALB gene in GSE73209.Conclusions: Our study revealed robust gene signatures in Wilms tumor. Dysregulations of the signaling pathways were associated with the development and progression of the Wilms tumor, and 10 hub genes may play important roles in its diagnosis and therapy.

Exploration of biological significance of m6A-related genes in Wilms tumor

“…Although our study focused on m6A-related genes, we found in many results of our studies that the DEGs between WT tissues and normal tissues partially overlapped with another study. A study by Li et al compared the DEGs between WT and normal tissues from the GEO (Gene Expression Omnibus) database by bioinformatics methods, and 10 DEGs ( ALB, CDH1, EGF, AQP2, REN, SLC2A2, SPP1, UMOD, NPHS2 and FOXM1 ) were screened [30]. The AQP2, SPP1 and UMOD in the results of this study coincided with the DEGs we screened.…”

Integrative Transcriptomic Profiling of the Wilms Tumor

“…Although the treatment of the WT is successful, advanced comprehensive approaches are needed for personalized therapy. The main goal is to improve outcomes by combining the results of recent research, including molecular genetics, with potential novel biomarkers independent of WT histology and prognostic significance [5,11]. Thus, our study aimed to identify WT-related transcriptomic markers independent of the WT subtype and tumor stage, which represent potential diagnostic and therapeutic targets.…”

Integrative Transcriptomic Profiling Reveals Novel Biomarkers in Wilms Tumor

“…Although the treatment of WT is successful, advanced comprehensive approaches are needed for personalized therapy. The main goal is to improve outcomes by combining the results of recent research, including molecular genetics, with potential novel biomarkers independent of WT histology and prognostic signi cance [5,11]. Thus, our study aimed to identify universal transcriptomic markers independent of the WT subtype and tumor stage, which represent potential diagnostic and therapeutic targets.…”