Decoding hub gene networks and miRNA interplay in Wilms tumor pathogenesis and therapeutic sensitivity.

Abstract

Objectives: This study aims to explore the expression and functional significance of hub genes in Wilms tumors and their potential as diagnostic biomarkers and therapeutic targets.

Methods: Gene expression data from Wilms tumors and normal control samples were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified using the limma package in R, followed by Venn diagram analysis to identify common DEGs. STRING and Cytoscape were employed to construct a protein-protein interaction (PPI) network and identify hub genes. Cell culture of five Wilms tumor cell lines and normal controls was performed to validate gene expression. Functional assays including proliferation, colony formation, and wound healing assays were conducted to assess the impact of SLC12A3 and GSTM3 overexpression. Immune infiltration analysis was carried out using ssGSEA.

Results: We identified SLC12A3, CLCNKB, REN, and GSTM3 as hub genes with significant down-regulation across Wilms tumor cell lines and normal controls. Immune infiltration analysis revealed that the expression of these genes was associated with altered levels of immune cell populations, such as activated dendritic cells, CD8+ T cells, macrophages, and NK cells. GSTM3 overexpression enhanced the inflammatory response and reduced DNA damage, indicated by lower γ-H2AX expression. Functional assays showed that induction of SLC12A3 and GSTM3 overexpression significantly inhibited cell proliferation, colony formation, and migration.

Conclusion: SLC12A3, CLCNKB, REN, and GSTM3 hub genes play key roles in regulating cellular functions and the immune microenvironment in Wilms tumors. Therefore, these genes could serve as potential biomarker and therapeutic targets in Wilms tumor patients.