Bioinformatics analysis and experimental validation of SH2B adaptor protein 3 as a prognostic biomarker for gastric cancer

Objective To investigate the expression of SH2B adaptor protein 3 (SH2B3) in gastric cancer cells by combining of bioinformatics methods with experimental validation.

Methods RNA-seq data and microarray datasets of gastric cancer from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) databases were integrated to screen for differentially expressed genes and identify their intersections. Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) network analysis were performed on the intersecting genes. The expression of SH2B3 and its correlation with clinical characteristics and immune infiltration were explored based on databases, and its expression level in gastric cancer cells was validated by RT-qPCR.

Results GO analysis revealed that the genes were primarily involved in processes such as vascular development, extracellular matrix, and oxidoreductase activity. KEGG analysis indicated that the genes were enriched in pathways including the PI3K-Akt pathway, cytokine interactions, and cancer pathways. Gene set enrichment analysis (GSEA) showed that SH2B3 was significantly enriched in epithelial-mesenchymal transition, IL-6/JAK/STAT3 signaling pathway, KRAS-UP signaling pathway, and KRAS-DN signaling pathway. SH2B3 expression was significantly elevated in gastric cancer cells and was associated with poor survival prognosis, with a hazard ratio (HR) of 1.62 for overall survival in patients with high SH2B3 expression. SH2B3 exhibited negative regulation of resting CD4⁺ memory T cells, plasma cells, and activated NK cells, while showing positive regulation of activated CD4⁺ memory T cells and resting NK cells. RT-qPCR analysis revealed high expression of SH2B3 in the gastric cancer cell lines AGS (P < 0.01), HGC-27 (P < 0.05), and NCI-N87 (P < 0.05).

Conclusion SH2B3 is highly expressed in gastric cancer cells and is closely associated with poor prognosis and regulation of the tumor immune microenvironment. SH2B3 may mediate gastric cancer progression through the epithelial-mesenchymal transition signaling pathway.