Conserved sphingolipid metabolism under transcriptomic diversity: a prognostic and therapeutic target in triple-negative breast cancer

Triple-negative breast cancer (TNBC) exhibits significant transcriptomic diversity, limiting treatment efficacy. This study aims to identify conserved molecular pathways that remain stable in heterogeneous TNBC, providing reliable therapeutic and prognostic targets. Genomic diversity was assessed via Mutant-Allele Tumor Heterogeneity (MATH) in TCGA-TNBC cohorts. Single-cell RNA sequencing from TNBC samples (GSE176078) underwent non-negative matrix factorization (NMF) to identify intratumoral heterogeneity (ITH) metaprograms. Transcriptomic diversity was quantified using PCA-based cell-cell Euclidean distances. CellChat analyzed cellular communication in high- and low-diversity groups. Conserved pathways were identified using KEGG enrichment, ssGSEA, and spatial transcriptomics. And we confirmed the feasibility of targeting sphingolipid metabolism through in vitro and in vivo experiments. TNBC showed elevated genomic diversity, inversely correlated with immune infiltration and pathway activity. Single-cell RNA sequencing revealed ITH metaprograms across malignant subtypes, with Cancer Cycling cells showing proliferative enrichment. High transcriptomic diversity tumors exhibited enhanced Cancer Basal SC interactions with CAFs, promoting stemness and EMT. Multi-region TNBC dataset analysis confirmed sphingolipid metabolism as the most conserved pathway (high interpatient and low intratumoral heterogeneity), enriched in malignant regions and negatively correlated with immune cells. A prognostic model incorporating sphingolipid genes (SPTLC2, SGMS1, SGPP2) stratified high-risk patients. Inhibiting SPHK1 via PF-543 induced dose-dependent cell death. Sphingolipid metabolism could be a transcriptionally conserved pathway in TNBC. Its inhibition may overcome heterogeneity-driven resistance, and its prognostic value enables precise patient stratification, offering a potential strategy against TNBC plasticity.