Gene signatures of palmitoylation and fatty acid metabolism predict prognosis and immunotherapy response in breast cancer patients by machine learning, single-cell analysis, and experimental validation

Abstract

Background Palmitoylation and dysregulated fatty acid metabolism are key components of tumor metabolic reprogramming and play important roles in the initiation, progression, and immune regulation of breast cancer (BRCA). However, their systemic molecular characteristics and clinical predictive value remain incompletely understood. Methods This study integrated transcriptomic and clinical data from The Cancer Genome Atlas, GTEx, and Gene Expression Omnibus databases to identify genes associated with fatty acid metabolism and palmitoylation that are aberrantly expressed in tumors. Using Cox and LASSO regression analyses, we constructed a prognostic risk model to stratify patients into distinct risk groups and evaluated differences in survival outcomes, immune profiles, and predicted therapeutic responses. Furthermore, we performed additional analyses, including pan-cancer analysis, tumor microenvironment characterization, drug sensitivity prediction, single-cell RNA sequencing analysis, and in vitro and in vivo functional experiments, to investigate the potential biological and clinical relevance of these findings. Results This study identified a set of genes associated with palmitoylation and fatty acid metabolism that are significantly linked to BRCA prognosis, and constructed a prognostic risk model to stratify patients into distinct risk groups. Significant differences were observed between the high- and low-risk groups regarding overall survival, immune cell infiltration, immune checkpoint expression, and predicted immunotherapy efficacy. Further analysis identified G6PD as a key gene associated with poor prognosis. Epithelial cells with high G6PD expression exhibited enhanced activity in palmitoylation and fatty acid metabolism pathways, accompanied by altered intercellular communication within the TME. Knockdown of G6PD inhibited the proliferation and migration of BRCA cells and suppressed tumor growth in vivo. Potential interactions between G6PD and candidate compounds suggest its therapeutic potential. Conclusion This study indicates that gene signatures associated with palmitoylation and fatty acid metabolism may be relevant to prognostic stratification and the prediction of immunotherapy efficacy in BRCA. Furthermore, the study identifies G6PD as a key metabolic gene linked to tumor progression; this finding not only offers potential insights into the molecular mechanisms of BRCA but also supports further exploration of metabolism-related therapeutic strategies.