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 clinical and laboratory studies. To address these discrepancies, we conducted an integrated omics analysis of effects of agonist-activated PR in MCF-7 cells with elevated PR expression. PR agonist R5020 exerted strong antiproliferative and proapoptotic effects in these cells. 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 signalling, TNFA signalling via NFKB, epithelial-mesenchymal transition, and KRAS signalling, 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 all components of the Ndc80 complex 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, Smac/DIABLO) and downregulating anti-apoptotic proteins (BCL-2, BCL-XL). This culminated in mitochondria-mediated apoptosis independent of effector caspases. The omics analysis also detected previously reported upregulation of pro-growth proteins such as EGFR, IRS2, and CCND1, but the upregulation was functionally futile and inhibitory phosphorylation of IRS2 at S306 increased 4-fold. In conclusion, this omics study achieved to date the most comprehensive and holistic understanding of PR-regulated proteins and molecular networks that are strongly anti-proliferative and proapoptotic with significant involvement of mitochondria. These findings suggest that pure PR agonists warrant evaluation as first-line endocrine therapy for breast cancer with high PR expression.