1
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Mays SG, D'Agostino EH, Flynn AR, Huang X, Wang G, Liu X, Millings EJ, Okafor CD, Patel A, Cato ML, Cornelison JL, Melchers D, Houtman R, Moore DD, Calvert JW, Jui NT, Ortlund EA. A phospholipid mimetic targeting LRH-1 ameliorates colitis. Cell Chem Biol 2022; 29:1174-1186.e7. [PMID: 35316658 DOI: 10.1016/j.chembiol.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/14/2021] [Accepted: 02/27/2022] [Indexed: 12/14/2022]
Abstract
Phospholipids are ligands for nuclear hormone receptors (NRs) that regulate transcriptional programs relevant to normal physiology and disease. Here, we demonstrate that mimicking phospholipid-NR interactions is a robust strategy to improve agonists of liver receptor homolog-1 (LRH-1), a therapeutic target for colitis. Conventional LRH-1 modulators only partially occupy the binding pocket, leaving vacant a region important for phospholipid binding and allostery. Therefore, we constructed a set of molecules with elements of natural phospholipids appended to a synthetic LRH-1 agonist. We show that the phospholipid-mimicking groups interact with the targeted residues in crystal structures and improve binding affinity, LRH-1 transcriptional activity, and conformational changes at a key allosteric site. The best phospholipid mimetic markedly improves colonic histopathology and disease-related weight loss in a murine T cell transfer model of colitis. This evidence of in vivo efficacy for an LRH-1 modulator in colitis represents a leap forward in agonist development.
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Affiliation(s)
- Suzanne G Mays
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | | | - Autumn R Flynn
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Xiangsheng Huang
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Guohui Wang
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Xu Liu
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Elizabeth J Millings
- Department of Biochemistry, Emory University, Atlanta, GA, USA; Department of Surgery, Emory University, Atlanta, GA, USA
| | - C Denise Okafor
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Anamika Patel
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Michael L Cato
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | | | | | | | - David D Moore
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - John W Calvert
- Department of Surgery, Emory University, Atlanta, GA, USA
| | - Nathan T Jui
- Department of Chemistry, Emory University, Atlanta, GA, USA.
| | - Eric A Ortlund
- Department of Biochemistry, Emory University, Atlanta, GA, USA.
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2
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Abstract
Efforts to improve estrogen receptor-α (ER)-targeted therapies in breast cancer have relied upon a single mechanism, with ligands having a single side chain on the ligand core that extends outward to determine antagonism of breast cancer growth. Here, we describe inhibitors with two ER-targeting moieties, one of which uses an alternate structural mechanism to generate full antagonism, freeing the side chain to independently determine other critical properties of the ligands. By combining two molecular targeting approaches into a single ER ligand, we have generated antiestrogens that function through new mechanisms and structural paradigms to achieve antagonism. These dual-mechanism ER inhibitors (DMERIs) cause alternate, noncanonical structural perturbations of the receptor ligand-binding domain (LBD) to antagonize proliferation in ER-positive breast cancer cells and in allele-specific resistance models. Our structural analyses with DMERIs highlight marked differences from current standard-of-care, single-mechanism antiestrogens. These findings uncover an enhanced flexibility of the ER LBD through which it can access nonconsensus conformational modes in response to DMERI binding, broadly and effectively suppressing ER activity.
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3
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Chemical systems biology reveals mechanisms of glucocorticoid receptor signaling. Nat Chem Biol 2021; 17:307-316. [PMID: 33510451 PMCID: PMC8783757 DOI: 10.1038/s41589-020-00719-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 12/04/2020] [Indexed: 02/07/2023]
Abstract
Glucocorticoids display remarkable anti-inflammatory activity, but their use is limited by on-target adverse effects including insulin resistance and skeletal muscle atrophy. We used a chemical systems biology approach, ligand class analysis, to examine ligands designed to modulate glucocorticoid receptor activity through distinct structural mechanisms. These ligands displayed diverse activity profiles, providing the variance required to identify target genes and coregulator interactions that were highly predictive of their effects on myocyte glucose disposal and protein balance. Their anti-inflammatory effects were linked to glucose disposal but not muscle atrophy. This approach also predicted selective modulation in vivo, identifying compounds that were muscle-sparing or anabolic for protein balance and mitochondrial potential. Ligand class analysis defined the mechanistic links between the ligand-receptor interface and ligand-driven physiological outcomes, a general approach that can be applied to any ligand-regulated allosteric signaling system.
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4
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Skowron KJ, Booker K, Cheng C, Creed S, David BP, Lazzara PR, Lian A, Siddiqui Z, Speltz TE, Moore TW. Steroid receptor/coactivator binding inhibitors: An update. Mol Cell Endocrinol 2019; 493:110471. [PMID: 31163202 PMCID: PMC6645384 DOI: 10.1016/j.mce.2019.110471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]
Abstract
The purpose of this review is to highlight recent developments in small molecules and peptides that block the binding of coactivators to steroid receptors. These coactivator binding inhibitors bind at the coregulator binding groove, also known as Activation Function-2, rather than at the ligand-binding site of steroid receptors. Steroid receptors that have been targeted with coactivator binding inhibitors include the androgen receptor, estrogen receptor and progesterone receptor. Coactivator binding inhibitors may be useful in some cases of resistance to currently prescribed therapeutics. The scope of the review includes small-molecule and peptide coactivator binding inhibitors for steroid receptors, with a particular focus on recent compounds that have been assayed in cell-based models.
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Affiliation(s)
- Kornelia J Skowron
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Kenneth Booker
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Changfeng Cheng
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Simone Creed
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Brian P David
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Phillip R Lazzara
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Amy Lian
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Zamia Siddiqui
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Thomas E Speltz
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA; Department of Chemistry, University of Chicago, 929 E. 57th Street, E547, Chicago, IL, 60637, USA
| | - Terry W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA; University of Illinois Cancer Center, University of Illinois at Chicago, 1801 W. Taylor Street, Chicago, IL, 60612, USA.
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5
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Broekema MF, Hollman DAA, Koppen A, van den Ham HJ, Melchers D, Pijnenburg D, Ruijtenbeek R, van Mil SWC, Houtman R, Kalkhoven E. Profiling of 3696 Nuclear Receptor-Coregulator Interactions: A Resource for Biological and Clinical Discovery. Endocrinology 2018; 159:2397-2407. [PMID: 29718163 DOI: 10.1210/en.2018-00149] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/24/2018] [Indexed: 12/13/2022]
Abstract
Nuclear receptors (NRs) are ligand-inducible transcription factors that play critical roles in metazoan development, reproduction, and physiology and therefore are implicated in a broad range of pathologies. The transcriptional activity of NRs critically depends on their interaction(s) with transcriptional coregulator proteins, including coactivators and corepressors. Short leucine-rich peptide motifs in these proteins (LxxLL in coactivators and LxxxIxxxL in corepressors) are essential and sufficient for NR binding. With 350 different coregulator proteins identified to date and with many coregulators containing multiple interaction motifs, an enormous combinatorial potential is present for selective NR-mediated gene regulation. However, NR-coregulator interactions have often been determined experimentally on a one-to-one basis across diverse experimental conditions. In addition, NR-coregulator interactions are difficult to predict because the molecular determinants that govern specificity are not well established. Therefore, many biologically and clinically relevant NR-coregulator interactions may remain to be discovered. Here, we present a comprehensive overview of 3696 NR-coregulator interactions by systematically characterizing the binding of 24 nuclear receptors with 154 coregulator peptides. We identified unique ligand-dependent NR-coregulator interaction profiles for each NR, confirming many well-established NR-coregulator interactions. Hierarchical clustering based on the NR-coregulator interaction profiles largely recapitulates the classification of NR subfamilies based on the primary amino acid sequences of the ligand-binding domains, indicating that amino acid sequence is an important, although not the only, molecular determinant in directing and fine-tuning NR-coregulator interactions. This NR-coregulator peptide interactome provides an open data resource for future biological and clinical discovery as well as NR-based drug design.
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Affiliation(s)
- Marjoleine F Broekema
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - Danielle A A Hollman
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - Arjen Koppen
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | | | - Diana Melchers
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Dirk Pijnenburg
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Rob Ruijtenbeek
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Saskia W C van Mil
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
| | - René Houtman
- PamGene International B. V., BJ 's-Hertogenbosch, Netherlands
| | - Eric Kalkhoven
- Molecular Cancer Research and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, CG Utrecht, Netherlands
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6
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Miro Estruch I, de Haan LHJ, Melchers D, Houtman R, Louisse J, Groten JP, Rietjens IMCM. The effects of all-trans retinoic acid on estrogen receptor signaling in the estrogen-sensitive MCF/BUS subline. J Recept Signal Transduct Res 2018; 38:112-121. [PMID: 29447503 DOI: 10.1080/10799893.2018.1436559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Estrogen receptor alpha (ERα) and retinoic acid receptors (RARs) play important and opposite roles in breast cancer growth. While exposure to ERα agonists such as 17β-estradiol (E2) is related to proliferation, RAR agonists such as all-trans retinoic acid (AtRA) induce anti-proliferative effects. Although crosstalk between these pathways has been proposed, the molecular mechanisms underlying this interplay are still not completely unraveled. The aim of this study was to evaluate the effects of AtRA on ERα-mediated signaling in the ERα positive cell lines MCF7/BUS and U2OS-ERα-Luc to investigate some of the possible underlying modes of action. To do so, this study assessed the effects of AtRA on different ERα-related events such as ERα-mediated cell proliferation and gene expression, ERα-coregulator binding and ERα subcellular localization. AtRA-mediated antagonism of E2-induced signaling was observed in the proliferation and gene expression studies. However, AtRA showed no remarkable effects on the E2-driven coregulator binding and subcellular distribution of ERα. Interestingly, in the absence of E2, ERα-mediated gene expression, ERα-coregulator binding and ERα subcellular mobilization were increased upon exposure to micromolar concentrations of AtRA found to inhibit cell proliferation after long-term exposure. Nevertheless, experiments using purified ERα showed that direct binding of AtRA to ERα does not occur. Altogether, our results using MCF7/BUS and U2OS-ERα-Luc cells suggest that AtRA, without being a direct ligand of ERα, can indirectly interfere on basal ERα-coregulator binding and basal ERα subcellular localization in addition to the previously described crosstalk mechanisms such as competition of ERs and RARs for DNA binding sites.
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Affiliation(s)
| | - Laura H J de Haan
- a Division of Toxicology , Wageningen University , Wageningen , The Netherlands
| | - Diana Melchers
- b PamGene International B.V , Hertogenbosch , The Netherlands
| | - René Houtman
- b PamGene International B.V , Hertogenbosch , The Netherlands
| | - Jochem Louisse
- a Division of Toxicology , Wageningen University , Wageningen , The Netherlands
| | - John P Groten
- a Division of Toxicology , Wageningen University , Wageningen , The Netherlands.,b PamGene International B.V , Hertogenbosch , The Netherlands
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7
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Guo S, Zhang C, Bratton M, Mottamal M, Liu J, Ma P, Zheng S, Zhong Q, Yang L, Wiese TE, Wu Y, Ellis MJ, Matossian M, Burow ME, Miele L, Houtman R, Wang G. ZB716, a steroidal selective estrogen receptor degrader (SERD), is orally efficacious in blocking tumor growth in mouse xenograft models. Oncotarget 2018; 9:6924-6937. [PMID: 29467940 PMCID: PMC5805526 DOI: 10.18632/oncotarget.24023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/27/2017] [Indexed: 12/16/2022] Open
Abstract
Advances in oral SERDs development so far have been confined to nonsteroidal molecules such as those containing a cinnamic acid moiety, which are in earlystage clinical evaluation. ZB716 was previously reported as an orally bioavailable SERD structurally analogous to fulvestrant. In this study, we examined the binding details of ZB716 to the estrogen receptor alpha (ERα) by computer modeling to reveal its interactions with the ligand binding domain as a steroidal molecule. We also found that ZB716 modulates ERα-coregulator interactions in nearly identical manner to fulvestrant. The ability of ZB716 to inhibit cell growth and downregulate ER expression in endocrine resistant, ERα mutant breast cancer cells was demonstrated. Moreover, in both the MCF-7 xenograft and a patient derived xenograft model, orally administered ZB716 showed superior efficacy in blocking tumor growth when compared to fulvestrant. Importantly, such enhanced efficacy of ZB716 was shown to be attributable to its markedly higher bioavailability, as evidenced in the final plasma and tumor tissue concentrations of ZB716 in mice where drug concentrations were found significantly higher than in the fulvestrant treatment group.
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Affiliation(s)
- Shanchun Guo
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.,RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Changde Zhang
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.,RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Melyssa Bratton
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.,College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Madhusoodanan Mottamal
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.,RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Jiawang Liu
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.,RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Peng Ma
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.,College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Shilong Zheng
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.,RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Qiu Zhong
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.,RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Lin Yang
- College of Pharmacy Chongqing Medical and Pharmaceutical College, University Town, Chongqing, 401331, China
| | - Thomas E Wiese
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA.,College of Pharmacy, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Yong Wu
- Department of Internal Medicine, Charles Drew University, Los Angeles, CA 90059, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margarite Matossian
- Section of Hematology & Medical Oncology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Matthew E Burow
- Section of Hematology & Medical Oncology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - René Houtman
- Nuclear Receptor Group, PamGene International, 5211HH Den Bosch, The Netherlands
| | - Guangdi Wang
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 70125, USA.,RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA 70125, USA
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8
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Clarisse D, Thommis J, Van Wesemael K, Houtman R, Ratman D, Tavernier J, Offner F, Beck I, De Bosscher K. Coregulator profiling of the glucocorticoid receptor in lymphoid malignancies. Oncotarget 2017; 8:109675-109691. [PMID: 29312638 PMCID: PMC5752551 DOI: 10.18632/oncotarget.22764] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 11/14/2017] [Indexed: 12/11/2022] Open
Abstract
Coregulators cooperate with nuclear receptors, such as the glucocorticoid receptor (GR), to enhance or repress transcription. These regulatory proteins are implicated in cancer, yet, their role in lymphoid malignancies, including multiple myeloma (MM) and acute lymphoblastic leukemia (ALL), is largely unknown. Here, we report the use and extension of the microarray assay for real-time nuclear receptor coregulator interactions (MARCoNI) technology to detect coregulator associations with endogenous GR in cell lysates. We use MARCoNI to determine the GR coregulator profile of glucocorticoid-sensitive (MM and ALL) and glucocorticoid-resistant (ALL) cells, and identify common and unique coregulators for different cell line comparisons. Overall, we identify SRC-1/2/3, PGC-1α, RIP140 and DAX-1 as the strongest interacting coregulators of GR in MM and ALL cells and show that the interaction strength does not correlate with GR protein levels. Lastly, as a step towards patient samples, we determine the GR coregulator profile of peripheral blood mononuclear cells. We profile the interactions between GR and coregulators in MM and ALL cells and suggest to further explore the GR coregulator profile in hematological patient samples.
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Affiliation(s)
- Dorien Clarisse
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium.,Laboratory of Experimental Cancer Research (LECR), Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jonathan Thommis
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
| | - Karlien Van Wesemael
- Laboratory of Experimental Cancer Research (LECR), Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium.,Hematology, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - René Houtman
- PamGene International B.V., 's Hertogenbosch, The Netherlands
| | - Dariusz Ratman
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium.,Current/Present address: Roche Global IT Solutions, Roche-Polska, Warsaw, Poland
| | - Jan Tavernier
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Fritz Offner
- Hematology, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ilse Beck
- Laboratory of Experimental Cancer Research (LECR), Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium.,Department of Health Sciences, Odisee University College, Ghent, Belgium
| | - Karolien De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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9
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Xue A, Szymczak LC, Mrksich M, Bagheri N. Machine Learning on Signal-to-Noise Ratios Improves Peptide Array Design in SAMDI Mass Spectrometry. Anal Chem 2017; 89:9039-9047. [PMID: 28719743 PMCID: PMC5588089 DOI: 10.1021/acs.analchem.7b01728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/18/2017] [Indexed: 12/15/2022]
Abstract
Emerging peptide array technologies are able to profile molecular activities within cell lysates. However, the structural diversity of peptides leads to inherent differences in peptide signal-to-noise ratios (S/N). These complex effects can lead to potentially unrepresentative signal intensities and can bias subsequent analyses. Within mass spectrometry-based peptide technologies, the relation between a peptide's amino acid sequence and S/N remains largely nonquantitative. To address this challenge, we present a method to quantify and analyze mass spectrometry S/N of two peptide arrays, and we use this analysis to portray quality of data and to design future arrays for SAMDI mass spectrometry. Our study demonstrates that S/N varies significantly across peptides within peptide arrays, and variation in S/N is attributable to differences of single amino acids. We apply supervised machine learning to predict peptide S/N based on amino acid sequence, and identify specific physical properties of the amino acids that govern variation of this metric. We find low peptide-S/N concordance between arrays, demonstrating that different arrays require individual characterization and that global peptide-S/N relationships are difficult to identify. However, with proper peptide sampling, this study illustrates how machine learning can accurately predict the S/N of a peptide in an array, allowing for the efficient design of arrays through selection of high S/N peptides.
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Affiliation(s)
- Albert
Y. Xue
- Department of Chemical & Biological Engineering, Department of Chemistry, Department of Biomedical
Engineering, Department of Cell & Molecular Biology, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208 United States
| | - Lindsey C. Szymczak
- Department of Chemical & Biological Engineering, Department of Chemistry, Department of Biomedical
Engineering, Department of Cell & Molecular Biology, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208 United States
| | - Milan Mrksich
- Department of Chemical & Biological Engineering, Department of Chemistry, Department of Biomedical
Engineering, Department of Cell & Molecular Biology, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208 United States
| | - Neda Bagheri
- Department of Chemical & Biological Engineering, Department of Chemistry, Department of Biomedical
Engineering, Department of Cell & Molecular Biology, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208 United States
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10
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Perera L, Li Y, Coons LA, Houtman R, van Beuningen R, Goodwin B, Auerbach SS, Teng CT. Binding of bisphenol A, bisphenol AF, and bisphenol S on the androgen receptor: Coregulator recruitment and stimulation of potential interaction sites. Toxicol In Vitro 2017; 44:287-302. [PMID: 28751236 DOI: 10.1016/j.tiv.2017.07.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/20/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022]
Abstract
Bisphenol A (BPA), bisphenol AF (BPAF), and bisphenol S (BPS) are well known endocrine disruptors. Previous in vitro studies showed that these compounds antagonize androgen receptor (AR) transcriptional activity; however, the mechanisms of action are unclear. In the present study, we investigated interactions of coregulator peptides with BPA, BPAF, or BPS at the AR complexes using Micro Array for Real-time Coregulator Nuclear Receptor Interaction (MARCoNI) assays and assessed the binding of these compounds on AR by molecular dynamics (MD) simulations. The set of coregulator peptides that are recruited by BPA-bound AR, either positively/or negatively, are different from those recruited by the agonist R1881-bound AR. Therefore, the data indicates that BPA shows no similarities to R1881 and suggests that it may recruit other coregulators to the AR complex. BPAF-bound AR recruits about 70-80% of the same coregulator peptides as BPA-bound AR. Meanwhile, BPS-bound AR interacts with only few peptides compared to BPA or BPAF-bound AR. MD results show that multiple binding sites with varying binding affinities are available on AR for BPA, BPAF, and BPS, indicating the availability of modified binding surfaces on AR for coregulator interactions. These findings help explain some of the distinct AR-related toxicities observed with bisphenol chemicals and raise concern for the use of substitutes for BPA in commercial products.
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Affiliation(s)
- Lalith Perera
- Genome Integrity and Structural Biology Laboratory, United States
| | - Yin Li
- Reproductive and Developmental Biology Laboratory, DIR, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States
| | - Laurel A Coons
- Reproductive and Developmental Biology Laboratory, DIR, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States
| | - Rene Houtman
- PamGene International B.V., Wolvenhoek 10, NL-5211 HH 's-Hertogenboch, The Netherlands
| | - Rinie van Beuningen
- PamGene International B.V., Wolvenhoek 10, NL-5211 HH 's-Hertogenboch, The Netherlands
| | - Bonnie Goodwin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, United States
| | - Scott S Auerbach
- Biomolecular Screening Branch, DNTP, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States
| | - Christina T Teng
- Biomolecular Screening Branch, DNTP, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States.
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11
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Experimental and computational insights on the recognition mechanism between the estrogen receptor α with bisphenol compounds. Arch Toxicol 2017; 91:3897-3912. [DOI: 10.1007/s00204-017-2011-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 06/08/2017] [Indexed: 01/31/2023]
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12
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Denison MS, Faber SC. And Now for Something Completely Different: Diversity in Ligand-Dependent Activation of Ah Receptor Responses. CURRENT OPINION IN TOXICOLOGY 2017; 2:124-131. [PMID: 28845473 PMCID: PMC5570615 DOI: 10.1016/j.cotox.2017.01.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ligand-dependent activation of the Ah receptor (AhR) can result in an extremely diverse spectrum of biological and toxic effects that occur in a ligand-, species- and tissue-specific manner. While the classical mechanism of AhR-dependent signal transduction is directly related to its ability to modulate gene expression, the dramatic diversity in responses observed following AhR activation or inhibition is inconsistent with a single molecular mechanism of AhR action. Recent studies have revealed that key molecular events underlying the AhR signaling pathway are significantly more varied and complex than previously established, and the specificity and diversity in AhR response can be selectively modulated by a variety of factors. Here we describe new insights into the mechanistic diversity in AhR signal transduction that can contribute to ligand-, species- and tissue-specific differences in AhR reponse.
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Affiliation(s)
- Michael S Denison
- Department of Environmental Toxicology, University of California, Davis, CA, 95616, USA
| | - Samantha C Faber
- Department of Environmental Toxicology, University of California, Davis, CA, 95616, USA
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13
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Hsu CW, Hsieh JH, Huang R, Pijnenburg D, Khuc T, Hamm J, Zhao J, Lynch C, van Beuningen R, Chang X, Houtman R, Xia M. Differential modulation of FXR activity by chlorophacinone and ivermectin analogs. Toxicol Appl Pharmacol 2016; 313:138-148. [PMID: 27773686 DOI: 10.1016/j.taap.2016.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 09/10/2016] [Accepted: 10/18/2016] [Indexed: 02/02/2023]
Abstract
Chemicals that alter normal function of farnesoid X receptor (FXR) have been shown to affect the homeostasis of bile acids, glucose, and lipids. Several structural classes of environmental chemicals and drugs that modulated FXR transactivation were previously identified by quantitative high-throughput screening (qHTS) of the Tox21 10K chemical collection. In the present study, we validated the FXR antagonist activity of selected structural classes, including avermectin anthelmintics, dihydropyridine calcium channel blockers, 1,3-indandione rodenticides, and pyrethroid pesticides, using in vitro assay and quantitative structural-activity relationship (QSAR) analysis approaches. (Z)-Guggulsterone, chlorophacinone, ivermectin, and their analogs were profiled for their ability to alter CDCA-mediated FXR binding using a panel of 154 coregulator motifs and to induce or inhibit transactivation and coactivator recruitment activities of constitutive androstane receptor (CAR), liver X receptor alpha (LXRα), or pregnane X receptor (PXR). Our results showed that chlorophacinone and ivermectin had distinct modes of action (MOA) in modulating FXR-coregulator interactions and compound selectivity against the four aforementioned functionally-relevant nuclear receptors. These findings collectively provide mechanistic insights regarding compound activities against FXR and possible explanations for in vivo toxicological observations of chlorophacinone, ivermectin, and their analogs.
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Affiliation(s)
- Chia-Wen Hsu
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Jui-Hua Hsieh
- National Toxicology Program, National Institutes of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Ruili Huang
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Dirk Pijnenburg
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - Thai Khuc
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Jon Hamm
- Integrated Laboratory System, Inc., Morrisville, NC, USA
| | - Jinghua Zhao
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Caitlin Lynch
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Rinie van Beuningen
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - Xiaoqing Chang
- Integrated Laboratory System, Inc., Morrisville, NC, USA
| | - René Houtman
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - Menghang Xia
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
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14
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Nwachukwu JC, Srinivasan S, Zheng Y, Wang S, Min J, Dong C, Liao Z, Nowak J, Wright NJ, Houtman R, Carlson KE, Josan JS, Elemento O, Katzenellenbogen JA, Zhou HB, Nettles KW. Predictive features of ligand-specific signaling through the estrogen receptor. Mol Syst Biol 2016; 12:864. [PMID: 27107013 PMCID: PMC4848761 DOI: 10.15252/msb.20156701] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Some estrogen receptor‐α (ERα)‐targeted breast cancer therapies such as tamoxifen have tissue‐selective or cell‐specific activities, while others have similar activities in different cell types. To identify biophysical determinants of cell‐specific signaling and breast cancer cell proliferation, we synthesized 241 ERα ligands based on 19 chemical scaffolds, and compared ligand response using quantitative bioassays for canonical ERα activities and X‐ray crystallography. Ligands that regulate the dynamics and stability of the coactivator‐binding site in the C‐terminal ligand‐binding domain, called activation function‐2 (AF‐2), showed similar activity profiles in different cell types. Such ligands induced breast cancer cell proliferation in a manner that was predicted by the canonical recruitment of the coactivators NCOA1/2/3 and induction of the GREB1 proliferative gene. For some ligand series, a single inter‐atomic distance in the ligand‐binding domain predicted their proliferative effects. In contrast, the N‐terminal coactivator‐binding site, activation function‐1 (AF‐1), determined cell‐specific signaling induced by ligands that used alternate mechanisms to control cell proliferation. Thus, incorporating systems structural analyses with quantitative chemical biology reveals how ligands can achieve distinct allosteric signaling outcomes through ERα.
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Affiliation(s)
- Jerome C Nwachukwu
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - Sathish Srinivasan
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - Yangfan Zheng
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Song Wang
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Jian Min
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Chune Dong
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Zongquan Liao
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Jason Nowak
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - Nicholas J Wright
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, USA
| | - René Houtman
- PamGene International, Den Bosch, The Netherlands
| | | | | | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Hai-Bing Zhou
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Kendall W Nettles
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, USA
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15
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Shi J, Sharif S, Ruijtenbeek R, Pieters RJ. Activity Based High-Throughput Screening for Novel O-GlcNAc Transferase Substrates Using a Dynamic Peptide Microarray. PLoS One 2016; 11:e0151085. [PMID: 26960196 PMCID: PMC4784888 DOI: 10.1371/journal.pone.0151085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/23/2016] [Indexed: 11/22/2022] Open
Abstract
O-GlcNAcylation is a reversible and dynamic protein post-translational modification in mammalian cells. The O-GlcNAc cycle is catalyzed by O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). O-GlcNAcylation plays important role in many vital cellular events including transcription, cell cycle regulation, stress response and protein degradation, and altered O-GlcNAcylation has long been implicated in cancer, diabetes and neurodegenerative diseases. Recently, numerous approaches have been developed to identify OGT substrates and study their function, but there is still a strong demand for highly efficient techniques. Here we demonstrated the utility of the peptide microarray approach to discover novel OGT substrates and study its specificity. Interestingly, the protein RBL-2, which is a key regulator of entry into cell division and may function as a tumor suppressor, was identified as a substrate for three isoforms of OGT. Using peptide Ala scanning, we found Ser 420 is one possible O-GlcNAc site in RBL-2. Moreover, substitution of Ser 420, on its own, inhibited OGT activity, raising the possibility of mechanism-based development for selective OGT inhibitors. This approach will prove useful for both discovery of novel OGT substrates and studying OGT specificity.
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Affiliation(s)
- Jie Shi
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
| | - Suhela Sharif
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
| | - Rob Ruijtenbeek
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
- PamGene International BV, ‘s-Hertogenbosch, The Netherlands
| | - Roland J. Pieters
- Department of Medicinal Chemistry and Chemical Biology, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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16
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Simon TW, Budinsky RA, Rowlands JC. A model for aryl hydrocarbon receptor-activated gene expression shows potency and efficacy changes and predicts squelching due to competition for transcription co-activators. PLoS One 2015; 10:e0127952. [PMID: 26039703 PMCID: PMC4454675 DOI: 10.1371/journal.pone.0127952] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 04/22/2015] [Indexed: 12/17/2022] Open
Abstract
A stochastic model of nuclear receptor-mediated transcription was developed based on activation of the aryl hydrocarbon receptor (AHR) by 2,3,7,8-tetrachlorodibenzodioxin (TCDD) and subsequent binding the activated AHR to xenobiotic response elements (XREs) on DNA. The model was based on effects observed in cells lines commonly used as in vitro experimental systems. Following ligand binding, the AHR moves into the cell nucleus and forms a heterodimer with the aryl hydrocarbon nuclear translocator (ARNT). In the model, a requirement for binding to DNA is that a generic coregulatory protein is subsequently bound to the AHR-ARNT dimer. Varying the amount of coregulator available within the nucleus altered both the potency and efficacy of TCDD for inducing for transcription of CYP1A1 mRNA, a commonly used marker for activation of the AHR. Lowering the amount of available cofactor slightly increased the EC50 for the transcriptional response without changing the efficacy or maximal response. Further reduction in the amount of cofactor reduced the efficacy and produced non-monotonic dose-response curves (NMDRCs) at higher ligand concentrations. The shapes of these NMDRCs were reminiscent of the phenomenon of squelching. Resource limitations for transcriptional machinery are becoming apparent in eukaryotic cells. Within single cells, nuclear receptor-mediated gene expression appears to be a stochastic process; however, intercellular communication and other aspects of tissue coordination may represent a compensatory process to maintain an organism’s ability to respond on a phenotypic level to various stimuli within an inconstant environment.
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Affiliation(s)
- Ted W. Simon
- Ted Simon LLC, Winston, GA, United States of America
- * E-mail:
| | - Robert A. Budinsky
- The Dow Chemical Company, Toxicology and Environmental Research & Consulting. Midland, MI, United States of America
| | - J. Craig Rowlands
- The Dow Chemical Company, Toxicology and Environmental Research & Consulting. Midland, MI, United States of America
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17
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Le Grand A, Bouter A, Couturier A, Mulner-Lorillon O, Le Goff X, Chesnel F, Sire O, Le Tilly V. Investigation of the functional properties and subcellular localization of alpha human and rainbow trout estrogen receptors within a unique yeast cellular context. J Steroid Biochem Mol Biol 2015; 149:17-26. [PMID: 25595040 DOI: 10.1016/j.jsbmb.2015.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/26/2014] [Accepted: 01/11/2015] [Indexed: 12/22/2022]
Abstract
Estrogens are steroid hormones that play a pivotal role in growth, differentiation and function of reproductive and non-reproductive tissues, mediated through estrogen receptors (ERs). Estrogens are involved in different genomic and non-genomic cell signaling pathways which involve well-defined subcellular ER localizations. Thus, ER activity results from complex interplays between intrinsic binding properties and specific subcellular localization. Since these two factors are deeply intricate, we carried out, in a unique yeast cell context, a comparative study to better understand structure/function/subcellular distribution relationships. This was carried out by comparing two ERs: the human ER α subtype (hERα) and the short form of the α isoform of the rainbow trout ER (rtERαS). Their distinct binding properties to agonist and antagonist ligands and subcellular localizations were characterized in Saccharomyces cerevisiae yeast cells. An unexpected partial agonistic effect of ICI 182-780 was observed for rtERαS. Concomitant to distinct binding properties, distinct subcellular localizations were observed before and after ligand stimulation. Due to the unique cell context, the link between ERs intrinsic binding properties and subcellular localizations is partly unveiled and issues are hypothesized based on the role of cytoplasmic transient complexes which play a role in the ER cytoplasmic/nuclear partition, which in turn is critical for the recruitment of co-regulators in the nucleus.
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Affiliation(s)
- Adélaïde Le Grand
- Laboratoire d'Ingénierie des Matériaux de Bretagne, Université de Bretagne-Sud, CER Yves Coppens, BP573, 56017 Vannes Cedex, France
| | - Anthony Bouter
- Molecular Imaging and NanoBioTechnology, UMR 5248 CBMN, CNRS-Université Bordeaux 1-ENITAB, IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Anne Couturier
- CNRS/Université de Rennes 1, Institut de Génétique & Développement de Rennes, UMR 6290, 2 Ave. Prof. Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Odile Mulner-Lorillon
- CNRS/UPMC Université Paris 06, UMR 8227 LBI2M, Traduction, Cycle Cellulaire et Développement, Station Biologique, CS 90074, 29688 Roscoff Cedex, France
| | - Xavier Le Goff
- CNRS/Université de Rennes 1, Institut de Génétique & Développement de Rennes, UMR 6290, 2 Ave. Prof. Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Franck Chesnel
- CNRS/Université de Rennes 1, Institut de Génétique & Développement de Rennes, UMR 6290, 2 Ave. Prof. Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Olivier Sire
- Laboratoire d'Ingénierie des Matériaux de Bretagne, Université de Bretagne-Sud, CER Yves Coppens, BP573, 56017 Vannes Cedex, France
| | - Véronique Le Tilly
- Laboratoire d'Ingénierie des Matériaux de Bretagne, Université de Bretagne-Sud, CER Yves Coppens, BP573, 56017 Vannes Cedex, France.
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18
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An exposure:activity profiling method for interpreting high-throughput screening data for estrogenic activity—Proof of concept. Regul Toxicol Pharmacol 2015; 71:398-408. [DOI: 10.1016/j.yrtph.2015.01.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/13/2015] [Accepted: 01/17/2015] [Indexed: 11/17/2022]
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19
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Evers NM, van den Berg JHJ, Wang S, Melchers D, Houtman R, de Haan LHJ, Ederveen AGH, Groten JP, Rietjens IMCM. Cell proliferation and modulation of interaction of estrogen receptors with coregulators induced by ERα and ERβ agonists. J Steroid Biochem Mol Biol 2014; 143:376-85. [PMID: 24923734 DOI: 10.1016/j.jsbmb.2014.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 05/27/2014] [Accepted: 06/06/2014] [Indexed: 12/13/2022]
Abstract
The aim of the present study was to investigate modulation of the interaction of the ERα and ERβ with coregulators in the ligand responses induced by estrogenic compounds. To this end, selective ERα and ERβ agonists were characterized for intrinsic relative potency reflected by EC50 and maximal efficacy towards ERα and ERβ mediated response in ER selective reporter gene assays, and subsequently tested for induction of cell proliferation in T47D-ERβ cells with variable ERα/ERβ ratio, and finally for ligand dependent modulation of the interaction of ERα and ERβ with coregulators using the MARCoNI assay, with 154 unique nuclear receptor coregulator peptides derived from 66 different coregulators. Results obtained reveal an important influence of the ERα/ERβ ratio and receptor selectivity of the compounds tested on induction of cell proliferation. ERα agonists activate cell proliferation whereas ERβ suppresses ERα mediated cell proliferation. The responses in the MARCoNI assay reveal that upon ERα or ERβ activation by a specific agonist, the modulation of the interaction of the ERs with coregulators is very similar indicating only a limited number of differences upon ERα or ERβ activation by a specific ligand. Differences in the modulation of the interaction of the ERs with coregulators between the different agonists were more pronounced. Based on ligand dependent differences in the modulation of the interaction of the ERs with coregulators, the MARCoNI assay was shown to be able to classify the ER agonists discriminating between different agonists for the same receptor, a characteristic not defined by the ER selective reporter gene or proliferation assays. It is concluded that the ultimate effect of the model compounds on proliferation of estrogen responsive cells depends on the intrinsic relative potency of the agonist towards ERα and ERβ and the cellular ERα/ERβ ratio whereas differences in the modulation of the interaction of the ERα and ERβ with coregulators contribute to the ligand dependent responses induced by estrogenic compounds.
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Affiliation(s)
- Nynke M Evers
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, the Netherlands.
| | | | - Si Wang
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, the Netherlands
| | - Diana Melchers
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's Hertogenbosch, the Netherlands
| | - René Houtman
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's Hertogenbosch, the Netherlands
| | - Laura H J de Haan
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, the Netherlands
| | - Antwan G H Ederveen
- Pharmacokinetics Pharmacodynamics & Drug Metabolism, MSD, P.O. Box 20, 5340 BH Oss, the Netherlands
| | - John P Groten
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, the Netherlands; PamGene International B.V., Wolvenhoek 10, 5211 HH 's Hertogenbosch, the Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, the Netherlands
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20
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Evers NM, Wang S, van den Berg JHJ, Houtman R, Melchers D, de Haan LHJ, Ederveen AGH, Groten JP, Rietjens IMCM. Identification of coregulators influenced by estrogen receptor subtype specific binding of the ER antagonists 4-hydroxytamoxifen and fulvestrant. Chem Biol Interact 2014; 220:222-30. [PMID: 25014417 DOI: 10.1016/j.cbi.2014.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/07/2014] [Accepted: 06/19/2014] [Indexed: 11/18/2022]
Abstract
The aim of the present study was to investigate modulation of the interaction of ERα and ERβ with coregulators in the ligand dependent responses induced by the ER antagonistic compounds 4OHT and fulvestrant. Comparison with the modulation index (MI) profiles for the ER agonist estradiol (E2) will elucidate whether differences in the (ant)agonist dependent interaction of ERα and ERβ with coregulators expressed in MI profiles contribute to the differences in (ant)agonist responses. To this end, the selected ER antagonistic compounds were first characterized for intrinsic relative potency and efficacy towards ERα and ERβ using ER selective U2OS reporter gene assays, and subsequently tested for ligand dependent modulation of the interaction of ERα and ERβ with coregulators using the MARCoNI assay. Results obtained indicate a preference of 4OHT to antagonize ERβ and find fulvestrant to be less ER specific. MARCoNI assay responses reveal that ERα and ERβ mediated interaction with coregulators expressed in MI profiles are similar for 4OHT and fulvestrant and generally opposite to the MI profile of the ER agonist E2. Hierarchical clustering based on the MI profiles appeared able to clearly discriminate the two compounds with ER antagonistic properties from the ER agonist E2. Taken together the data reveal that modulation of the interaction of ERs with coregulators discriminates ER agonists from antagonists but does not discriminate between the less specific ER antagonist fulvestrant and the preferential ERβ antagonistic compound 4OHT. It is concluded that differences in modulation of the interaction of ERα and ERβ with coregulators contribute to the differences in ligand dependent responses induced by ER agonists and ER antagonists but the importance of the subtle differences in modulation of the interaction of ERs with coregulators between the ER antagonistic compounds 4OHT and fulvestrant for the ultimate biological effect remains to be established.
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Affiliation(s)
- Nynke M Evers
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands.
| | - Si Wang
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands
| | | | - René Houtman
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's Hertogenbosch, The Netherlands
| | - Diana Melchers
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's Hertogenbosch, The Netherlands
| | - Laura H J de Haan
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands
| | - Antwan G H Ederveen
- Pharmacokinetics Pharmacodynamics & Drug Metabolism, MSD, P.O. Box 20, 5340 BH Oss, The Netherlands
| | - John P Groten
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands; PamGene International B.V., Wolvenhoek 10, 5211 HH 's Hertogenbosch, The Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University, Tuinlaan 5, 6703 HE Wageningen, The Netherlands
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21
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Wang S, Rijk JCW, Besselink HT, Houtman R, Peijnenburg AACM, Brouwer A, Rietjens IMCM, Bovee TFH. Extending an in vitro panel for estrogenicity testing: the added value of bioassays for measuring antiandrogenic activities and effects on steroidogenesis. Toxicol Sci 2014; 141:78-89. [PMID: 24928889 DOI: 10.1093/toxsci/kfu103] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the present study, a previously established integrated testing strategy (ITS) for in vitro estrogenicity testing was extended with additional in vitro assays in order to broaden its sensitivity to different modes of action resulting in apparent estrogenicity, i.e., other than estrogen receptor (ER) binding. To this end, an extra set of 10 estrogenic compounds with modes of action in part different from ER binding, were tested in the previously defined ITS, consisting of a yeast estrogen reporter gene assay, an U2OS ERα CALUX reporter gene assay and a cell-free coregulator binding assay. Two androgen reporter gene assays and the enhanced H295R steroidogenesis assay were added to that previous defined ITS. These assays had added value, as several estrogenic model compounds also elicited clear and potent antiandrogenic properties and in addition also showed effects on steroidogenesis that might potentiate their apparent estrogenic effects in vivo. Adding these assays, examining mechanisms of action for estrogenicity apart from ERα binding, gives a more complete and comprehensive assessment of the ability of test compounds to interfere with endocrine signaling. It was concluded that the extended ITS will go beyond in vivo estrogenicity testing by the uterotrophic assay, thereby contributing to the 3R-principles.
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Affiliation(s)
- Si Wang
- Division of Toxicology, Wageningen University and Research Centre, Tuinlaan 5, 6703 HE Wageningen, The Netherlands Business Unit of Toxicology & Bioassays, RIKILT - Institute of Food Safety, Wageningen University and Research Centre, Akkermaalsbos 2, 6708 WB Wageningen, The Netherlands
| | - Jeroen C W Rijk
- Business Unit of Toxicology & Bioassays, RIKILT - Institute of Food Safety, Wageningen University and Research Centre, Akkermaalsbos 2, 6708 WB Wageningen, The Netherlands
| | - Harrie T Besselink
- BioDetection Systems B.V., Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - René Houtman
- PamGene International B.V., Wolvenhoek 10, 5211 HH 's-Hertogenbosch, The Netherlands
| | - Ad A C M Peijnenburg
- Business Unit of Toxicology & Bioassays, RIKILT - Institute of Food Safety, Wageningen University and Research Centre, Akkermaalsbos 2, 6708 WB Wageningen, The Netherlands
| | - Abraham Brouwer
- BioDetection Systems B.V., Science Park 406, 1098 XH Amsterdam, The Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research Centre, Tuinlaan 5, 6703 HE Wageningen, The Netherlands
| | - Toine F H Bovee
- Business Unit of Toxicology & Bioassays, RIKILT - Institute of Food Safety, Wageningen University and Research Centre, Akkermaalsbos 2, 6708 WB Wageningen, The Netherlands
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22
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Nwachukwu JC, Srinivasan S, Bruno NE, Parent AA, Hughes TS, Pollock JA, Gjyshi O, Cavett V, Nowak J, Garcia-Ordonez RD, Houtman R, Griffin PR, Kojetin DJ, Katzenellenbogen JA, Conkright MD, Nettles KW. Resveratrol modulates the inflammatory response via an estrogen receptor-signal integration network. eLife 2014; 3:e02057. [PMID: 24771768 PMCID: PMC4017646 DOI: 10.7554/elife.02057] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Resveratrol has beneficial effects on aging, inflammation and metabolism, which are thought to result from activation of the lysine deacetylase, sirtuin 1 (SIRT1), the cAMP pathway, or AMP-activated protein kinase. In this study, we report that resveratrol acts as a pathway-selective estrogen receptor-α (ERα) ligand to modulate the inflammatory response but not cell proliferation. A crystal structure of the ERα ligand-binding domain (LBD) as a complex with resveratrol revealed a unique perturbation of the coactivator-binding surface, consistent with an altered coregulator recruitment profile. Gene expression analyses revealed significant overlap of TNFα genes modulated by resveratrol and estradiol. Furthermore, the ability of resveratrol to suppress interleukin-6 transcription was shown to require ERα and several ERα coregulators, suggesting that ERα functions as a primary conduit for resveratrol activity.DOI: http://dx.doi.org/10.7554/eLife.02057.001.
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Affiliation(s)
- Jerome C Nwachukwu
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, United States
| | - Sathish Srinivasan
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, United States
| | - Nelson E Bruno
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, United States
| | | | - Travis S Hughes
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, United States
| | - Julie A Pollock
- Department of Chemistry, University of Illinois, Urbana, United States
| | - Olsi Gjyshi
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, United States
| | - Valerie Cavett
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, United States
| | - Jason Nowak
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, United States
| | - Ruben D Garcia-Ordonez
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, United States
| | - René Houtman
- Nuclear Receptor Group, PamGene International, Den Bosch, Netherlands
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, United States
| | - Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, United States
| | | | - Michael D Conkright
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, United States
| | - Kendall W Nettles
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, United States
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Wang S, Aarts JMMJG, de Haan LHJ, Argyriou D, Peijnenburg AACM, Rietjens IMCM, Bovee TFH. Towards an integratedin vitrostrategy for estrogenicity testing. J Appl Toxicol 2013; 34:1031-40. [DOI: 10.1002/jat.2928] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 07/11/2013] [Accepted: 08/04/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Si Wang
- Division of Toxicology; Wageningen University and Research Centre; Tuinlaan 5 6703 HE Wageningen The Netherlands
- Business Unit of Toxicology & Bioassays, RIKILT - Institute of Food Safety; Wageningen University and Research Centre; Akkermaalsbos 2 6708 WB Wageningen The Netherlands
| | - Jac M. M. J. G. Aarts
- Business Unit of Toxicology & Bioassays, RIKILT - Institute of Food Safety; Wageningen University and Research Centre; Akkermaalsbos 2 6708 WB Wageningen The Netherlands
| | - Laura H. J. de Haan
- Division of Toxicology; Wageningen University and Research Centre; Tuinlaan 5 6703 HE Wageningen The Netherlands
| | - Dimitrios Argyriou
- Division of Toxicology; Wageningen University and Research Centre; Tuinlaan 5 6703 HE Wageningen The Netherlands
| | - Ad A. C. M. Peijnenburg
- Business Unit of Toxicology & Bioassays, RIKILT - Institute of Food Safety; Wageningen University and Research Centre; Akkermaalsbos 2 6708 WB Wageningen The Netherlands
| | - Ivonne M. C. M. Rietjens
- Division of Toxicology; Wageningen University and Research Centre; Tuinlaan 5 6703 HE Wageningen The Netherlands
| | - Toine F. H. Bovee
- Business Unit of Toxicology & Bioassays, RIKILT - Institute of Food Safety; Wageningen University and Research Centre; Akkermaalsbos 2 6708 WB Wageningen The Netherlands
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