Isoform-Specific Gene Regulation by Progesterone Receptors Drives Divergent Phenotypes in Breast Cancer Cells [CUT&Run]
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE293884 | GEO | 2025/06/24
REPOSITORIES: GEO
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Project description:Exposure to progesterone is a recognized risk factor for breast cancer, and PGR polymorphisms are associated with various malignancies. The two progesterone receptor (PR) isoforms, full length PR-B and truncated PR-A, are expressed from the PGR gene in breast tissue and play crucial roles in normal physiology and breast cancer progression. An imbalance in the expression ratio of these isoforms, favoring increased levels of PR-A, is common in breast cancer and is associated with resistance to tamoxifen in Luminal A-type tumors. Notably, PRs have recently been implicated in promoting endocrine resistance and driving the expansion of cancer stem-like cell (CSC) populations. Despite this insight, the isoform-specific molecular and epigenetic mechanisms underlying PR action in ER+ breast cancers remain understudied. Phenotypic studies of T47D cell lines that express exclusively PR-A or PR-B showed that PR isoforms regulate divergent cell fates. PR-B expressing cells have a higher proliferation rate, while PR-A expressing cells produce more mammospheres. We profiled progesterone-driven gene expression in cells grown in both adherent (2D) and mammosphere (3D) growth conditions and found differential gene regulation by PR-A and PR-B that is consistent with the observed divergent phenotypes. We then performed CUT&RUN to identify the genomic binding patterns unique to each PR isoform and their suite of target genes. Our findings indicate that PR-A acts as a regulator of the cell cycle and senescence, while PR-B plays a pivotal role in metabolism and intracellular signaling. Our genomic profiling of PRs in this model system has unveiled novel isoform-specific functions of PR. This work has shifted our prior understanding of the role of PRs in gene regulation, offering potential insights for therapeutic interventions in ER+ breast cancer.
2025-06-24 | GSE293885 | GEO
Project description:Background Estrogen and progesterone are potent breast mitogens. In addition to steroid hormones, multiple signaling pathways input to estrogen receptor (ER) and progesterone receptor (PR) actions via posttranslational events. Protein kinases commonly activated in breast cancers phosphorylate steroid hormone receptors (SRs) and profoundly impact their activities. Methods To better understand the role of modified PRs in breast cancer, we measured total and phospho-Ser294 PRs in 209 human breast tumors represented on 2754 individual tissue spots within a tissue microarray and assayed the regulation of this site in human tumor explants cultured ex vivo. To complement this analysis, we assayed PR target gene regulation in T47D luminal breast cancer models following treatment with progestin (promegestone; R5020) and antiprogestins (mifepristone, onapristone, or aglepristone) in conditions under which the receptor is regulated by Lys388 SUMOylation (K388 intact) or is SUMO-deficient (via K388R mutation to mimic persistent Ser294 phosphorylation). Selected phospho-PR-driven target genes were validated by qRT-PCR and following RUNX2 shRNA knockdown in breast cancer cell lines. Primary and secondary mammosphere assays were performed to implicate phospho-Ser294 PRs, epidermal growth factor signaling, and RUNX2 in breast cancer stem cell biology. Results Phospho-Ser294 PR species were abundant in a majority (54%) of luminal breast tumors, and PR promoter selectivity was exquisitely sensitive to posttranslational modifications. Phospho-PR expression and target gene programs were significantly associated with invasive lobular carcinoma (ILC). Consistent with our finding that activated phospho-PRs undergo rapid ligand-dependent turnover, unique phospho-PR gene signatures were most prevalent in breast tumors clinically designated as PR-low to PR-null (luminal B) and included gene sets associated with cancer stem cell biology (HER2, PAX2, AHR, AR, RUNX). Validation studies demonstrated a requirement for RUNX2 in the regulation of selected phospho-PR target genes (SLC37A2). In vitro mammosphere formation assays support a role for phospho-Ser294-PRs via growth factor (EGF) signaling as well as RUNX2 as potent drivers of breast cancer stem cell fate. Conclusions We conclude that PR Ser294 phosphorylation is a common event in breast cancer progression that is required to maintain breast cancer stem cell fate, in part via cooperation with growth factor-initiated signaling pathways and key phospho-PR target genes including SLC37A2 and RUNX2. Clinical measurement of phosphorylated PRs should be considered a useful marker of breast tumor stem cell potential. Alternatively, unique phospho-PR target gene sets may provide useful tools with which to identify patients likely to respond to selective PR modulators that block PR Ser294 phosphorylation as part of rational combination (i.e., with antiestrogens) endocrine therapies designed to durably block breast cancer recurrence.
2017-04-10 | GSE94363 | GEO
Project description:The nuclear steroid hormone receptor Progesterone Receptor (PGR) is expressed in granulosa cells in the ovarian follicle in a tightly regulated pattern in response to the surge of Luteinizing Hormone (LH) that stimulates ovulation. PGR plays a critical role in mediating ovulation in response to LH, however the mechanism for this is still unknown. Using the KGN human granulosa cell line expressing the primary PGR isoforms PGR-A or PGR-B, we performed immunoprecipitation-mass spectrometry to identify novel interacting proteins that regulate PGR function in these ovary-specific target cells. Proteomic analysis revealed protein interactions with both PGR isoforms that were gained (e.g. transcriptional coactivators) or lost (e.g. chaperone proteins) in response to the PGR agonist R5020. Additionally, isoform-specific interactions, including different families of transcriptional regulators, were identified. Comparison with published datasets of PGR interacting proteins in human breast cancer cell lines and decidualised endometrial stromal cells demonstrated a remarkable number of tissue-specific interactions, shedding light on how PGR can maintain diverse functions in different tissues. In conclusion, our dataset provides new insights into ovary-specific PGR transcriptional mechanisms.
2025-05-06 | PXD056566 | Pride
Project description:Progesterone receptors (PRs) are critical context-dependent transcription factors required for normal uterine (PR-A) and mammary gland (PR-B) development. Progesterone is proliferative in the breast, where PR-target genes include paracrine factors that mediate mammary stem cell self-renewal. In the context of altered signal transduction that typifies breast tumorigenesis, dysregulated (i.e. hyper-phosphorylated) PRs likely contribute to tumor progression by promoting cancer cell pro-survival and proliferation. Notably, in breast cancer cells, progestin-bound PRs induce rapid MAPK activation leading to selective regulation of growth-promoting genes by phosphorylated PR species. Functional domains within PR that interact with c-Src and estrogen receptors (ER) have been identified as indirect routes to MAPK activation. Herein, we describe a common docking (CD) domain located within the PR-B N-terminus, a motif first described in MAPKs that facilitates direct interactions between MAPKs and MEK1 or MAPK-phosphatases (MKPs). Mutation of negatively-charged amino acids, previously determined to be critical for CD domain function in MAPKs, within PR-B (mCD PR) did not alter MEK-binding or progestin-induced rapid signaling (i.e. MAPK activation) and PR transcriptional activity as measured by PRE-luciferase (reporter) assays. Microarray gene-expression analysis revealed that endogenous genes regulated by wt PR, but not mCD PR, are involved in critical cellular pathways regulating growth, proliferation, survival, and cancer. mCD PR failed to undergo ligand-induced phosphorylation on Ser81, a ck2-dependent site required for progestin-regulation of select growth-promoting genes (BIRC3, HSD11β2, HbEGF). Progestin-induced PR Ser81 phosphorylation mapped to CD domain-dependent binding of PR-B to MKP3, but did not require phosphatase activity. Receptors containing either mutant CD domains (mCD PR) or point mutations of Ser81 (S79/81A PR) failed to upregulate STAT5 and Wnt1, key PR-target gene products that act as critical mediators of mammary stem cell expansion. Inhibition of JAK/STAT signaling blocked progestin-induced STAT5 and Wnt1 expression. ChIP assays demonstrated that wt, but not phospho-mutant (S79/81A), PR-B was co-recruited to a PRE-containing enhancer region of the Wnt1 gene along with MKP3, ck2 and STAT5. Our studies reveal a novel scaffolding action of MKP3 mediated by interaction with the PR CD domain and required for ck2-dependent PR Ser81 phosphorylation. Co-regulation of select target genes by phospho-Ser81 PR and phospho-STAT5 is likely a global mechanism required for the activation of growth promoting programs active during normal mammary gland development and relevant to mechanisms of breast cancer progression. The study contains 6 different sample groups measured in triplicate, for a total of 18 individual samples (18 arrays). From parental T47D-Y human breast cancer cell lines, we created three stable clones expressing (1) an empty vector (pSG5), (2) the wild type progesterone receptor isoform B (pSG5-PR-B), or (3) a mutant mutant CD domain PR-B. These cell lines were treated with either (1) vehicle control (ethanol) or (2) R5020 10e-8 M for 6 hours before total RNA harvest. Thus, the experiment contains three cell lines, and two treatments (6 sample groups) treated and analyzed in triplicate (18 microarrays). Standard Illumina HT-12v4 chip controls were used during hybridization.
2013-09-06 | E-GEOD-46850 | biostudies-arrayexpress
Project description:The progesterone receptor (PR) and its coactivators are direct targets of activated cyclin-dependent kinases (CDKs) in response to peptide growth factors, progesterone, and deregulation of cell cycle inhibitors. Herein, using the T47D breast cancer model, we probed mechanisms of cell cycle-dependent PR action. In the absence of exogenous progestin, the PR is specifically phosphorylated during the G2/M phase. Accordingly, numerous PR target genes are cell cycle regulated, including HSPB8, a heat-shock protein whose high expression is associated with tamoxifen resistance. Progestin-induced HSPB8 expression required cyclin D1 and was insensitive to antiestrogens but blocked by antiprogestins or inhibition of specificity factor 1 (SP1). HSPB8 expression increased with or without ligand when cells were G2/M synchronized or contained high levels of cyclin D1. Knockdown of PRs abrogated ligand-independent HSPB8 expression in synchronized cells. Notably, PRs and cyclin D1 copurified in whole-cell lysates of transiently transfected COS-1 cells and in PR-positive T47D breast cancer cells expressing endogenous cyclin D1. PRs, cyclin D1, and SP1 were recruited to the HSPB8 promoter in progestin-treated T47D breast cancer cells. Mutation of PR Ser345 to Ala (S345A) or inhibition of CDK2 activity using roscovitine disrupted PR/cyclin D1 interactions with DNA and blocked HSPB8 mRNA expression. Interaction of phosphorylated PRs with SP1 and cyclin D1 provides a mechanism for targeting transcriptionally active PRs to selected gene promoters relevant to breast cancer progression. Understanding the functional linkage between PRs and cell cycle regulatory proteins will provide keys to targeting novel PR/cyclin D1 cross talk in both hormone-responsive disease and HSPB8-high refractory disease with high HSPB8 expression.
2014-02-27 | GSE46715 | GEO
Project description:The progesterone receptor isoforms PRA and PRB are implicated in breast cancer development and metastasis. Expression ratio PRA/PRB is imbalanced in such cancers under the influence of MAPK-dependent extracellular stimuli that strongly impact progesterone-responsiveM- transcriptional regulation. In order to determine the isoform-specific regulated genes M- in a metastatic cancer cell, we established the iPRAB cell line derived from MDA-MB-231 mammary cancer cells (ER-, PR-). This cell lineM- conditionally expressed PRA and/or PRB under the control of RSL1 and doxycycline (Dox) non-steroid ligands, respectively, in a dose-dependent manner. The bi-inducible expression system was generated using a combination of the Rheoswitch (NE Biolabs) and T-Rex (Invitrogen) vector systems as described in the article. We investigated the transcriptomes obtained in cells treated by either RSL1 (for PRA), or Dox (for PRB), or RSL1 + Dox (for PRA + PRB) for 24 h and then by either 10 nM progesterone (+) or vehicle (-) for 6 h. Control experiments were obtained from cells grown in the absence of RSL1, doxycycline and in the presence of progesterone (O+) or vehicle (O-). Experimental conditions of PRA/PRB expression ratio were ranged from 0.1 to 10, and the maximum expression of a given isoform was set to 300 fmol per mg proteins following 24 h induction. After removing redundant probes and pseudogens, the processed data identified 1014 distinct regulated genes subdivised in 3 classes : genes responding either only to unliganded PR isoforms (-), or only to liganded (+) or to both conditions (mixed M-1). Each classe was subdivided according to isoform specificity criteria (A, B, AB, A&B, A&AB, B&AB, A&B&AB) leading to define 3X7 clusters of genes per classe. Each subset was then further analyzed by complete hierarchical clustering through up or down-regulation criteria. These data indicated that PR target genes selectivity is highly dependent of PRA/PRB expression ratio as well as ligand status and highlight the major impact of PR on transcriptional regulation of genes involved in breast cancer and metastasis.
2012-06-11 | E-TABM-1215 | biostudies-arrayexpress
Project description:Major roadblocks to developing effective progesterone receptor (PR)-targeted therapies in breast cancer include the lack of highly-specific PR modulators, a poor understanding of the pro- or anti-tumorigenic networks for PR isoforms and ligands, and an incomplete understanding of the cross talk between PR and estrogen receptor (ER) signaling. Through genomic analyses of xenografts treated with various clinically-relevant ER and PR-targeting drugs, we describe how the activation or inhibition of PR differentially reprograms estrogen signaling, resulting in the segregation of transcriptomes into separate PR agonist and antagonist-mediated groups. These findings address an ongoing controversy regarding the clinical utility of PR agonists and antagonists, alone or in combination with tamoxifen, for breast cancer management. Additionally, the two PR isoforms PRA and PRB, bind distinct genomic sites and interact with different sets of co-regulators to differentially modulate estrogen signaling to be either pro- or anti-tumorigenic. Of the two isoforms, PRA inhibited gene expression and ER chromatin binding significantly more than PRB. Differential gene expression was observed in PRA and PRB-rich patient tumors and importantly, PRA-rich gene signatures had poorer survival outcomes. In support of antiprogestin responsiveness of PRA-rich tumors, gene signatures associated with PR antagonists, but not PR agonists, predicted better survival outcomes. This better patient survival associated with PR antagonists versus PR agonists treatments was further reflected in the higher anti-tumor activity of combination therapies of tamoxifen with PR antagonists and modulators. The study suggests that distinguishing common effects observed due to concomitant interaction of another receptor with its ligand (agonist or antagonist) from unique isoform and ligand-specific effects will guide the development of biomarkers for patient selection and translation of PR-targeted therapies to the clinic.
2017-12-31 | GSE80619 | GEO
Project description:Major roadblocks to developing effective progesterone receptor (PR)-targeted therapies in breast cancer include the lack of highly-specific PR modulators, a poor understanding of the pro- or anti-tumorigenic networks for PR isoforms and ligands, and an incomplete understanding of the cross talk between PR and estrogen receptor (ER) signaling. Through genomic analyses of xenografts treated with various clinically-relevant ER and PR-targeting drugs, we describe how the activation or inhibition of PR dictates distinct ER and PR chromatin binding and differentially reprograms estrogen signaling, resulting in the segregation of transcriptomes into separate PR agonist and antagonist-mediated groups. These findings address an ongoing controversy regarding the clinical utility of PR agonists and antagonists, alone or in combination with tamoxifen, for breast cancer management. Genomic analyses of the two PR isoforms, PRA and PRB, indicate that these isoforms bind distinct genomic sites and interact with different sets of co-regulators to differentially modulate gene expression as well as pro- or anti-tumorigenic phenotypes. Of the two isoforms, PRA inhibited gene expression and ER chromatin binding significantly more than PRB. Of note, the two isoforms reprogrammed estrogen activity to be either pro or anti-tumorigenic. In concordance to the in-vitro observations, differential gene expression was observed in PRA and PRB-rich patient tumors and importantly, PRA-rich gene signatures had poorer survival outcomes. In support of antiprogestin responsiveness of PRA-rich tumors, gene signatures associated with PR antagonists, but not PR agonists, predicted better survival outcomes. This differential of better patient survival associated with PR antagonists versus PR agonists treatments was further reflected in the higher anti-tumor activity of combination therapies of tamoxifen with PR antagonists and modulators. Knowledge of various determinants of PR action and their interactions with estrogen signaling to differentially modulate breast cancer biology should serve as a guide to the development of biomarkers for patient selection and translation of PR-targeted therapies to the clinic.
2017-12-31 | GSE80358 | GEO
Project description:How breast cancers respond to endocrine therapy strongly depends on the expression of the estrogen and progesterone receptors (ER and PR, respectively), with doublenegative ER-/PR- breast cancers having worse clinical outcome than ER+/PR+ breast cancers. Although much is known about ERα gene (ESR1) regulation after hormonal stimulation, how it is regulated in the absence of hormones is not fully understood. We used ER+/PR+ positive breast cancer cells to investigate the role of PR in ESR1 gene regulation in the absence of hormones. We show that PR binds to the low-methylated ESR1 promoter and maintains both gene expression and the DNA methylation profile of the ESR1 locus in hormone-deprived breast cancer cells. Depletion of PR reduces ESR1 expression, with a concomitant increase in gene promoter methylation. The high amount of DNA methylation in the ESR1 promoter of PR-depleted cells persists after the stable re-expression of PR and inhibits PR binding to this genomic region. Consequently, the rescue of PR expression in PR-depleted cells is insufficient to restore ESR1 expression. Consistent with these data, DNA methylation impedes PR binding to consensus progesterone responsive elements in vitro. These findings help us understand the complex crosstalk between PR and ER, and suggest that the analysis of DNA methylation of ESR1 promoter in breast cancer cells can help to design the appropriate targeted therapies for different types of breast cancer patients.
2018-10-04 | GSE107966 | GEO
Project description:Progesterone and estrogen are important drivers of breast cancer proliferation. Herein, we probed estrogen receptor-α (ER) and progesterone receptor (PR) cross-talk in breast cancer models. Stable expression of PR-B in PR-low/ER+ MCF7 cells increased cellular sensitivity to estradiol and insulin-like growth factor 1 (IGF1), as measured in growth assays performed in the absence of exogenous progestin; similar results were obtained in PR-null/ER+ T47D cells stably expressing PR-B. Genome-wide microarray analyses revealed that unliganded PR-B induced robust expression of a subset of estradiol-responsive ER target genes, including cathepsin-D (CTSD). Estradiol-treated MCF7 cells stably expressing PR-B exhibited enhanced ER Ser167 phosphorylation and recruitment of ER, PR and the proline-, glutamate- and leucine-rich protein 1 (PELP1) to an estrogen response element in the CTSD distal promoter; this complex co-immunoprecipitated with IGF1 receptor (IGFR1) in whole-cell lysates. Importantly, ER/PR/PELP1 complexes were also detected in human breast cancer samples. Inhibition of IGF1R or phosphoinositide 3-kinase blocked PR-B-dependent CTSD mRNA upregulation in response to estradiol. Similarly, inhibition of IGF1R or PR significantly reduced ER recruitment to the CTSD promoter. Stable knockdown of endogenous PR or onapristone treatment of multiple unmodified breast cancer cell lines blocked estradiol-mediated CTSD induction, inhibited growth in soft agar and partially restored tamoxifen sensitivity of resistant cells. Further, combination treatment of breast cancer cells with both onapristone and IGF1R tyrosine kinase inhibitor AEW541 was more effective than either agent alone. In summary, unliganded PR-B enhanced proliferative responses to estradiol and IGF1 via scaffolding of ER-α/PELP1/IGF1R-containing complexes. Our data provide a strong rationale for targeting PR in combination with ER and IGF1R in patients with luminal breast cancer.
2015-03-15 | GSE45643 | GEO