Multi-omics landscape and functional validation of HCCS in breast cancer: from pan-cancer immunometabolic characterization to regulating tumor proliferation

Background Holocytochrome c synthase (HCCS) is an essential mitochondrial regulator; however, its pan-cancer significance and its direct functional role in breast cancer (BRCA) progression remain insufficiently explored. This study aimed to systematically characterize the pan-cancer landscape of HCCS and validate its biological impact on BRCA. Methods We integrated multi-omics data from 33 TCGA cancer types to investigate HCCS expression patterns, genomic alterations, and its correlation with the immune microenvironment. In breast cancer cell lines (MDA-MB-231), the effects of HCCS knockdown on cell proliferation and cell cycle distribution were assessed using CCK-8, colony formation, and flow cytometry assays. Finally, we constructed a machine learning-based prognostic signature and performed drug sensitivity analysis to evaluate its clinical relevance. Results HCCS was significantly upregulated in multiple malignancies, including BRCA, and correlated with poor patient prognosis. Pan-cancer analysis suggested that HCCS might act as a mitochondrial-immunometabolic hub involved in immune evasion. In vitro validation confirmed that HCCS is a key driver of tumor growth, as HCCS knockdown significantly inhibited cell proliferation and colony-forming ability by inducing G0/G1 phase arrest. By integrating these mechanistic findings with clinical data, we developed a robust HCCS-based prognostic model that demonstrated high predictive accuracy across independent BRCA cohorts. Furthermore, pharmacogenomic analysis identified candidate small molecules, such as MK-886 and mercaptopurine, as potential therapeutic options. Conclusion Our findings transition HCCS from a computational biomarker to a functionally validated regulator of breast cancer cell survival. By linking its systemic immunometabolic impact with its direct role in cell cycle control, this study identifies HCCS as a promising therapeutic target and a reliable prognostic indicator in BRCA.