Expression, prognostic association, and immune microenvironment correlates of C4orf50 in breast cancer: a The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) bioinformatics study

Abstract

Background Chromosome 4 open reading frame 50 (C4orf50) is a poorly characterized gene whose expression pattern and clinical relevance in breast cancer remain unclear. We aimed to evaluate the expression, prognostic association, immune microenvironment correlates, and transcriptional features associated with C4orf50 in breast cancer. Methods RNA-sequencing and clinical data from The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) cohort were analyzed. C4orf50 expression was compared between tumor and normal tissues and across clinicopathological subgroups. Continuous C4orf50 expression was evaluated in Cox proportional hazards models, including stage- and molecular-subtype-stratified sensitivity models. Immune-cell transcriptional enrichment was quantified using single-sample gene set enrichment analysis (ssGSEA) with the LM22 leukocyte signature matrix representing 22 immune-cell populations. Raw and Consensus Purity Estimate (CPE)-adjusted associations were examined, together with tumor microenvironment scores generated using the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm. Immune-checkpoint expression, patient-level coexpression, Gene Ontology, MSigDB C2 gene set enrichment analysis (GSEA), and consensus cancer-hallmark enrichment were also assessed. Results C4orf50 expression was higher in 1,093 breast tumor samples than in 111 normal samples (Wilcoxon P=4.6×10⁻11; Cliff’s delta =0.379), whereas no robust associations with pathological stage, molecular subtype, or receptor status remained after multiple-testing correction. In the primary stage-by-subtype-stratified Cox model, higher continuous C4orf50 expression was associated with poorer overall survival [hazard ratio (HR) per 1 standard deviation =1.41, 95% confidence interval (CI): 1.19–1.67; P<0.001]. The median-based Kaplan-Meier analysis was not significant (P=0.38). C4orf50 expression correlated positively with the ESTIMATE Immune Score (rho =0.372), Stromal Score (rho =0.198), and ESTIMATE Score (rho =0.340; all false discovery rate values <0.001). Tumor-purity adjustment attenuated but did not eliminate most associations with LM22 immune-cell and immune-checkpoint signatures. Coexpressed transcripts were enriched in regulated exocytosis, calcium-dependent exocytosis, dense-core granule exocytosis, and vesicle-related processes. No integrated cancer hallmark reached significance after multiple-testing correction. Conclusions C4orf50 is overexpressed in breast cancer and its continuous expression is associated with overall survival and immune-related transcriptional features in TCGA-BRCA. These observational findings do not establish a causal role for C4orf50 and require validation in independent cohorts and experimental models.