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Rashidian A, Dušek J, Drastik M, Smutná L, Fritsche K, Braeuning A, Pijnenburg D, van Beuningen R, Honkakoski P, Poso A, Kronenberger T, Pavek P. Filling the Blank Space: Branched 4-Nonylphenol Isomers Are Responsible for Robust Constitutive Androstane Receptor (CAR) Activation by Nonylphenol. Environ Sci Technol 2024; 58:6913-6923. [PMID: 38593436 DOI: 10.1021/acs.est.3c10096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
4-Nonylphenol (4-NP), a para-substituted phenolic compound with a straight or branched carbon chain, is a ubiquitous environmental pollutant and food contaminant. 4-NP, particularly the branched form, has been identified as an endocrine disruptor (ED) with potent activities on estrogen receptors. Constitutive Androstane Receptor (CAR) is another crucial nuclear receptor that regulates hepatic lipid, glucose, and steroid metabolism and is involved in the ED mechanism of action. An NP mixture has been described as an extremely potent activator of both human and rodent CAR. However, detailed mechanistic aspects of CAR activation by 4-NP are enigmatic, and it is not known if 4-NP can directly interact with the CAR ligand binding domain (LBD). Here, we examined interactions of individual branched (22NP, 33NP, and 353NP) and linear 4-NPs with CAR variants using molecular dynamics (MD) simulations, cellular experiments with various CAR expression constructs, recombinant CAR LBD in a TR-FRET assay, or a differentiated HepaRG hepatocyte cellular model. Our results demonstrate that branched 4-NPs display more stable poses to activate both wild-type CAR1 and CAR3 variant LBDs in MD simulations. Consistently, branched 4-NPs activated CAR3 and CAR1 LBD more efficiently than linear 4-NP. Furthermore, in HepaRG cells, we observed that all 4-NPs upregulated CYP2B6 mRNA, a relevant hallmark for CAR activation. This is the first study to provide detailed insights into the direct interaction between individual 4-NPs and human CAR-LBD, as well as its dominant variant CAR3. The work could contribute to the safer use of individual 4-NPs in many areas of industry.
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Affiliation(s)
- Azam Rashidian
- Department of Internal Medicine VIII, University Hospital of Tübingen, Tübingen, Baden-Württemberg 72076, Germany
| | - Jan Dušek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
- Department of Physiology, Faculty of Medicine in Hradec Kralove, Charles University, Šimkova 870, Hradec Králové 500 03, Czech Republic
| | - Martin Drastik
- Department of Biophysics and Physical Chemistry, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
| | - Lucie Smutná
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
| | - Kristin Fritsche
- Department Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Albert Braeuning
- Department Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, Berlin 10589, Germany
| | - Dirk Pijnenburg
- PamGene International B.V., Wolvenhoek 10, 's-Hertogenbosch 5211HH, Netherlands
| | - Rinie van Beuningen
- PamGene International B.V., Wolvenhoek 10, 's-Hertogenbosch 5211HH, Netherlands
| | - Paavo Honkakoski
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, Kuopio 72011, Finland
| | - Antti Poso
- Department of Internal Medicine VIII, University Hospital of Tübingen, Tübingen, Baden-Württemberg 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
| | - Thales Kronenberger
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove 500 05, Czech Republic
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Díaz‐Holguín A, Rashidian A, Pijnenburg D, Monteiro Ferreira G, Stefela A, Kaspar M, Kudova E, Poso A, van Beuningen R, Pavek P, Kronenberger T. Front Cover: When Two Become One: Conformational Changes in FXR/RXR Heterodimers Bound to Steroidal Antagonists (ChemMedChem 4/2023). ChemMedChem 2023. [DOI: 10.1002/cmdc.202300056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Alejandro Díaz‐Holguín
- School of Pharmacy Faculty of Health Sciences University of Eastern Finland Kuopio 70211 Finland
- Current address: Science for Life Laboratory Department of Cell and Molecular Biology Uppsala University 75124 Uppsala Sweden
| | - Azam Rashidian
- Institute of Pharmacy Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2) Eberhard Karls University Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Internal Medicine VIII University Hospital of Tübingen Otfried-Müller-Strasse 14 72076 Tübingen Germany
| | - Dirk Pijnenburg
- PamGene International B.V. Wolvenhoek 10 5211HH ‘s-Hertogenbosch Netherlands
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses School of Pharmaceutical Sciences University of São Paulo Av. Prof. Lineu Prestes 580 05508-000 São Paulo Brazil
| | - Alzbeta Stefela
- Department of Pharmacology and Toxicology Charles University Heyrovskeho 1203 50005 Hradec Kralove Czechia
| | - Miroslav Kaspar
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 542/2 16000 Prague Czechia
- Faculty of Sciences Charles University in Prague Albertov 6 Prague 2 12843 Czechia
| | - Eva Kudova
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 542/2 16000 Prague Czechia
| | - Antti Poso
- Institute of Pharmacy Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2) Eberhard Karls University Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Internal Medicine VIII University Hospital of Tübingen Otfried-Müller-Strasse 14 72076 Tübingen Germany
- School of Pharmacy Faculty of Health Sciences University of Eastern Finland Kuopio 70211 Finland
| | - Rinie van Beuningen
- PamGene International B.V. Wolvenhoek 10 5211HH ‘s-Hertogenbosch Netherlands
| | - Petr Pavek
- Department of Pharmacology and Toxicology Charles University Heyrovskeho 1203 50005 Hradec Kralove Czechia
| | - Thales Kronenberger
- Institute of Pharmacy Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2) Eberhard Karls University Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Internal Medicine VIII University Hospital of Tübingen Otfried-Müller-Strasse 14 72076 Tübingen Germany
- School of Pharmacy Faculty of Health Sciences University of Eastern Finland Kuopio 70211 Finland
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3
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Díaz-Holguín A, Rashidian A, Pijnenburg D, Monteiro Ferreira G, Stefela A, Kaspar M, Kudova E, Poso A, van Beuningen R, Pavek P, Kronenberger T. When Two Become One: Conformational Changes in FXR/RXR Heterodimers Bound to Steroidal Antagonists. ChemMedChem 2023; 18:e202200556. [PMID: 36398403 DOI: 10.1002/cmdc.202200556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/15/2022] [Indexed: 11/19/2022]
Abstract
Farnesoid X receptor (FXR) is a nuclear receptor with an essential role in regulating bile acid synthesis and cholesterol homeostasis. FXR activation by agonists is explained by an αAF-2-trapping mechanism; however, antagonism mechanisms are diverse. We discuss microsecond molecular dynamics (MD) simulations investigating our recently reported FXR antagonists 2a and 2 h. We study the antagonist-induced conformational changes in the FXR ligand-binding domain, when compared to the synthetic (GW4064) or steroidal (chenodeoxycholic acid, CDCA) FXR agonists in the FXR monomer or FXR/RXR heterodimer r, and in the presence and absence of the coactivator. Our MD data suggest ligand-specific influence on conformations of different FXR-LBD regions, including the α5/α6 region, αAF-2, and α9-11. Changes in the heterodimerization interface induced by antagonists seem to be associated with αAF-2 destabilization, which prevents both co-activator and co-repressor recruitment. Our results provide new insights into the conformational behaviour of FXR, suggesting that FXR antagonism/agonism shift requires a deeper assessment than originally proposed by crystal structures.
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Affiliation(s)
- Alejandro Díaz-Holguín
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland.,Current address: Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Azam Rashidian
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany
| | - Dirk Pijnenburg
- PamGene International B.V., Wolvenhoek 10, 5211HH, 's-Hertogenbosch, Netherlands
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, 05508-000, São Paulo, Brazil
| | - Alzbeta Stefela
- Department of Pharmacology and Toxicology, Charles University, Heyrovskeho 1203, 50005, Hradec Kralove, Czechia
| | - Miroslav Kaspar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 16000, Prague, Czechia.,Faculty of Sciences, Charles University in Prague, Albertov 6, Prague 2, 12843, Czechia
| | - Eva Kudova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 16000, Prague, Czechia
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Rinie van Beuningen
- PamGene International B.V., Wolvenhoek 10, 5211HH, 's-Hertogenbosch, Netherlands
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Charles University, Heyrovskeho 1203, 50005, Hradec Kralove, Czechia
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
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Rooney J, Ryan N, Liu J, Houtman R, van Beuningen R, Hsieh JH, Chang G, Chen S, Christopher Corton J. A Gene Expression Biomarker Identifies Chemical Modulators of Estrogen Receptor α in an MCF-7 Microarray Compendium. Chem Res Toxicol 2021; 34:313-329. [PMID: 33405908 PMCID: PMC10683854 DOI: 10.1021/acs.chemrestox.0c00243] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Identification of chemicals that affect hormone-regulated systems will help to predict endocrine disruption. In our previous study, a 46 gene biomarker was found to be an accurate predictor of estrogen receptor (ER) α modulation in chemically treated MCF-7 cells. Here, potential ERα modulators were identified using the biomarker by screening a microarray compendium consisting of ∼1600 gene expression comparisons representing exposure to ∼1200 chemicals. A total of ∼170 chemicals were identified as potential ERα modulators. In the Connectivity Map 2.0 collection, 75 and 39 chemicals were predicted to activate or suppress ERα, and they included 12 and six known ERα agonists and antagonists/selective ERα modulators, respectively. Nineteen and eight of the total number were also identified as active in an ERα transactivation assay carried out in an MCF-7-derived cell line used to screen the Tox21 10K chemical library in agonist or antagonist modes, respectively. Chemicals predicted to modulate ERα in MCF-7 cells were examined further using global and targeted gene expression in wild-type and ERα-null cells, transactivation assays, and cell-free ERα coregulator interaction assays. Environmental chemicals classified as weak and very weak agonists were confirmed to activate ERα including apigenin, kaempferol, and oxybenzone. Novel activators included digoxin, nabumetone, ivermectin, and six progestins. Novel suppressors included emetine, mifepristone, niclosamide, and proscillaridin. Our strategy will be useful to identify environmentally relevant ERα modulators in future high-throughput transcriptomic screens.
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Affiliation(s)
- John Rooney
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
- Present address: Integrated Lab Services, Research Triangle Park, NC
| | - Natalia Ryan
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
- Present address: Bayer Crop Science, Research Triangle Park, NC
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
| | - René Houtman
- PamGene International B.V., Den Bosch, The Netherlands
- Present address: Precision Medicine Lab, Oss, The Netherlands
| | | | - Jui-Hua Hsieh
- Kelly Government Solutions, Research Triangle Park, North Carolina
| | - Gregory Chang
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte,California 91010
| | - Shiuan Chen
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte,California 91010
| | - J. Christopher Corton
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, NC 27711
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Sawada T, Hilhorst R, Rangarajan S, Yoshida M, Tanabe Y, Tamura K, Kinoshita T, Shimoyama T, van Beuningen R, Ruijtenbeek R, Tsuda H, Koizumi F. Inactive immune pathways in triple negative breast cancers that showed resistance to neoadjuvant chemotherapy as inferred from kinase activity profiles. Oncotarget 2018; 9:34229-34239. [PMID: 30344939 PMCID: PMC6188135 DOI: 10.18632/oncotarget.26026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/02/2018] [Indexed: 12/15/2022] Open
Abstract
About 5% of Triple negative breast cancer patients (TNBCs) who receive neoadjuvant chemotherapy (NAC) experience progressive disease (PD). Few reports are published on TNBCs with PD during NAC, whereas TNBCs that respond to NAC have been well-studied. We investigated kinase activity profiles of TNBCs to explore the biological differences underlying the lack of response to NAC. Among 740 TNBCs, 20 non-responders were identified. Seven non-responders and 10 TNBCs that did not receive NAC (control group) were evaluated. No correlation was observed between NAC response and age, menopausal status, tumor size and axillary lymph node status. Tyrosine kinase activity profiles of TNBC primary tissues from NAC non-responders and the controls were determined with a peptide microarray system. Kinase activity measurements showed that 35 peptides had significantly (p < 0.05) lower phosphorylation in non-responders. ZAP70, LCK, SYK and JAK2 were identified as differentially active upstream kinases. Pathway analysis suggested lower activity in immune-related pathways in non-responders. The number of tumor infiltrating lymphocytes (TILs) was significantly lower (p = 0.0053) in non-responders. Kinases related to the immune system are less activated in non-responders. TILs evaluation suggested that the immune system is hardly active in non-responders and is not activated by NAC treatment.
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Affiliation(s)
- Takeshi Sawada
- Shien-Lab, National Cancer Center Hospital, Tokyo, Japan.,Division of Clinical Research Support, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Riet Hilhorst
- PamGene International BV, 's-Hertogenbosch, The Netherlands
| | | | - Masayuki Yoshida
- Department of Breast Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yuko Tanabe
- Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kenji Tamura
- Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Takayuki Kinoshita
- Department of Breast Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Tatsu Shimoyama
- Division of Clinical Research Support, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | | | | | - Hitoshi Tsuda
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan.,Department of Basic Pathology, National Defense Medical College, Saitama, Japan
| | - Fumiaki Koizumi
- Shien-Lab, National Cancer Center Hospital, Tokyo, Japan.,Division of Clinical Research Support, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
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Li Y, Perera L, Coons LA, Burns KA, Tyler Ramsey J, Pelch KE, Houtman R, van Beuningen R, Teng CT, Korach KS. Differential in Vitro Biological Action, Coregulator Interactions, and Molecular Dynamic Analysis of Bisphenol A (BPA), BPAF, and BPS Ligand-ERα Complexes. Environ Health Perspect 2018; 126:017012. [PMID: 29389661 PMCID: PMC6014695 DOI: 10.1289/ehp2505] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND Bisphenol A (BPA) is an endocrine-disrupting chemical (EDC) that might be harmful to human health. Recently, there has been widespread usage of bisphenol chemicals (BPs), such as bisphenol AF (BPAF) and bisphenol S (BPS), as replacements for BPA. However, the potential biological actions, toxicity, and the molecular mechanism of these compounds are still poorly understood. OBJECTIVES Our objective was to examine the estrogenic effects of BPA, BPAF, and BPS and the molecular mechanisms of action in the estrogen receptor alpha (ERα) complex. METHODS In vitro cell models were used to compare the estrogenic effects of BPA, BPAF, and BPS to estrogen. Microarray Assay for Real-Time Coregulator-Nuclear receptor Interaction (MARCoNI) analysis was used to identify coregulators of BPA, BPAF, and BPS, and molecular dynamic (MD) simulations were used to determine the compounds binding in the ERα complex. RESULTS We demonstrated that BPA and BPAF have agonistic activity for both ERα and ERβ, but BPS has ERα-selective specificity. We concluded that coregulators were differentially recruited in the presence of BPA, BPAF, or BPS. Interestingly, BPS recruited more corepressors when compared to BPA and BPAF. From a series of MD analysis, we concluded that BPA, BPAF, and BPS can bind to the ER-ligand-binding domain with differing energetics and conformations. In addition, the binding surface of coregulator interactions on ERα was characterized for the BPA, BPAF, and BPS complexes. CONCLUSION These findings further our understanding of the molecular mechanisms of EDCs, such as BPs, in ER-mediated transcriptional activation, biological activity, and their effects on physiological functions in human health. https://doi.org/10.1289/EHP2505.
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Affiliation(s)
- Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Laurel A Coons
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Katherine A Burns
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - J Tyler Ramsey
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Katherine E Pelch
- National Toxicology Program Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - René Houtman
- PamGene International B.V., NL-5211 HH 's-Hertogenbosch, Netherlands
| | | | - Christina T Teng
- National Toxicology Program Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Kenneth S Korach
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sawada T, Hilhorst R, Rangarajan S, Yoshida M, Tamura K, Beuningen RV, Ruijtenbeek R, Tsuda H, Koizumi F. Abstract 1792: Immune system pathway activation for prediction of the response to neoadjuvant chemotherapy in triple-negative breast cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Triple-negative breast cancer patients (TNBCs) who receive neoadjuvant chemotherapy (NAC) generally show a response to NAC, but about 5% experience progressive disease (PD). Although TNBCs that respond to NAC have been well-studied, reports about TNBCs with PD during NAC are absent. We aimed to compare kinase activity profiles of TNBCs of both groups to identify a biological predictor of NAC non-responders.
Methods: Tyrosine kinase activity profiles of lysates of fresh frozen cancer tissues from NAC non-responders and responders, the latter represented by TNBCs who did not receive NAC, were determined with a peptide microarray system (Cancer Res. 2009; 69(14):5987-95). Tumor infiltrating lymphocytes (TILs) were counted in these tissues.
Results: Among 740 TNBCs, 20 NAC non-responders were identified. For the 7 samples from PD confirmed patients and 10 TNBCs not receiving NAC, no correlation was observed between NAC response and age, menopausal status, tumor size or axillary lymph node status. Kinase activity measurements showed large differences in overall tyrosine kinase activity between responders and non-responders. 35 peptides had significantly (p < 0.05) higher phosphorylation in the responder group. Kinases that phosphorylate these peptides (upstream kinases) were identified from literature. Among others, the immune related kinases Zap70, Syk and JAK2 were identified as upstream kinases. Pathway analysis yielded evidence for increased activity in the responder group in immune-related pathways and in pathways involved in development and signal transduction. Responders had a significantly higher (p = 0.0053) TILs count.
Conclusion: Kinases related to the immune system are less activated in NAC non-responders. The low TILs count in the non-responders confirmed that activation of the immune system in non-responders is lower than in NAC responders. These data merit a further investigation of the use of kinase activity profiling either alone or in combination with TIL scoring for the prediction of the response to NAC in TNBC with a larger patient cohort.
Citation Format: Takeshi Sawada, Riet Hilhorst, Savithri Rangarajan, Masayuki Yoshida, Kenji Tamura, Rinie van Beuningen, Rob Ruijtenbeek, Hitoshi Tsuda, Fumiaki Koizumi. Immune system pathway activation for prediction of the response to neoadjuvant chemotherapy in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1792. doi:10.1158/1538-7445.AM2017-1792
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Affiliation(s)
- Takeshi Sawada
- 1Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Riet Hilhorst
- 2PamGene International BV, 's-Hertogenbosch, Netherlands
| | | | | | | | | | | | | | - Fumiaki Koizumi
- 1Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Murayama N, van Beuningen R, Suemizu H, Guillouzo CG, Shibata N, Yajima K, Utoh M, Shimizu M, Chesné C, Nakamura M, Guengerich FP, Houtman R, Yamazaki H. Thalidomide increases human hepatic cytochrome P450 3A enzymes by direct activation of the pregnane X receptor. Chem Res Toxicol 2014; 27:304-308. [PMID: 24460184 DOI: 10.1021/tx4004374] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heterotropic cooperativity of human cytochrome P450 (P450) 3A4/3A5 by the teratogen thalidomide was recently demonstrated by H. Yamazaki et al. ( ( 2013 ) Chem. Res. Toxicol. 26 , 486 - 489 ) using the model substrate midazolam in various in vitro and in vivo models. Chimeric mice with humanized liver also displayed enhanced midazolam clearance upon pretreatment with orally administered thalidomide, presumably because of human P450 3A induction. In the current study, we further investigated the regulation of human hepatic drug metabolizing enzymes. Thalidomide enhanced levels of P450 3A4 and 2B6 mRNA, protein expression, and/or oxidation activity in human hepatocytes, indirectly suggesting the activation of upstream transcription factors involved in detoxication, e.g., the nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR). A key event after ligand binding is an alteration of nuclear receptor conformation and recruitment of coregulator proteins that alter chromatin accessibility of target genes. To investigate direct engagement and functional alteration of PXR and CAR by thalidomide, we utilized a peptide microarray with 154 coregulator-derived nuclear receptor-interaction motifs and coregulator and nuclear receptor boxes, which serves as a sensor for nuclear receptor conformation and activity status as a function of ligand. Thalidomide and its human proximate metabolite 5-hydroxythalidomide displayed significant modulation of coregulator interaction with PXR and CAR ligand-binding domains, similar to established agonists for these receptors. These results collectively suggest that thalidomide acts as a ligand for PXR and CAR and causes enzyme induction leading to increased P450 enzyme activity. The possibilities of drug interactions during thalidomide therapy in humans require further evaluation.
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Yan JB, Xu M, Xiong C, Zhou DW, Ren ZR, Huang Y, Mommersteeg M, van Beuningen R, Wang YT, Liao SX, Zeng F, Wu Y, Zeng YT. Rapid screening for chromosomal aneuploidies using array-MLPA. BMC Med Genet 2011; 12:68. [PMID: 21575262 PMCID: PMC3111339 DOI: 10.1186/1471-2350-12-68] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/17/2011] [Indexed: 11/23/2022]
Abstract
Background Chromosome abnormalities, especially trisomy of chromosome 21, 13, or 18 as well as sex chromosome aneuploidy, are a well-established cause of pregnancy loss. Cultured cell karyotype analysis and FISH have been considered reliable detectors of fetal abnormality. However, results are usually not available for 3-4 days or more. Multiplex ligation-dependent probe amplification (MLPA) has emerged as an alternative rapid technique for detection of chromosome aneuploidies. However, conventional MLPA does not allow for relative quantification of more than 50 different target sequences in one reaction and does not detect mosaic trisomy. A multiplexed MLPA with more sensitive detection would be useful for fetal genetic screening. Methods We developed a method of array-based MLPA to rapidly screen for common aneuploidies. We designed 116 universal tag-probes covering chromosomes 13, 18, 21, X, and Y, and 8 control autosomal genes. We performed MLPA and hybridized the products on a 4-well flow-through microarray system. We determined chromosome copy numbers by analyzing the relative signals of the chromosome-specific probes. Results In a blind study of 161 peripheral blood and 12 amniotic fluid samples previously karyotyped, 169 of 173 (97.7%) including all the amniotic fluid samples were correctly identified by array-MLPA. Furthermore, we detected two chromosome X monosomy mosaic cases in which the mosaism rates estimated by array-MLPA were basically consistent with the results from karyotyping. Additionally, we identified five Y chromosome abnormalities in which G-banding could not distinguish their origins for four of the five cases. Conclusions Our study demonstrates the successful application and strong potential of array-MLPA in clinical diagnosis and prenatal testing for rapid and sensitive chromosomal aneuploidy screening. Furthermore, we have developed a simple and rapid procedure for screening copy numbers on chromosomes 13, 18, 21, X, and Y using array-MLPA.
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Affiliation(s)
- Jing-Bin Yan
- Institute of Medical Genetics, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai, P.R. China
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12
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Zeng F, Ren ZR, Huang SZ, Kalf M, Mommersteeg M, Smit M, White S, Jin CL, Xu M, Zhou DW, Yan JB, Chen MJ, van Beuningen R, Huang SZ, den Dunnen J, Zeng YT, Wu Y. Array-MLPA: comprehensive detection of deletions and duplications and its application to DMD patients. Hum Mutat 2008; 29:190-7. [PMID: 17854090 DOI: 10.1002/humu.20613] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Multiplex ligation-dependent probe amplification (MLPA) is widely used to screen genes of interest for deletions and duplications. Since MLPA is usually based on size-separation of the amplification products, the maximum number of target sequences that can be screened in parallel is usually limited to approximately 40. We report the design of a robust array-based MLPA format that uses amplification products of essentially uniform size (100-120 bp) and distinguishes between them by virtue of incorporated tag sequences. We were thus able to increase probe complexity to 124, with very uniform product yields and signals that have a low coefficient of variance. The assay designed was used to screen the largest set studied so far (249 patients) of unrelated Duchenne muscular dystrophy (DMD) cases from the Chinese population. In a blind study we correctly assigned 98% of the genotypes and detected rearrangements in 181 cases (73%); i.e., 163 deletions (65%), 13 duplications (5%), and five complex rearrangements (2%). Although this value is significantly higher for Chinese patients than previously reported, it is similar to that found for other populations. The location of the rearrangements (76% in the major deletion hotspot) is also in agreement with other findings. The 96-well flow-through microarray system used in this research provides high-throughput and speed; hybridization can be completed in 5 to 30 minutes. Since array processing and data analysis are fully automated, array-MLPA should be easy to implement in a standard diagnostic laboratory. The universal array can be used to analyze any tag-modified MLPA probe set.
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Affiliation(s)
- Fanyi Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, PR China
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13
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Wu Y, de Kievit P, Vahlkamp L, Pijnenburg D, Smit M, Dankers M, Melchers D, Stax M, Boender PJ, Ingham C, Bastiaensen N, de Wijn R, van Alewijk D, van Damme H, Raap AK, Chan AB, van Beuningen R. Quantitative assessment of a novel flow-through porous microarray for the rapid analysis of gene expression profiles. Nucleic Acids Res 2004; 32:e123. [PMID: 15333674 PMCID: PMC516077 DOI: 10.1093/nar/gnh118] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A novel microarray system that utilizes a porous aluminum-oxide substrate and flow-through incubation has been developed for rapid molecular biological testing. To assess its utility in gene expression analysis, we determined hybridization kinetics, variability, sensitivity and dynamic range of the system using amplified RNA. To show the feasibility with complex biological RNA, we subjected Jurkat cells to heat-shock treatment and analyzed the transcriptional regulation of 23 genes. We found that trends (regulation or no change) acquired on this platform are in good agreement with data obtained from real-time quantitative PCR and Affymetrix GeneChips. Additionally, the system demonstrates a linear dynamic range of 3 orders of magnitude and at least 10-fold decreased hybridization time compared to conventional microarrays. The minimum amount of transcript that could be detected in 20 microl volume is 2-5 amol, which enables the detection of 1 in 300,000 copies of a transcript in 1 microg of amplified RNA. Hybridization and subsequent analysis are completed within 2 h. Replicate hybridizations on 24 identical arrays with two complex biological samples revealed a mean coefficient of variation of 11.6%. This study shows the potential of flow-through porous microarrays for the rapid analysis of gene expression profiles in clinical applications.
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Affiliation(s)
- Ying Wu
- PamGene International BV, Nieuwstraat 30, PO Box 1345, 5200 BJ 's-Hertogenbosch, The Netherlands.
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van Beuningen R, van Damme H, Boender P, Bastiaensen N, Chan A, Kievits T. Fast and Specific Hybridization Using Flow-Through Microarrays on Porous Metal Oxide. Clin Chem 2001. [DOI: 10.1093/clinchem/47.10.1931] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Rinie van Beuningen
- PamGene B.V., Burgemeester Loeffplein 70a, 5211RX Den Bosch, The Netherlands
| | - Henk van Damme
- PamGene B.V., Burgemeester Loeffplein 70a, 5211RX Den Bosch, The Netherlands
| | - Piet Boender
- PamGene B.V., Burgemeester Loeffplein 70a, 5211RX Den Bosch, The Netherlands
| | - Niek Bastiaensen
- PamGene B.V., Burgemeester Loeffplein 70a, 5211RX Den Bosch, The Netherlands
| | - Alan Chan
- PamGene B.V., Burgemeester Loeffplein 70a, 5211RX Den Bosch, The Netherlands
| | - Tim Kievits
- PamGene B.V., Burgemeester Loeffplein 70a, 5211RX Den Bosch, The Netherlands
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