Omics analysis reveals striking effects of progesterone receptor on mitochondria and mitochondria-mediated apoptosis independent of caspases in Breast Cancer cells

The role of progesterone receptor (PR) in breast cancer remains controversial with conflicting reports from both clinical and laboratory studies. To address these discrepancies, we conducted an integrated omics analysis using MCF-7 cells with elevated PR expression (MCF-7PR) through transfection. Treatment with the pure PR agonist R5020 induced strong antiproliferative and proapoptotic effects. Quantitative proteomics identified 4,915 PR-regulated proteins and 678 phosphorylated peptides, with nearly 100% verifiable rate by Western blotting analysis. The proteomics data was closely correlated with transcriptomic data. Key pathways upregulated included hypoxia, p53 signaling, TNFA signaling via NFKB, epithelial-mesenchymal transition, and KRAS signaling, while E2F targets, G2/M checkpoint, and mitotic spindle assembly were downregulated. R5020 broadly suppressed cell cycle regulators, including CDKs, cyclins, DNA replication proteins, and components of the Ndc80 and chromosomal passenger complexes. Concurrently, it elicited significant changes in 200 mitochondrial proteins, upregulating many proapoptotic factors (e.g., BNIP3, NIX, AIF/AIFM1, AIFM2, ENDOG, HtrA2/Omi) and downregulating anti-apoptotic proteins (BCL-2, BCL-XL), leading to mitochondrial outer membrane permeability and caspase-independent apoptosis. Consistent with previous reports, we observed significant upregulation of pro-growth proteins such as EGFR, IRS2, and CCND1. However, these changes were functionally inconsequential, partly due to inhibitory phosphorylation, as IRS2 phosphorylation at S306 increased 4-fold. In conclusion, this omics study achieved to date the most comprehensive understanding of PR-regulated proteins and molecular networks, revealing a predominantly anti-proliferative and proapoptotic role with significant mitochondrial involvement. Our findings suggest that pure PR agonists warrant evaluation as first-line endocrine therapy for breast cancer with high PR expression.