Decreased Lipid Phosphate Phosphatase 1/3 and Increased Lipid Phosphate Phosphatase 2 Expression in the Human Breast Cancer Tumor Microenvironment Promotes Tumor Progression and Immune System Evasion

SIMPLE SUMMARY: The lipid phosphate phosphatases (LPPs) are a family of three enzymes that act at the cell surface and within the cell to modulate signaling. In many tumors, including breast cancers, LPP1 and LPP3 expression levels are decreased and LPP2 expression levels are increased relative to normal tissue, which stimulates a pro-cancerous phenotype by decreasing the turnover of bioactive lipids and promoting cell cycle progression. While most research has been conducted in the laboratory, validation in human tumors is lacking. We used three large independent patient cohorts and single-cell RNA-sequencing data to show that decreased LPP1/3 and increased LPP2 expression in cancers correlated to worse tumor biology, immune system evasion, and decreased survival. Most tumor LPP1/3 is produced by the stroma and LPP2 by cancer cells. Overall, our findings support pre-clinical evidence that restoring tumor LPP expression balance, particularly through LPP2 inhibition, could provide adjunct therapies for breast cancer patients. ABSTRACT: The LPP family is comprised of three enzymes that dephosphorylate bioactive lipid phosphates both intracellularly and extracellularly. Pre-clinical breast cancer models have demonstrated that decreased LPP1/3 with increased LPP2 expression correlates to tumorigenesis. This though has not been well verified in human specimens. In this study, we correlate LPP expression data to clinical outcomes in over 5000 breast cancers from three independent cohorts (TCGA, METABRIC, and GSE96058), investigate biological function using gene set enrichment analysis (GSEA) and the xCell cell-type enrichment analysis, and confirm sources of LPP production in the tumor microenvironment (TME) using single-cell RNA-sequencing (scRNAseq) data. Decreased LPP1/3 and increased LPP2 expression correlated to increased tumor grade, proliferation, and tumor mutational burden (all p < 0.001), as well as worse overall survival (hazard ratios 1.3–1.5). Further, cytolytic activity was decreased, consistent with immune system invasion. GSEA data demonstrated multiple increased inflammatory signaling, survival, stemness, and cell signaling pathways with this phenotype across all three cohorts. scRNAseq and the xCell algorithm demonstrated that most tumor LPP1/3 was expressed by endothelial cells and tumor-associated fibroblasts and LPP2 by cancer cells (all p < 0.01). Restoring the balance in LPP expression levels, particularly through LPP2 inhibition, could represent novel adjuvant therapeutic options in breast cancer treatment.