A pretreatment 15-gene signature predicts non-pCR in response to neoadjuvant chemotherapy in breast cancer and reveals a pyruvate-CCND1-MET therapeutic vulnerability.

BACKGROUND: In breast cancer (BC), neoadjuvant chemotherapy (NAC) improves surgical options, and pathologic complete response (pCR) predicts better outcomes. Patients with residual disease (non-pCR) have higher recurrence risk, yet robust pretreatment biomarkers remain limited. OBJECTIVE: To develop a pretreatment transcriptomic predictor of non-pCR and connect the predictive signal to an interpretable metabolic-transcriptional-signaling mechanism with potential therapeutic actionability. METHODS: Three Gene Expression Omnibus (GEO) pretreatment bulk-expression cohorts were analyzed (GSE25066, GSE20194, GSE32646). Differentially expressed genes (DEGs) were integrated and a least absolute shrinkage and selection operator (LASSO) logistic model (trained on GSE25066) generated a 15-gene risk score (RS), externally validated in GSE20194 and GSE32646. A hospital clinical cohort provided paired samples and serum metabolomics focusing on glycolysis-related metabolites. Functional assays and RNA-seq tested pyruvate effects and MET inhibition (capmatinib). Single-cell RNA-seq plus inferCNV was used to localize key signals and infer a regulatory axis. RESULTS: The 15-gene RS showed consistent discrimination for non-pCR (AUC: 0.823 training; 0.809 and 0.876 validations). Non-pCR tumors exhibited enriched cell-cycle programs (E2F/G2M), inflammatory signaling (TNFα/NF-κB), and estrogen-response pathways. Multi-omics highlighted CCND1 as a central hub; serum pyruvate was elevated in non-pCR and positively correlated with CCND1. Pyruvate enhanced malignant phenotypes and induced transcriptomic changes centered on MET signaling; capmatinib attenuated these effects. Single-cell analyses showed highest CCND1 expression in epithelial/malignant compartments and supported a YAP1-HIF1A/ARNT-MET transcriptional axis linking pyruvate-associated cues to MET activation. CONCLUSIONS: A pretreatment 15-gene RS enables risk stratification for NAC non-pCR, and mechanistic evidence supports a pyruvate-CCND1-MET vulnerability potentially addressable by MET-targeted combination strategies.