Investigating the prognostic role of citrullination-related genes in breast cancer by combining transcriptomics, single-cell analysis and verification

Abstract

Citrullination, a process linked to autoimmune diseases, has been implicated in cancer, but its role in breast cancer (BRCA) remains unclear. This study aimed to identify citrullination-related genes (CRGs) associated with prognosis in BRCA. We utilized datasets from The Cancer Genome Atlas (TCGA-BRCA) and Gene Expression Omnibus (GEO), pinpointing candidate genes by intersecting differentially expressed genes (DEGs) from TCGA-BRCA with known CRGs. Prognostic CRGs were selected using univariate Cox regression and Lasso regression analyses, and a predictive nomogram was created based on independent prognostic factors identified through multivariate Cox regression. Our findings revealed that SEZ6, S100B, SPIB, and TFF1 were key CRGs used to construct a risk model. High-risk BRCA patients exhibited immune-suppressive tumor microenvironments (TMEs) with low CD8⁺ T cell mutation and enrichment in C1/C4 immune subtypes. In contrast, low-risk patients displayed high immune infiltration and enrichment in C2/C3/C6 subtypes. High expression of S100B, SPIB, and TFF1 was associated with increased immune infiltration by NK cells and T cells, while high SEZ6 expression was linked to neutrophil mutations, PD-L1 upregulation, and low CD8⁺ T cell infiltration. Molecular docking studies explored the interactions of these CRGs with entinostat. In conclusion, SEZ6, S100B, SPIB, and TFF1 were identified as significant prognostic genes in BRCA, providing insights into BRCA pathogenesis and potential personalized treatment strategies.