PHGDH and LEP serve as prognostic markers associated with B cell and responses to immunotherapy in triple-negative breast cancer

Background. Triple-negative breast cancer (TNBC) is one of the most aggressive and prevalent cancers in women. This study aimed to identify target genes by integrating glutamine metabolism and cancer-immunity interactions in TNBC. Methods. Data were obtained from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO). Glutamine-related genes were extracted from the Gene Set Enrichment Analysis (GSEA) Database. Differential analysis and ESTIMATE were used to find immune-related and glutamine-related genes. The clusters were established by consensus clustering. Mechanistic insights were investigated through Gene set enrichment analysis (GSEA), ESTIMATE, epic, ssGSEA and weighted gene co-expression network analysis (WGCNA). Expression of immunomodulatory factors was used to assess immunotherapy response. Single cell RNA seq and RT-qPCR were used to validate the expression of PHGDH and LEP. Results. Analysis of The Cancer Genome Atlas (TCGA) dataset revealed that leptin (LEP) and phosphoglycerate dehydrogenase (PHGDH) are closely associated with immunity and glutamine metabolism in TNBC. Based on the expression profiles of LEP and PHGDH, TNBC samples were classified into two distinct clusters. Univariate logistic regression analysis demonstrated that clusters significantly influence TNBC prognosis. Gene set enrichment analysis (GSEA) highlighted potential pathways, showing that Cluster 2 correlates positively with immune cell infiltration and exhibits reduced oncogenic pathway activity. Utilizing Weighted gene co-expression network analysis (WGCNA), we identified a module strongly linked to immune response and clusters, along with eight B cell-associated genes. Notably, Cluster 2 displayed elevated expression of immunomodulatory factors, suggesting enhanced responsiveness to immunotherapy. Validation using the GSE76275 dataset confirmed these findings. Additionally, single-cell analysis revealed PHGDH expression in B cells within TNBC.The expression of PHGDH and LEP was validated in TNBC cell lines by RT-qPCR. Conclusion. These results suggested that LEP and PHGDH serve as prognostic markers associated with B cells and improved immunotherapy outcomes in TNBC.