Bladder cancer is a prevalent malignancy with high morbidity and mortality, necessitating the identification of novel biomarkers for improved diagnosis and treatment. CD22 and CD79A, traditionally recognized as B-cell surface markers, have emerged as genes of interest due to their roles in the tumor microenvironment and potential as immune markers and therapeutic targets.

Raw RNA-Seq data from the GSE133624 dataset were processed and analyzed using the Galaxy web server. The bioinformatics pipeline incorporated multiple tools, including HISAT2, featureCounts, and DESeq2 to identify genes with significant expression changes. CD22, CD79A, TCL1A, and VPREB3 were selected through STRING- and Cytoscape-based protein–protein interaction analysis with biological support. For validation, total RNA was isolated from peripheral blood of 27 patients and 25 healthy controls using TRIzol reagent. Complementary DNA (cDNA) was synthesized, and gene expression was measured by quantitative real-time PCR (qRT-PCR).

Bioinformatics analysis revealed significant downregulation of CD22 (log2FoldChange: -3.30, adjusted P = 2.49 × 10⁻¹⁰) and CD79A (log2FoldChange: -2.54, adjusted P = 1.13 × 10⁻⁵) in tumor tissues, with roles in immune and signaling pathways. qRT-PCR showed no significant expression differences in blood (P = 0.2361 for CD22, P = 0.531 for CD79A), with AUC values (0.5970 for CD22, 0.5215 for CD79A) indicating limited diagnostic potential. Significant expression reductions were observed in blood samples associated with comorbidities (diabetes, hypertension, ischemic heart disease) and risk factors (smoking, alcohol), and different stages and genders (P < 0.05). A positive correlation between CD22 and CD79A expression was found (r = 0.3521, P = 0.0105).

Although blood-based assessment of CD22 and CD79A showed no significant differences between patients and controls, significant expression alterations linked to metabolic comorbidities (e.g., diabetes) and environmental exposures (e.g., smoking) suggest their biological relevance in bladder cancer mechanisms. These findings highlight the compartment-specific expression of CD22 and CD79A and their possible relevance as candidate genes in blood in relation to comorbidities and risk factors.