Integrative Phosphoproteomic and Metabolomic Analysis of Disruption of Metabolic Homeostasis in Breast Cancer: A Pilot Study.

Breast cancer is a heterogeneous tumor with 4 major molecular subtypes. Hormone receptor (HR)-positive and HER2-negative breast cancer accounts for 70% of invasive breast cancers. In our study, we collected 15 original Luminal B breast cancer tissue (LBBC) and paired non-cancerous adjacent tissue (NATs) from patients and performed LC-MS/MS-based label-free quantitative phosphoproteomic analysis. The untargeted metabolomics analysis was also used to determine the differences in metabolic patterns between LBBC and NATs. In addition, an integrative analysis of phosphoproteomics and metabolomics data was performed to investigate regulatory metabolic pathways. The main regulatory proteins were verified by western blot. Phosphoproteomics analysis identified 1385 differentially phosphorylated sites in 785 proteins. The protein kinase A (PKA) and protein kinase C (PKC) families and p70 ribosomal S6 kinase (RPS6K) were strongly activated in LBBC, whereas the cycle-dependent kinases (CDKs) were markedly inhibited. Cancer-specific activation of PI3K-mTORC and Hippo signaling pathways were also highlighted. Metabolomic analysis showed that 223 metabolites were significantly differentially accumulated, including fatty acids (3-hydroxycapric acid; dodecanoic acid; linoleic acid; stearic acid), glycerophospholipids, glycerophosphatidylcholines, and sphingolipids, which were mainly involved in fatty acid oxidation metabolism, sphingolipid metabolism, purine metabolism, and amino acid metabolism pathway. After integrative analysis, we found that the sphingolipid metabolic pathway played the major regulatory role. We also validated 3 phosphorylated proteins (p-YAP, p-SGK1, and p-SGPP2) in the PI3K-mTORC, Hippo signaling pathway, and sphingolipid metabolic pathway, respectively. The present study provides the first integrative phosphoproteome and metabolome profiles of LBBC, mainly involving dysregulation of sphingolipid homeostasis mediated by PI3K-mTORC and Hippo signaling pathways. This study described two phosphorylation pathways and sphingolipid metabolism regulation module for a better understanding of LBBC carcinogenesis and therapy.