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Shukla V, Wang H, Varticovski L, Baek S, Wang R, Wu X, Echtenkamp F, Hernandez FV, Prothro KP, Gara SK, Zhang MR, Shiffka S, Raziuddin R, Neckers LM, Linehan WM, Chen H, Hager GL, Schrump DS. Genome-wide Analysis Identifies Nuclear Factor 1C as a Novel Transcription Factor and Potential Therapeutic Target in Small Cell Lung Cancer. J Thorac Oncol 2024:S1556-0864(24)00131-X. [PMID: 38583771 DOI: 10.1016/j.jtho.2024.03.023] [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: 10/31/2023] [Revised: 03/14/2024] [Accepted: 03/30/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND Recent insights regarding mechanisms mediating stemness, heterogeneity, and metastatic potential of lung cancers have yet to be fully translated to effective regimens for the treatment of these malignancies. This study sought to identify novel targets for lung cancer therapy. METHODS Transcriptomes and DNA methylomes of 14 SCLC and 10 NSCLC lines were compared to normal human small airway epithelial cells (SAEC) and induced pluripotent stem cell (iPSC) clones derived from SAEC. SCLC lines, lung iPSC (Lu-iPSC), and SAEC were further evaluated by DNase I hypersensitivity (DHS-seq). Changes in chromatin accessibility and depths of transcription factor (TF) footprints were quantified using Bivariate analysis of Genomic Footprint. Standard techniques were used to examine growth and tumorigenencity as well as changes in transcriptomes and glucose metabolism of SCLC cells following Nuclear Factor 1C (NFIC) knockdown, and to examine NFIC expression in SCLC cells following exposure to BET inhibitors. RESULTS Significant commonality of transcriptomes and DNA methylomes was observed between Lu-iPSC and SCLC; however, this analysis was uninformative regarding pathways unique to lung cancer. Linking results of DNase-seq to RNA-seq enabled identification of networks not previously associated with SCLC. When combined with footprint depth, NFIC, a transcription factor not previously associated with SCLC, had the highest score of occupancy at open chromatin sites. Knockdown of NFIC impaired glucose metabolism, decreased stemness, and inhibited growth of SCLC cells in-vitro and in-vivo. ChIP-seq analysis identified numerous sites occupied by Bromodomain-containing protein 4 (BRD4) in the NFIC promoter region. Knock-down of BRD4 or treatment with Bromodomain and extra-terminal domain (BET) inhibitors (BETi) markedly reduced NFIC expression in SCLC cells and SCLC PDX models. Approximately 8% of genes downregulated by BETi treatment were repressed by NFIC knockdown in SCLC, while 34% of genes repressed following NFIC knockdown were also downregulated in SCLC cells following BETi treatment. CONCLUSIONS NFIC is a key TF and possible mediator of transcriptional regulation by BET family proteins in SCLC. Our findings highlight the potential of genome-wide chromatin accessibility analysis for elucidating mechanisms of pulmonary carcinogenesis and identifying novel targets for lung cancer therapy.
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Affiliation(s)
- Vivek Shukla
- Thoracic Epigenetics Section, Thoracic Surgery Branch
| | - Haitao Wang
- Thoracic Epigenetics Section, Thoracic Surgery Branch
| | | | | | - Ruihong Wang
- Thoracic Epigenetics Section, Thoracic Surgery Branch
| | - Xinwei Wu
- Thoracic Epigenetics Section, Thoracic Surgery Branch
| | | | | | | | | | - Mary R Zhang
- Thoracic Epigenetics Section, Thoracic Surgery Branch
| | | | | | | | | | - Haobin Chen
- Thoracic Epigenetics Section, Thoracic Surgery Branch
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Stavreva DA, Varticovski L, Raziuddin R, Pegoraro G, Schiltz RL, Hager GL. Novel biosensor for high-throughput detection of progesterone receptor-interacting endocrine disruptors. Sci Rep 2024; 14:5567. [PMID: 38448539 PMCID: PMC10917811 DOI: 10.1038/s41598-024-55254-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
Progesterone receptor (PR)-interacting compounds in the environment are associated with serious health hazards. However, methods for their detection in environmental samples are cumbersome. We report a sensitive activity-based biosensor for rapid and reliable screening of progesterone receptor (PR)-interacting endocrine disrupting chemicals (EDCs). The biosensor is a cell line which expresses nuclear mCherry-NF1 and a green fluorescent protein (GFP)-tagged chimera of glucocorticoid receptor (GR) N terminus fused to the ligand binding domain (LBD) of PR (GFP-GR-PR). As this LBD is shared by the PRA and PRB, the biosensor reports on the activation of both PR isoforms. This GFP-GR-PR chimera is cytoplasmic in the absence of hormone and translocates rapidly to the nucleus in response to PR agonists or antagonists in concentration- and time-dependent manner. In live cells, presence of nuclear NF1 label eliminates cell fixation and nuclear staining resulting in efficient screening. The assay can be used in screens for novel PR ligands and PR-interacting contaminants in environmental samples. A limited screen of river water samples indicated a widespread, low-level contamination with PR-interacting contaminants in all tested samples.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, 41 Medlars Dr., Bethesda, MD, 20892-5055, USA.
| | - Lyuba Varticovski
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, 41 Medlars Dr., Bethesda, MD, 20892-5055, USA
| | - Razi Raziuddin
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, 41 Medlars Dr., Bethesda, MD, 20892-5055, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, 41 Medlars Dr., Bethesda, MD, 20892-5055, USA
| | - R Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, 41 Medlars Dr., Bethesda, MD, 20892-5055, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, 41 Medlars Dr., Bethesda, MD, 20892-5055, USA.
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Fettweis G, Johnson TA, Almeida‐Prieto B, Weller‐Pérez J, Presman DM, Hager GL, Alvarez de la Rosa D. The mineralocorticoid receptor forms higher order oligomers upon DNA binding. Protein Sci 2024; 33:e4890. [PMID: 38160317 PMCID: PMC10868434 DOI: 10.1002/pro.4890] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/30/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
The prevailing model of steroid hormone nuclear receptor function assumes ligand-induced homodimer formation followed by binding to DNA hormone response elements (HREs). This model has been challenged by evidence showing that the glucocorticoid receptor (GR) forms tetramers upon ligand and DNA binding, which then drive receptor-mediated gene transactivation and transrepression. GR and the closely-related mineralocorticoid receptors (MR) interact to transduce corticosteroid hormone signaling, but whether they share the same quaternary arrangement is unknown. Here, we used a fluorescence imaging technique, Number & Brightness, to study oligomerization in a cell system allowing real-time analysis of receptor-DNA interactions. Agonist-bound MR forms tetramers in the nucleoplasm and higher order oligomers upon binding to HREs. Antagonists form intermediate-size quaternary arrangements, suggesting that large oligomers are essential for function. Divergence between MR and GR quaternary structure is driven by different functionality of known and new multimerization interfaces, which does not preclude formation of heteromers. Thus, influencing oligomerization may be important to selectively modulate corticosteroid signaling.
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Affiliation(s)
- Gregory Fettweis
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
- Present address:
Laboratory of Gene Expression and Cancer, GIGA‐Molecular Biology of DiseaseUniversity of LiègeLiègeBelgium
| | - Thomas A. Johnson
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Brian Almeida‐Prieto
- Departmento de Ciencias Médicas Básicas and Instituto de Tecnologías BiomédicasUniversidad de La LagunaLa LagunaSpain
| | - Julián Weller‐Pérez
- Departmento de Ciencias Médicas Básicas and Instituto de Tecnologías BiomédicasUniversidad de La LagunaLa LagunaSpain
| | - Diego M. Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET‐Universidad de Buenos AiresFacultad de Ciencias Exactas y NaturalesBuenos AiresArgentina
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Diego Alvarez de la Rosa
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
- Departmento de Ciencias Médicas Básicas and Instituto de Tecnologías BiomédicasUniversidad de La LagunaLa LagunaSpain
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Abstract
Cells must tightly regulate their gene expression programs and yet rapidly respond to acute biochemical and biophysical cues within their environment. This information is transmitted to the nucleus through various signaling cascades, culminating in the activation or repression of target genes. Transcription factors (TFs) are key mediators of these signals, binding to specific regulatory elements within chromatin. While live-cell imaging has conclusively proven that TF-chromatin interactions are highly dynamic, how such transient interactions can have long-term impacts on developmental trajectories and disease progression is still largely unclear. In this review, we summarize our current understanding of the dynamic nature of TF functions, starting with a historical overview of early live-cell experiments. We highlight key factors that govern TF dynamics and how TF dynamics, in turn, affect downstream transcriptional bursting. Finally, we conclude with open challenges and emerging technologies that will further our understanding of transcriptional regulation.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
- Department of Physics, University of Maryland, College Park, Maryland, USA;
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, Maryland, USA;
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; , ,
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Abstract
The human genome is organized into multiple structural layers, ranging from chromosome territories to progressively smaller substructures, such as topologically associating domains (TADs) and chromatin loops. These substructures, collectively referred to as long-range chromatin interactions (LRIs), have a significant role in regulating gene expression. TADs are regions of the genome that harbour groups of genes and regulatory elements that frequently interact with each other and are insulated from other regions, thereby preventing widespread uncontrolled DNA contacts. Chromatin loops formed within TADs through enhancer and promoter interactions are elastic, allowing transcriptional heterogeneity and stochasticity. Over the past decade, it has become evident that the 3D genome structure, also referred to as the chromatin architecture, is central to many transcriptional cellular decisions. In this Review, we delve into the intricate relationship between steroid receptors and LRIs, discussing how steroid receptors interact with and modulate these chromatin interactions. Genetic alterations in the many processes involved in organizing the nuclear architecture are often associated with the development of hormone-dependent cancers. A better understanding of the interplay between architectural proteins and hormone regulatory networks can ultimately be exploited to develop improved approaches for cancer treatment.
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Affiliation(s)
- Theophilus T Tettey
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA.
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Nigam N, Bernard B, Sevilla S, Kim S, Dar MS, Tsai D, Robbins Y, Burkitt K, Sievers C, Allen CT, Bennett RL, Tettey TT, Carter B, Rinaldi L, Lingen MW, Sater H, Edmondson EF, Moshiri A, Saeed A, Cheng H, Luo X, Brennan K, Koparde V, Chen C, Das S, Andresson T, Abdelmaksoud A, Murali M, Sakata S, Takeuchi K, Chari R, Nakamura Y, Uppaluri R, Sunwoo JB, Van Waes C, Licht JD, Hager GL, Saloura V. SMYD3 represses tumor-intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck. Cell Rep 2023; 42:112823. [PMID: 37463106 PMCID: PMC10407766 DOI: 10.1016/j.celrep.2023.112823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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] [Received: 09/30/2022] [Revised: 04/03/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Cancers often display immune escape, but the mechanisms are incompletely understood. Herein, we identify SMYD3 as a mediator of immune escape in human papilloma virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC), an aggressive disease with poor response to immunotherapy with pembrolizumab. SMYD3 depletion induces upregulation of multiple type I interferon (IFN) response and antigen presentation machinery genes in HNSCC cells. Mechanistically, SMYD3 binds to and regulates the transcription of UHRF1, encoding for a reader of H3K9me3, which binds to H3K9me3-enriched promoters of key immune-related genes, recruits DNMT1, and silences their expression. SMYD3 further maintains the repression of immune-related genes through intragenic deposition of H4K20me3. In vivo, Smyd3 depletion induces influx of CD8+ T cells and increases sensitivity to anti-programmed death 1 (PD-1) therapy. SMYD3 overexpression is associated with decreased CD8 T cell infiltration and poor response to neoadjuvant pembrolizumab. These data support combining SMYD3 depletion strategies with checkpoint blockade to overcome anti-PD-1 resistance in HPV-negative HNSCC.
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Affiliation(s)
- Nupur Nigam
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Benjamin Bernard
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Samantha Sevilla
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD 20892, USA
| | - Mohd Saleem Dar
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Daniel Tsai
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Yvette Robbins
- Translational Tumor Immunology Program, NIDCD, NIH, Bethesda, MD 20892, USA
| | - Kyunghee Burkitt
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Cem Sievers
- Translational Tumor Immunology Program, NIDCD, NIH, Bethesda, MD 20892, USA
| | - Clint T Allen
- Translational Tumor Immunology Program, NIDCD, NIH, Bethesda, MD 20892, USA
| | | | - Theophilus T Tettey
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD 20892, USA
| | - Benjamin Carter
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD 20892, USA
| | - Mark W Lingen
- University of Chicago, Department of Pathology, Chicago, IL 60637, USA
| | - Houssein Sater
- GU Malignancies Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Elijah F Edmondson
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, NIH, Frederick, MD 21702, USA
| | - Arfa Moshiri
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Abbas Saeed
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Hui Cheng
- National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Xiaolin Luo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Kevin Brennan
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vishal Koparde
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Chen Chen
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD 21702, USA
| | - Abdalla Abdelmaksoud
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Madhavi Murali
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Seiji Sakata
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan; Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan; Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan; Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Yusuke Nakamura
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
| | | | - John B Sunwoo
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carter Van Waes
- National Institute of Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | | | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD 20892, USA
| | - Vassiliki Saloura
- Thoracic and GI Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
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Johnson TA, Fettweis G, Wagh K, Almeida-Prieto B, Krishnamurthy M, Upadhyaya A, Hager GL, Alvarez de la Rosa D. The Glucocorticoid Receptor is Required for Efficient Aldosterone-Induced Transcription by the Mineralocorticoid Receptor. bioRxiv 2023:2023.01.26.525745. [PMID: 36789429 PMCID: PMC9928040 DOI: 10.1101/2023.01.26.525745] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The glucocorticoid and mineralocorticoid receptors (GR and MR, respectively) have distinct, yet overlapping physiological and pathophysiological functions. There are indications that both receptors interact functionally and physically, but the precise role of this interdependence is poorly understood. Here, we analyzed the impact of GR co-expression on MR genome-wide chromatin binding and transcriptional responses to aldosterone and glucocorticoids, both physiological ligands of this receptor. Our data show that GR co-expression alters MR genome-wide binding to consensus DNA sequences in a locus- and ligand-specific way. MR binding to consensus DNA sequences is affected by GR. Transcriptional responses of MR in the absence of GR are weak and show poor correlation with chromatin binding. In contrast, co-expression of GR potentiates MR-mediated transcription, particularly in response to aldosterone. Finally, single-molecule tracking of MR suggests that the presence of GR contributes to productive binding of MR/aldosterone complexes to chromatin. Together, our data indicate that co-expression of GR potentiates aldosterone-mediated MR transcriptional activity, even in the absence of glucocorticoids.
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Affiliation(s)
- Thomas A. Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD, USA
| | - Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD, USA
- Department of Physics, University of Maryland, College Park, 4296 Stadium Drive, College Park, MD, USA
| | - Brian Almeida-Prieto
- Departamento de Ciencias Médicas Básicas and Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Campus de Ciencias de la Salud sn, 38200 San Cristóbal de La Laguna, Spain
| | - Manan Krishnamurthy
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, 4296 Stadium Drive, College Park, MD, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD, USA
| | - Diego Alvarez de la Rosa
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD, USA
- Departamento de Ciencias Médicas Básicas and Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Campus de Ciencias de la Salud sn, 38200 San Cristóbal de La Laguna, Spain
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Wagh K, Stavreva DA, Jensen RAM, Paakinaho V, Fettweis G, Schiltz RL, Wüstner D, Mandrup S, Presman DM, Upadhyaya A, Hager GL. Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states. Sci Adv 2023; 9:eade1122. [PMID: 37315128 PMCID: PMC10954219 DOI: 10.1126/sciadv.ade1122] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/25/2022] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
How chromatin dynamics relate to transcriptional activity remains poorly understood. Using single-molecule tracking, coupled with machine learning, we show that histone H2B and multiple chromatin-bound transcriptional regulators display two distinct low-mobility states. Ligand activation results in a marked increase in the propensity of steroid receptors to bind in the lowest-mobility state. Mutational analysis revealed that interactions with chromatin in the lowest-mobility state require an intact DNA binding domain and oligomerization domains. These states are not spatially separated as previously believed, but individual H2B and bound-TF molecules can dynamically switch between them on time scales of seconds. Single bound-TF molecules with different mobilities exhibit different dwell time distributions, suggesting that the mobility of TFs is intimately coupled with their binding dynamics. Together, our results identify two unique and distinct low-mobility states that appear to represent common pathways for transcription activation in mammalian cells.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Diana A. Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rikke A. M. Jensen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Institute of Biomedicine, University of Eastern Finland, Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - R. Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Diego M. Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Fettweis G, Johnson TA, Almeida-Prieto B, Presman DM, Hager GL, Alvarez de la Rosa D. The mineralocorticoid receptor forms higher order oligomers upon DNA binding. bioRxiv 2023:2023.01.26.525752. [PMID: 36789424 PMCID: PMC9928021 DOI: 10.1101/2023.01.26.525752] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The prevailing model of steroid hormone nuclear receptor function assumes ligand-induced homodimer formation followed by binding to DNA hormone response elements (HREs). This model has been challenged by evidence showing that the glucocorticoid receptor (GR) forms tetramers upon ligand and DNA binding, which then drive receptor-mediated gene transactivation and transrepression. GR and the closely-related mineralocorticoid receptors (MR) interact to transduce corticosteroid hormone signaling, but whether they share the same quaternary arrangement is unknown. Here, we used a fluorescence imaging technique, Number & Brightness, to study oligomerization in a cell system allowing real-time analysis of receptor-DNA interactions. Agonist-bound MR forms tetramers in the nucleoplasm and higher order oligomers upon binding to HREs. Antagonists form intermediate quaternary arrangements, suggesting that large oligomers are essential for function. Divergence between MR and GR quaternary structure is driven by different functionality of known and new multimerization interfaces, which does not preclude formation of heteromers. Thus, influencing oligomerization may be important to selectively modulate corticosteroid signaling.
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Affiliation(s)
- Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
| | - Thomas A. Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
| | - Brian Almeida-Prieto
- Departmento de Ciencias Médicas Básicas and Instituto de Tecnologías Biomédicas, Universidad de La Laguna, La Laguna 38200, Spain
| | - Diego M. Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
| | - Diego Alvarez de la Rosa
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
- Departmento de Ciencias Médicas Básicas and Instituto de Tecnologías Biomédicas, Universidad de La Laguna, La Laguna 38200, Spain
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10
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Bradley PM, Kolpin DW, Thompson DA, Romanok KM, Smalling KL, Breitmeyer SE, Cardon MC, Cwiertny DM, Evans N, Field RW, Focazio MJ, Beane Freeman LE, Givens CE, Gray JL, Hager GL, Hladik ML, Hofmann JN, Jones RR, Kanagy LK, Lane RF, McCleskey RB, Medgyesi D, Medlock-Kakaley EK, Meppelink SM, Meyer MT, Stavreva DA, Ward MH. Juxtaposition of intensive agriculture, vulnerable aquifers, and mixed chemical/microbial exposures in private-well tapwater in northeast Iowa. Sci Total Environ 2023; 868:161672. [PMID: 36657670 PMCID: PMC9976626 DOI: 10.1016/j.scitotenv.2023.161672] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
In the United States and globally, contaminant exposure in unregulated private-well point-of-use tapwater (TW) is a recognized public-health data gap and an obstacle to both risk-management and homeowner decision making. To help address the lack of data on broad contaminant exposures in private-well TW from hydrologically-vulnerable (alluvial, karst) aquifers in agriculturally-intensive landscapes, samples were collected in 2018-2019 from 47 northeast Iowa farms and analyzed for 35 inorganics, 437 unique organics, 5 in vitro bioassays, and 11 microbial assays. Twenty-six inorganics and 51 organics, dominated by pesticides and related transformation products (35 herbicide-, 5 insecticide-, and 2 fungicide-related), were observed in TW. Heterotrophic bacteria detections were near ubiquitous (94 % of the samples), with detection of total coliform bacteria in 28 % of the samples and growth on at least one putative-pathogen selective media across all TW samples. Health-based hazard index screening levels were exceeded frequently in private-well TW and attributed primarily to inorganics (nitrate, uranium). Results support incorporation of residential treatment systems to protect against contaminant exposure and the need for increased monitoring of rural private-well homes. Continued assessment of unmonitored and unregulated private-supply TW is needed to model contaminant exposures and human-health risks.
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Affiliation(s)
| | | | | | | | | | | | - Mary C Cardon
- U.S. Environmental Protection Agency, Durham, NC, USA
| | | | - Nicola Evans
- U.S. Environmental Protection Agency, Durham, NC, USA
| | | | | | | | | | | | | | | | | | - Rena R Jones
- National Cancer Institute/NIH, Rockville, MD, USA
| | | | | | | | | | | | | | | | | | - Mary H Ward
- National Cancer Institute/NIH, Rockville, MD, USA
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11
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Pongor LS, Schultz CW, Rinaldi L, Wangsa D, Redon CE, Takahashi N, Fialkoff G, Desai P, Zhang Y, Burkett S, Hermoni N, Vilk N, Gutin J, Gergely R, Zhao Y, Nichols S, Vilimas R, Sciuto L, Graham C, Caravaca JM, Turan S, Tsai-Wei S, Rajapakse VN, Kumar R, Upadhyay D, Kumar S, Kim YS, Roper N, Tran B, Hewitt SM, Kleiner DE, Aladjem MI, Friedman N, Hager GL, Pommier Y, Ried T, Thomas A. Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes. Cancer Discov 2023; 13:928-949. [PMID: 36715552 PMCID: PMC10073312 DOI: 10.1158/2159-8290.cd-22-0796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/10/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Small-cell lung cancer (SCLC) is an aggressive neuroendocrine lung cancer. Oncogenic MYC amplifications drive SCLC heterogeneity, but the genetic mechanisms of MYC amplification and phenotypic plasticity, characterized by neuroendocrine and nonneuroendocrine cell states, are not known. Here, we integrate whole-genome sequencing, long-range optical mapping, single-cell DNA sequencing, and fluorescence in situ hybridization to find extrachromosomal DNA (ecDNA) as a primary source of SCLC oncogene amplifications and driver fusions. ecDNAs bring to proximity enhancer elements and oncogenes, creating SCLC transcription-amplifying units, driving exceptionally high MYC gene dosage. We demonstrate that cell-free nucleosome profiling can noninvasively detect ecDNA amplifications in plasma, facilitating its genome-wide interrogation in SCLC and other cancers. Altogether, our work provides the first comprehensive map of SCLC ecDNA and describes a new mechanism that governs MYC-driven SCLC heterogeneity. ecDNA-enabled transcriptional flexibility may explain the significantly worse survival outcomes of SCLC harboring complex ecDNA amplifications. SIGNIFICANCE MYC drives SCLC progression, but the genetic basis of MYC-driven SCLC evolution is unknown. Using SCLC as a paradigm, we report how ecDNA amplifications function as MYC-amplifying units, fostering tumor plasticity and a high degree of tumor heterogeneity. This article is highlighted in the In This Issue feature, p. 799.
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Affiliation(s)
- Lőrinc Sándor Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- HCEMM Cancer Genomics and Epigenetics Research Group, Szeged, Hungary
| | - Christopher W Schultz
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Nobuyuki Takahashi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Gavriel Fialkoff
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Parth Desai
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yang Zhang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sandra Burkett
- Molecular Cytogenetic Core Facility, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Nadav Hermoni
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- School of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Noa Vilk
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- School of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jenia Gutin
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rona Gergely
- Department of Biochemistry and Molecular Pharmacology, NYU, New York, New York
- Laura and Isaac Perlmutter NYU Cancer Center, New York, New York
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, New York
| | - Yongmei Zhao
- Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Samantha Nichols
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Rasa Vilimas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Linda Sciuto
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Chante Graham
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Juan Manuel Caravaca
- Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Sevilay Turan
- Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Shen Tsai-Wei
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, New York
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Rajesh Kumar
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Deep Upadhyay
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Suresh Kumar
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yoo Sun Kim
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Nitin Roper
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Bao Tran
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Stephen M Hewitt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David E Kleiner
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- School of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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12
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Bissa M, Kim S, Galli V, Fourati S, Sarkis S, Arakelyan A, de Castro IS, Rahman MA, Fujiwara S, Vaccari M, Tomalka JA, Stamos JD, Schifanella L, Gorini G, Moles R, Gutowska A, Ferrari G, Lobanov A, Montefiori DC, Nelson GW, Cam MC, Chakhtoura M, Haddad EK, Doster MN, McKinnon K, Brown S, Venzon DJ, Choo-Wosoba H, Breed MW, Killoran KE, Kramer J, Margolis L, Sekaly RP, Hager GL, Franchini G. HIV vaccine candidate efficacy in female macaques mediated by cAMP-dependent efferocytosis and V2-specific ADCC. Nat Commun 2023; 14:575. [PMID: 36732510 PMCID: PMC9894672 DOI: 10.1038/s41467-023-36109-8] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 01/15/2023] [Indexed: 02/04/2023] Open
Abstract
The development of an effective vaccine to protect against HIV acquisition will be greatly bolstered by in-depth understanding of the innate and adaptive responses to vaccination. We report here that the efficacy of DNA/ALVAC/gp120/alum vaccines, based on V2-specific antibodies mediating apoptosis of infected cells (V2-ADCC), is complemented by efferocytosis, a cyclic AMP (cAMP)-dependent antiphlogistic engulfment of apoptotic cells by CD14+ monocytes. Central to vaccine efficacy is the engagement of the CCL2/CCR2 axis and tolerogenic dendritic cells producing IL-10 (DC-10). Epigenetic reprogramming in CD14+ cells of the cyclic AMP/CREB pathway and increased systemic levels of miRNA-139-5p, a negative regulator of expression of the cAMP-specific phosphodiesterase PDE4D, correlated with vaccine efficacy. These data posit that efferocytosis, through the prompt and effective removal of apoptotic infected cells, contributes to vaccine efficacy by decreasing inflammation and maintaining tissue homeostasis.
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Affiliation(s)
- Massimiliano Bissa
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA.
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Veronica Galli
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Slim Fourati
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Pathology, Emory University, Atlanta, GA, USA
| | - Sarkis Sarkis
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Anush Arakelyan
- Section on Intercellular Interactions, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - Mohammad Arif Rahman
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Saori Fujiwara
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Monica Vaccari
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
- Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Jeffrey A Tomalka
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Pathology, Emory University, Atlanta, GA, USA
| | - James D Stamos
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Luca Schifanella
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Giacomo Gorini
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Ramona Moles
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Anna Gutowska
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Guido Ferrari
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Alexei Lobanov
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - David C Montefiori
- Division of Surgical Sciences, Duke University School of Medicine, Durham, NC, USA
| | - George W Nelson
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Margaret C Cam
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Marita Chakhtoura
- Department of Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Elias K Haddad
- Department of Medicine, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Melvin N Doster
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Katherine McKinnon
- Vaccine Branch Flow Cytometry Core, National Cancer Institute, Bethesda, MD, USA
| | - Sophia Brown
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
- Vaccine Branch Flow Cytometry Core, National Cancer Institute, Bethesda, MD, USA
| | - David J Venzon
- Biostatistics and Data Management Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hyoyoung Choo-Wosoba
- Biostatistics and Data Management Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Matthew W Breed
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD, USA
| | - Kristin E Killoran
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD, USA
| | - Joshua Kramer
- Laboratory Animal Sciences Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD, USA
| | - Leonid Margolis
- Section on Intercellular Interactions, Eunice Kennedy-Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Rafick P Sekaly
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- Department of Pathology, Emory University, Atlanta, GA, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA.
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13
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Stubbs FE, Flynn BP, Rivers CA, Birnie MT, Herman A, Swinstead EE, Baek S, Fang H, Temple J, Carroll JS, Hager GL, Lightman SL, Conway-Campbell BL. Identification of a novel GR-ARID1a-P53BP1 protein complex involved in DNA damage repair and cell cycle regulation. Oncogene 2022; 41:5347-5360. [PMID: 36344675 PMCID: PMC9734058 DOI: 10.1038/s41388-022-02516-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022]
Abstract
ARID1a (BAF250), a component of human SWI/SNF chromatin remodeling complexes, is frequently mutated across numerous cancers, and its loss of function has been putatively linked to glucocorticoid resistance. Here, we interrogate the impact of siRNA knockdown of ARID1a compared to a functional interference approach in the HeLa human cervical cancer cell line. We report that ARID1a knockdown resulted in a significant global decrease in chromatin accessibility in ATAC-Seq analysis, as well as affecting a subset of genome-wide GR binding sites determined by analyzing GR ChIP-Seq data. Interestingly, the specific effects on gene expression were limited to a relatively small subset of glucocorticoid-regulated genes, notably those involved in cell cycle regulation and DNA repair. The vast majority of glucocorticoid-regulated genes were largely unaffected by ARID1a knockdown or functional interference, consistent with a more specific role for ARID1a in glucocorticoid function than previously speculated. Using liquid chromatography-mass spectrometry, we have identified a chromatin-associated protein complex comprising GR, ARID1a, and several DNA damage repair proteins including P53 binding protein 1 (P53BP1), Poly(ADP-Ribose) Polymerase 1 (PARP1), DNA damage-binding protein 1 (DDB1), DNA mismatch repair protein MSH6 and splicing factor proline and glutamine-rich protein (SFPQ), as well as the histone acetyltransferase KAT7, an epigenetic regulator of steroid-dependent transcription, DNA damage repair and cell cycle regulation. Not only was this protein complex ablated with both ARID1a knockdown and functional interference, but spontaneously arising DNA damage was also found to accumulate in a manner consistent with impaired DNA damage repair mechanisms. Recovery from dexamethasone-dependent cell cycle arrest was also significantly impaired. Taken together, our data demonstrate that although glucocorticoids can still promote cell cycle arrest in the absence of ARID1a, the purpose of this arrest to allow time for DNA damage repair is hindered.
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Affiliation(s)
- Felicity E Stubbs
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, US National Institutes of Health, 41 Medlars Drive, Bethesda, MD, 20892, USA
| | - Benjamin P Flynn
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
| | - Caroline A Rivers
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
| | - Matthew T Birnie
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
| | - Andrew Herman
- Flow Cytometry Facility, Faculty of Life Sciences, School of Cellular & Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Erin E Swinstead
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, US National Institutes of Health, 41 Medlars Drive, Bethesda, MD, 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, US National Institutes of Health, 41 Medlars Drive, Bethesda, MD, 20892, USA
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jillian Temple
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, US National Institutes of Health, 41 Medlars Drive, Bethesda, MD, 20892, USA
| | - Stafford L Lightman
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK
| | - Becky L Conway-Campbell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, Translational Health Sciences, Faculty of Health Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1 3NY, UK.
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14
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Ren G, Lai B, Harly C, Baek S, Ding Y, Zheng M, Cao Y, Cui K, Yang Y, Zhu J, Hager GL, Bhandoola A, Zhao K. Transcription factors TCF-1 and GATA3 are key factors for the epigenetic priming of early innate lymphoid progenitors toward distinct cell fates. Immunity 2022; 55:1402-1413.e4. [PMID: 35882235 PMCID: PMC9393082 DOI: 10.1016/j.immuni.2022.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022]
Abstract
The differentiation of innate lymphoid cells (ILCs) from hematopoietic stem cells needs to go through several multipotent progenitor stages. However, it remains unclear whether the fates of multipotent progenitors are predefined by epigenetic states. Here, we report the identification of distinct accessible chromatin regions in all lymphoid progenitors (ALPs), EILPs, and ILC precursors (ILCPs). Single-cell MNase-seq analyses revealed that EILPs contained distinct subpopulations epigenetically primed toward either dendritic cell lineages or ILC lineages. We found that TCF-1 and GATA3 co-bound to the lineage-defining sites for ILCs (LDS-Is), whereas PU.1 binding was enriched in the LDSs for alternative dendritic cells (LDS-As). TCF-1 and GATA3 were indispensable for the epigenetic priming of LDSs at the EILP stage. Our results suggest that the multipotency of progenitor cells is defined by the existence of a heterogeneous population of cells epigenetically primed for distinct downstream lineages, which are regulated by key transcription factors.
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Affiliation(s)
- Gang Ren
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA; Northwest Agriculture and Forest University, College of Animal Science and Technology, Yangling, Shaanxi 712100, China
| | - Binbin Lai
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA; Biomedical Engineering Department, Peking University, Beijing 100191, China; Department of Dermatology and Venereology, Peking University First Hospital, Beijing 100034, China
| | - Christelle Harly
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Ding
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mingzhu Zheng
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Department of Microbiology and Immunology, School of Medicine, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yaqiang Cao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Yu Yang
- Biomedical Engineering Department, Peking University, Beijing 100191, China; Department of Dermatology and Venereology, Peking University First Hospital, Beijing 100034, China
| | - Jinfang Zhu
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA.
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15
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Rinaldi L, Fettweis G, Kim S, Garcia DA, Fujiwara S, Johnson TA, Tettey TT, Ozbun L, Pegoraro G, Puglia M, Blagoev B, Upadhyaya A, Stavreva DA, Hager GL. The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation. Sci Adv 2022; 8:eabj8360. [PMID: 35353576 PMCID: PMC8967222 DOI: 10.1126/sciadv.abj8360] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 02/07/2022] [Indexed: 05/13/2023]
Abstract
The cohesin complex is central to chromatin looping, but mechanisms by which these long-range chromatin interactions are formed and persist remain unclear. We demonstrate that interactions between a transcription factor (TF) and the cohesin loader NIPBL regulate enhancer-dependent gene activity. Using mass spectrometry, genome mapping, and single-molecule tracking methods, we demonstrate that the glucocorticoid (GC) receptor (GR) interacts with NIPBL and the cohesin complex at the chromatin level, promoting loop extrusion and long-range gene regulation. Real-time single-molecule experiments show that loss of cohesin markedly diminishes the concentration of TF molecules at specific nuclear confinement sites, increasing TF local concentration and promoting gene regulation. Last, patient-derived acute myeloid leukemia cells harboring cohesin mutations exhibit a reduced response to GCs, suggesting that the GR-NIPBL-cohesin interaction is defective in these patients, resulting in poor response to GC treatment.
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Affiliation(s)
- Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A. Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Saori Fujiwara
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas A. Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Theophilus T. Tettey
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laurent Ozbun
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD 20892, USA
| | - Michele Puglia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Diana A. Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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16
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Varticovski L, Stavreva DA, McGowan A, Raziuddin R, Hager GL. Endocrine disruptors of sex hormone activities. Mol Cell Endocrinol 2022; 539:111415. [PMID: 34339825 PMCID: PMC8762672 DOI: 10.1016/j.mce.2021.111415] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022]
Abstract
Sex hormones, such as androgens, estrogens and progestins are naturally occurring compounds that tightly regulate endocrine systems in a variety of living organisms. Uncontrolled environmental exposure to these hormones or their biological and synthetic mimetics has been widely documented. Furthermore, water contaminants penetrate soil to affect flora, fauna and ultimately humans. Because endocrine systems evolved to respond to very small changes in hormone levels, the low levels found in the environment cannot be ignored. The combined actions of sex hormones with glucocorticoids and other nuclear receptors disruptors creates additional level of complexity including the newly described "dynamic assisted loading" mechanism. We reviewed the extensive literature pertaining to world-wide detection of these disruptors and created a detailed Table on the development and current status of methods used for their analysis.
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Affiliation(s)
- L Varticovski
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - D A Stavreva
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A McGowan
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - R Raziuddin
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - G L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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17
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Amin R, Shukla A, Zhu JJ, Kim S, Wang P, Tian SZ, Tran AD, Paul D, Cappell SD, Burkett S, Liu H, Lee MP, Kruhlak MJ, Dwyer JE, Simpson RM, Hager GL, Ruan Y, Hunter KW. Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response. Nat Commun 2021; 12:7216. [PMID: 34903738 PMCID: PMC8669001 DOI: 10.1038/s41467-021-27451-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022] Open
Abstract
Mechanical signals from the extracellular microenvironment have been implicated in tumor and metastatic progression. Here, we identify nucleoporin NUP210 as a metastasis susceptibility gene for human estrogen receptor positive (ER+) breast cancer and a cellular mechanosensor. Nup210 depletion suppresses lung metastasis in mouse models of breast cancer. Mechanistically, NUP210 interacts with LINC complex protein SUN2 which connects the nucleus to the cytoskeleton. In addition, the NUP210/SUN2 complex interacts with chromatin via the short isoform of BRD4 and histone H3.1/H3.2 at the nuclear periphery. In Nup210 knockout cells, mechanosensitive genes accumulate H3K27me3 heterochromatin modification, mediated by the polycomb repressive complex 2 and differentially reposition within the nucleus. Transcriptional repression in Nup210 knockout cells results in defective mechanotransduction and focal adhesion necessary for their metastatic capacity. Our study provides an important role of nuclear pore protein in cellular mechanosensation and metastasis. The involvement of nuclear pore proteins in cellular mechanosensing and metastasis is unclear. Here the authors identify that nuclear pore protein NUP210 promotes metastasis through the interaction with mechanotransducer LINC complex protein and chromatin to regulate mechanosensitive genes.
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Affiliation(s)
- Ruhul Amin
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - Anjali Shukla
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Andy D Tran
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,Confocal Microscopy Core Facility, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Debasish Paul
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Steven D Cappell
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, NIH, Frederick, MD, USA
| | - Huaitian Liu
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,High-Dimension Data Analysis Group, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Maxwell P Lee
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,High-Dimension Data Analysis Group, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael J Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,Confocal Microscopy Core Facility, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jennifer E Dwyer
- Molecular Pathology Unit, Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - R Mark Simpson
- Molecular Pathology Unit, Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kent W Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
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18
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Bruno NE, Nwachukwu JC, Hughes DC, Srinivasan S, Hawkins R, Sturgill D, Hager GL, Hurst S, Sheu SS, Bodine SC, Conkright MD, Nettles KW. Activation of Crtc2/Creb1 in skeletal muscle enhances weight loss during intermittent fasting. FASEB J 2021; 35:e21999. [PMID: 34748223 DOI: 10.1096/fj.202100171r] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 11/11/2022]
Abstract
The Creb-Regulated Transcriptional Coactivator (Crtc) family of transcriptional coregulators drive Creb1-mediated transcription effects on metabolism in many tissues, but the in vivo effects of Crtc2/Creb1 transcription on skeletal muscle metabolism are not known. Skeletal muscle-specific overexpression of Crtc2 (Crtc2 mice) induced greater mitochondrial activity, metabolic flux capacity for both carbohydrates and fats, improved glucose tolerance and insulin sensitivity, and increased oxidative capacity, supported by upregulation of key metabolic genes. Crtc2 overexpression led to greater weight loss during alternate day fasting (ADF), selective loss of fat rather than lean mass, maintenance of higher energy expenditure during the fast and reduced binge-eating during the feeding period. ADF downregulated most of the mitochondrial electron transport genes, and other regulators of mitochondrial function, that were substantially reversed by Crtc2-driven transcription. Glucocorticoids acted with AMPK to drive atrophy and mitophagy, which was reversed by Crtc2/Creb1 signaling. Crtc2/Creb1-mediated signaling coordinates metabolic adaptations in skeletal muscle that explain how Crtc2/Creb1 regulates metabolism and weight loss.
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Affiliation(s)
- Nelson E Bruno
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Jerome C Nwachukwu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - David C Hughes
- Section for Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Sathish Srinivasan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Richard Hawkins
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Stephen Hurst
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Shey-Shing Sheu
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sue C Bodine
- Section for Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Michael D Conkright
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Kendall W Nettles
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, USA
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19
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Hager GL, Kurumizaka H. Editorial overview: New insights and complexities for chromatin interacting proteins. Curr Opin Struct Biol 2021; 71:vi-viii. [PMID: 34690049 DOI: 10.1016/j.sbi.2021.09.004] [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: 10/20/2022]
Affiliation(s)
- Gordon L Hager
- Lab of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Hitoshi Kurumizaka
- Lab of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
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20
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Flynn BP, Birnie MT, Kershaw YM, Pauza AG, Kim S, Baek S, Rogers MF, Paterson AR, Stavreva DA, Murphy D, Hager GL, Lightman SL, Conway-Campbell BL. Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver. PLoS Genet 2021; 17:e1009737. [PMID: 34375333 PMCID: PMC8378686 DOI: 10.1371/journal.pgen.1009737] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/20/2021] [Accepted: 07/23/2021] [Indexed: 12/21/2022] Open
Abstract
Ultradian glucocorticoid rhythms are highly conserved across mammalian species, however, their functional significance is not yet fully understood. Here we demonstrate that pulsatile corticosterone replacement in adrenalectomised rats induces a dynamic pattern of glucocorticoid receptor (GR) binding at ~3,000 genomic sites in liver at the pulse peak, subsequently not found during the pulse nadir. In contrast, constant corticosterone replacement induced prolonged binding at the majority of these sites. Additionally, each pattern further induced markedly different transcriptional responses. During pulsatile treatment, intragenic occupancy by active RNA polymerase II exhibited pulsatile dynamics with transient changes in enrichment, either decreased or increased depending on the gene, which mostly returned to baseline during the inter-pulse interval. In contrast, constant corticosterone exposure induced prolonged effects on RNA polymerase II occupancy at the majority of gene targets, thus acting as a sustained regulatory signal for both transactivation and repression of glucocorticoid target genes. The nett effect of these differences were consequently seen in the liver transcriptome as RNA-seq analysis indicated that despite the same overall amount of corticosterone infused, twice the number of transcripts were regulated by constant corticosterone infusion, when compared to pulsatile. Target genes that were found to be differentially regulated in a pattern-dependent manner were enriched in functional pathways including carbohydrate, cholesterol, glucose and fat metabolism as well as inflammation, suggesting a functional role for dysregulated glucocorticoid rhythms in the development of metabolic dysfunction. Adrenal glucocorticoid hormones are released in a characteristic ultradian rhythm that becomes dysregulated during chronic stress, disease, or synthetic corticosteroid treatment. Metabolic dysfunction is a comorbidity associated with all these conditions, but the role that altered glucocorticoid dynamics play is unknown. As the liver is a major site of glucocorticoid action on metabolic homeostasis regulated by the glucocorticoid receptor, we have assessed how different patterns of hormone replacement in adrenalectomised rats differentially regulate gene pathways involved in type II diabetes, cirrhosis, and fatty liver development, via altering the pattern of glucocorticoid receptor binding to regulatory sites. We believe our findings have important implications for therapies that can reproduce the endogenous glucocorticoid rhythm and thus minimize adverse metabolic side-effects in patients.
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Affiliation(s)
- Benjamin P. Flynn
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Matthew T. Birnie
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Yvonne M. Kershaw
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Audrys G. Pauza
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States of America
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States of America
| | - Mark F. Rogers
- Intelligent Systems Laboratory, University of Bristol, Bristol, United Kingdom
| | - Alex R. Paterson
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Diana A. Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States of America
| | - David Murphy
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States of America
| | - Stafford L. Lightman
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Becky L. Conway-Campbell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
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21
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Garcia DA, Fettweis G, Presman DM, Paakinaho V, Jarzynski C, Upadhyaya A, Hager GL. Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model. Nucleic Acids Res 2021; 49:6605-6620. [PMID: 33592625 DOI: 10.1093/nar/gkab072] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/13/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the diffusion and binding behavior of these proteins in the nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed to two discrete populations of TFs-one non-specifically bound to chromatin and another specifically bound to target sites, as implied by decades of biochemical studies. However, emerging studies suggest alternate models for dwell-time distributions, indicating the existence of more than two populations of TFs (multi-exponential distribution), or even the absence of discrete states altogether (power-law distribution). Here, we present an analytical pipeline to evaluate which model best explains SMT data. We find that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution of dwell-times, blurring the temporal line between non-specific and specific binding, suggesting that productive binding may involve longer binding events than previously believed. From these observations, we propose a continuum of affinities model to explain TF dynamics, that is consistent with complex interactions of TFs with multiple nuclear domains as well as binding and searching on the chromatin template.
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Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA, Buenos Aires, Argentina
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Institute of Biomedicine, University of Eastern Finland, Kuopio, PO Box 1627, FI-70211 Kuopio, Finland
| | - Christopher Jarzynski
- Department of Physics, University of Maryland, College Park, MD 20742, USA.,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
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22
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Stavreva DA, Collins M, McGowan A, Varticovski L, Raziuddin R, Brody DO, Zhao J, Lee J, Kuehn R, Dehareng E, Mazza N, Pegoraro G, Hager GL. Mapping multiple endocrine disrupting activities in Virginia rivers using effect-based assays. Sci Total Environ 2021; 773:145602. [PMID: 33592464 PMCID: PMC8026610 DOI: 10.1016/j.scitotenv.2021.145602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/23/2021] [Accepted: 01/29/2021] [Indexed: 06/01/2023]
Abstract
Water sources are frequently contaminated with natural and anthropogenic substances having known or suspected endocrine disrupting activities; however, these activities are not routinely measured and monitored. Phenotypic bioassays are a promising new approach for detection and quantitation of endocrine disrupting chemicals (EDCs). We developed cell lines expressing fluorescent chimeric constructs capable of detecting environmental contaminants which interact with multiple nuclear receptors. Using these assays, we tested water samples collected in the summers of 2016, 2017 and 2018 from two major Virginia rivers. Samples were concentrated 200× and screened for contaminants interacting with the androgen (AR), glucocorticoid (GR), aryl hydrocarbon (AhR) and thyroid receptors. Among 45 tested sites, over 70% had AR activity and 60% had AhR activity. Many sites were also positive for GR and TRβ activation (22% and 42%, respectively). Multiple sites were positive for more than one type of contaminants, indicating presence of complex mixtures. These activities may negatively impact river ecosystems and consequently human health.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
| | - Michael Collins
- Center for Natural Capital, PO Box 901, Orange, VA, United States
| | - Andrew McGowan
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Lyuba Varticovski
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Razi Raziuddin
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - David Owen Brody
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States; Walt Whitman High School, 7100 Whittier Blvd, Bethesda, MD 20817, United States
| | - Jerry Zhao
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States; Walt Whitman High School, 7100 Whittier Blvd, Bethesda, MD 20817, United States
| | - Johnna Lee
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States; Walt Whitman High School, 7100 Whittier Blvd, Bethesda, MD 20817, United States
| | - Riley Kuehn
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States; Walt Whitman High School, 7100 Whittier Blvd, Bethesda, MD 20817, United States
| | - Elisabeth Dehareng
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States; Walt Whitman High School, 7100 Whittier Blvd, Bethesda, MD 20817, United States
| | - Nicholas Mazza
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States; Walt Whitman High School, 7100 Whittier Blvd, Bethesda, MD 20817, United States
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
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23
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Wagh K, Ishikawa M, Garcia DA, Stavreva DA, Upadhyaya A, Hager GL. Mechanical Regulation of Transcription: Recent Advances. Trends Cell Biol 2021; 31:457-472. [PMID: 33712293 PMCID: PMC8221528 DOI: 10.1016/j.tcb.2021.02.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [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] [Received: 10/30/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/01/2023]
Abstract
Mechanotransduction is the ability of a cell to sense mechanical cues from its microenvironment and convert them into biochemical signals to elicit adaptive transcriptional and other cellular responses. Here, we describe recent advances in the field of mechanical regulation of transcription, highlight mechanical regulation of the epigenome as a key novel aspect of mechanotransduction, and describe recent technological advances that could further elucidate the link between mechanical stimuli and gene expression. In this review, we emphasize the importance of mechanotransduction as one of the governing principles of cancer progression, underscoring the need to conduct further studies of the molecular mechanisms involved in sensing mechanical cues and coordinating transcriptional responses.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Momoko Ishikawa
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Stavreva DA, Varticovski L, Raziuddin R, Hager GL. Novel Assay for Detection of Progesterone Receptor-Interacting Endocrine Disruptors. J Endocr Soc 2021. [PMCID: PMC8090675 DOI: 10.1210/jendso/bvab048.1015] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The presence of progesterone receptor (PR)-interacting compounds in the environment may have serious health consequences for humans and wildlife, but the methods for their detection and monitoring are limited. Here we report the development and testing of a cell line expressing a chimeric construct containing ligand-binding domain of progesterone receptor and green fluorescent protein-tagged domain of the glucocorticoid receptor (GFP-GR-PR) under tetracycline regulation. Unlike the constitutively nuclear PR, this chimera is cytoplasmic in the absence of the ligand and translocates to the nucleus in response to the hormone or its analogues. The GFP-GR-PR chimera maintains specificity for binding to progesterone and does not cross-react with GR-activating hormones. A concentration- and time-dependent translocation in response to progesterone confirmed picomolar sensitivity for detecting PR ligands. Importantly, the assay can detect both agonist and antagonist activities and thus can be used for screening environmental samples for contamination with endocrine disruptors and for drug development. Using this approach, we screened water samples collected at 23 sites along 2 major rivers in Virginia: Mattaponi and Rappahannock Rivers. We detected a low, but reproducible PR-binding activity in 34.8 % of the sites tested. The calculated progesterone equivalent concentration (EQ) in some of these sites reached ~ 0.8 ng/L. The assay provides an effect-based approach for screening PR-interacting endocrine disrupting chemicals regardless of whether they exert agonist or antagonist activities. Either one could be seriously disruptive for the health of humans and wildlife.
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25
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Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL. An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Mol Cell 2021; 81:1484-1498.e6. [PMID: 33561389 DOI: 10.1016/j.molcel.2021.01.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific consensus motifs within the local chromatin context. The mechanisms by which TFs navigate the nuclear environment as they search for binding sites remain unclear. Here, we used single-molecule tracking and machine-learning-based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells. We revealed two distinct and dynamic low-mobility populations. One accounts for specific binding to chromatin, while the other represents a confinement state that requires an intrinsically disordered region (IDR), implicated in liquid-liquid condensate subdomains. Further analysis showed that the dwell times of both subpopulations follow a power-law distribution, consistent with a broad distribution of affinities on the GR cistrome and interactome. Together, our data link IDRs with a confinement state that is functionally distinct from specific chromatin binding and modulates the transcriptional output by increasing the local concentration of TFs at specific sites.
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Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Rikke A M Jensen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.
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Paakinaho V, Swinstead EE, Presman DM, Grøntved L, Hager GL. Meta-analysis of Chromatin Programming by Steroid Receptors. Cell Rep 2020; 28:3523-3534.e2. [PMID: 31553919 DOI: 10.1016/j.celrep.2019.08.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 05/15/2019] [Revised: 08/08/2019] [Accepted: 08/12/2019] [Indexed: 12/13/2022] Open
Abstract
Transcription factors (TFs) must access chromatin to bind to their response elements and regulate gene expression. A widely accepted model proposes that only a special subset of TFs, pioneer factors, can associate with condensed chromatin and initiate chromatin opening. We previously reported that steroid receptors (SRs), not considered pioneer factors, can assist the binding of an archetypal pioneer, the forkhead box protein 1 (FOXA1), at a subset of receptor-activated enhancers. These findings have been challenged recently, with the suggestion that newly acquired data fully support the prevailing pioneer model. Here, we reexamine our results and confirm the original conclusions. We also analyze and discuss a number of available datasets relevant to chromatin penetration by SRs and find a general consensus supporting our original observations. Hence, we propose that chromatin opening at some sites can be initiated by SRs, with a parallel recruitment of factors often treated as having a unique pioneer function. This Matters Arising paper is in response to Glont et al. (2019), published in Cell Reports.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, 70211 Kuopio, Finland
| | - Erin E Swinstead
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892-5055, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892-5055, USA.
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Taves MD, Mittelstadt PR, Presman DM, Hager GL, Ashwell JD. Single-Cell Resolution and Quantitation of Targeted Glucocorticoid Delivery in the Thymus. Cell Rep 2020; 26:3629-3642.e4. [PMID: 30917317 DOI: 10.1016/j.celrep.2019.02.108] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 08/24/2018] [Revised: 12/20/2018] [Accepted: 02/27/2019] [Indexed: 10/27/2022] Open
Abstract
Glucocorticoids are lipid-soluble hormones that signal via the glucocorticoid receptor (GR), a ligand-dependent transcription factor. Circulating glucocorticoids derive from the adrenals, but it is now apparent that paracrine glucocorticoid signaling occurs in multiple tissues. Effective local glucocorticoid concentrations and whether glucocorticoid delivery can be targeted to specific cell subsets are unknown. We use fluorescence detection of chromatin-associated GRs as biosensors of ligand binding and observe signals corresponding to steroid concentrations over physiological ranges in vitro and in vivo. In the thymus, where thymic epithelial cell (TEC)-synthesized glucocorticoids antagonize negative selection, we find that CD4+CD8+TCRhi cells, a small subset responding to self-antigens and undergoing selection, are specific targets of TEC-derived glucocorticoids and are exposed to 3-fold higher levels than other cells. These results demonstrate and quantitate targeted delivery of paracrine glucocorticoids. This approach may be used to assess in situ nuclear receptor signaling in a variety of physiological and pathological contexts.
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Affiliation(s)
- Matthew D Taves
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Paul R Mittelstadt
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Instituto de Fisiología, Biología Molecular y Neurosciencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jonathan D Ashwell
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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de la Rosa DA, Johnson TA, Fettweis G, Hager GL. OR12-03 Mineralocorticoid and Glucocorticoid Receptors Adopt Distinct Quaternary Structures and Can Form Heteromultimers That Affect Chromatin-Binding Profiles. J Endocr Soc 2020. [PMCID: PMC7209005 DOI: 10.1210/jendso/bvaa046.1651] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The mineralocorticoid and glucocorticoid receptors (MR and GR) are evolutionarily related nuclear receptors with high sequence conservation and a shared hormone response element (HRE). Both receptors are activated by glucocorticoids, but MR can be selectively activated by aldosterone. Using the imaging technique Number & Brightness (N&B) it has recently been proposed that liganded GR dimers form tetramers upon binding to HREs in live cells. We now show that agonist-bound MR adopts a tetrameric organization in the nucleoplasm and forms complexes with an average of 7 receptor units upon binding an HRE. Interestingly, MR antagonists eplerenone and spironolactone induced intermediate oligomerization arrangements, strongly suggesting that higher order oligomerization is essential for receptor activity. Site-directed mutagenesis and deletion analysis suggest that the N-terminus of MR is a main determinant of higher order oligomerization. Both with corticosterone and aldosterone, GR can incorporate into MR complexes partially displacing MR monomers. Genome-wide chromatin binding studies suggest that the presence of GR in the same cells profoundly change MR interaction with distinct sets of enhancers in a ligand-dependent way, contributing to receptor-specific signaling. Certain genes respond to only one receptor while others respond to both receptors. The interaction of these two closely related receptors has important implications for the mechanisms for glucocorticoid signaling and transcription factors in general.
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Jones RR, Stavreva DA, Weyer PJ, Varticovski L, Inoue-Choi M, Medgyesi DN, Chavis N, Graubard BI, Cain T, Wichman M, Beane Freeman LE, Hager GL, Ward MH. Pilot study of global endocrine disrupting activity in Iowa public drinking water utilities using cell-based assays. Sci Total Environ 2020; 714:136317. [PMID: 32018941 PMCID: PMC8459208 DOI: 10.1016/j.scitotenv.2019.136317] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/15/2019] [Accepted: 12/22/2019] [Indexed: 06/02/2023]
Abstract
Some anthropogenic substances in drinking water are known or suspected endocrine disrupting compounds (EDCs), but EDCs are not routinely measured. We conducted a pilot study of 10 public drinking water utilities in Iowa, where common contaminants (e.g., pesticides) are suspected EDCs. Raw (untreated) and finished (treated) drinking water samples were collected in spring and fall and concentrated using solid phase extraction. We assessed multiple endocrine disrupting activities using novel mammalian cell-based assays that express nuclear steroid receptors (aryl hydrocarbon [AhR], androgenic [AR], thyroid [TR], estrogenic [ER] and glucocorticoid [GR]). We quantified each receptor's activation relative to negative controls and compared activity by season and utility/sample characteristics. Among 62 samples, 69% had AhR, 52% AR, 3% TR, 2% ER, and 0% GR activity. AhR and AR activities were detected more frequently in spring (p =0 .002 and < 0.001, respectively). AR activity was more common in samples of raw water (p =0 .02) and from surface water utilities (p =0 .05), especially in fall (p =0 .03). Multivariable analyses suggested spring season, surface water, and nitrate and disinfection byproduct concentrations as determinants of bioactivity. Our results demonstrate that AR and AhR activities are commonly found in Iowa drinking water, and that their detection varies by season and utility/sample characteristics. Screening EDCs with cell-based bioassays holds promise for characterizing population exposure to diverse EDCs mixtures.
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Affiliation(s)
- Rena R Jones
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
| | - Diana A Stavreva
- Laboratory of Receptor Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Peter J Weyer
- Center for Health Effects of Environmental Contamination, University of Iowa, Iowa City, IA, United States
| | - Lyuba Varticovski
- Laboratory of Receptor Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Maki Inoue-Choi
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Danielle N Medgyesi
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Nicole Chavis
- Milken Institute of Public Health, George Washington University, Washington, DC, United States
| | - Barry I Graubard
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Terence Cain
- State Hygienic Laboratory, University of Iowa, Coralville, IA, United States
| | - Michael Wichman
- State Hygienic Laboratory, University of Iowa, Coralville, IA, United States
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Gordon L Hager
- Laboratory of Receptor Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mary H Ward
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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Stavreva DA, Garcia DA, Fettweis G, Gudla PR, Zaki GF, Soni V, McGowan A, Williams G, Huynh A, Palangat M, Schiltz RL, Johnson TA, Presman DM, Ferguson ML, Pegoraro G, Upadhyaya A, Hager GL. Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility. Mol Cell 2019; 75:1161-1177.e11. [PMID: 31421980 PMCID: PMC6754282 DOI: 10.1016/j.molcel.2019.06.042] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [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] [Received: 11/15/2018] [Revised: 02/07/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
Genes are transcribed in a discontinuous pattern referred to as RNA bursting, but the mechanisms regulating this process are unclear. Although many physiological signals, including glucocorticoid hormones, are pulsatile, the effects of transient stimulation on bursting are unknown. Here we characterize RNA synthesis from single-copy glucocorticoid receptor (GR)-regulated transcription sites (TSs) under pulsed (ultradian) and constant hormone stimulation. In contrast to constant stimulation, pulsed stimulation induces restricted bursting centered around the hormonal pulse. Moreover, we demonstrate that transcription factor (TF) nuclear mobility determines burst duration, whereas its bound fraction determines burst frequency. Using 3D tracking of TSs, we directly correlate TF binding and RNA synthesis at a specific promoter. Finally, we uncover a striking co-bursting pattern between TSs located at proximal and distal positions in the nucleus. Together, our data reveal a dynamic interplay between TF mobility and RNA bursting that is responsive to stimuli strength, type, modality, and duration.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA.
| | - David A Garcia
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA; Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Prabhakar R Gudla
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - George F Zaki
- High Performance Computing Group, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vikas Soni
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Andrew McGowan
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Geneva Williams
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Anh Huynh
- Department of Physics and Graduate Program in Biomolecular Science, Boise State University, Boise, ID 83725, USA
| | - Murali Palangat
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - R Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Matthew L Ferguson
- Department of Physics and Graduate Program in Biomolecular Science, Boise State University, Boise, ID 83725, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Arpita Upadhyaya
- Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA.
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31
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Paul-Friedman K, Martin M, Crofton KM, Hsu CW, Sakamuru S, Zhao J, Xia M, Huang R, Stavreva DA, Soni V, Varticovski L, Raziuddin R, Hager GL, Houck KA. Limited Chemical Structural Diversity Found to Modulate Thyroid Hormone Receptor in the Tox21 Chemical Library. Environ Health Perspect 2019; 127:97009. [PMID: 31566444 PMCID: PMC6792352 DOI: 10.1289/ehp5314] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND Thyroid hormone receptors (TRs) are critical endocrine receptors that regulate a multitude of processes in adult and developing organisms, and thyroid hormone disruption is of high concern for neurodevelopmental and reproductive toxicities in particular. To date, only a small number of chemical classes have been identified as possible TR modulators, and the receptors appear highly selective with respect to the ligand structural diversity. Thus, the question of whether TRs are an important screening target for protection of human and wildlife health remains. OBJECTIVE Our goal was to evaluate the hypothesis that there is limited structural diversity among environmentally relevant chemicals capable of modulating TR activity via the collaborative interagency Tox21 project. METHODS We screened the Tox21 chemical library (8,305 unique structures) in a quantitative high-throughput, cell-based reporter gene assay for TR agonist or antagonist activity. Active compounds were further characterized using additional orthogonal assays, including mammalian one-hybrid assays, coactivator recruitment assays, and a high-throughput, fluorescent imaging, nuclear receptor translocation assay. RESULTS Known agonist reference chemicals were readily identified in the TR transactivation assay, but only a single novel, direct agonist was found, the pharmaceutical betamipron. Indirect activation of TR through activation of its heterodimer partner, the retinoid-X-receptor (RXR), was also readily detected by confirmation in an RXR agonist assay. Identifying antagonists with high confidence was a challenge with the presence of significant confounding cytotoxicity and other, non-TR-specific mechanisms common to the transactivation assays. Only three pharmaceuticals-mefenamic acid, diclazuril, and risarestat-were confirmed as antagonists. DISCUSSION The results support limited structural diversity for direct ligand effects on TR and imply that other potential target sites in the thyroid hormone axis should be a greater priority for bioactivity screening for thyroid axis disruptors. https://doi.org/10.1289/EHP5314.
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Affiliation(s)
- Katie Paul-Friedman
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Matt Martin
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Kevin M Crofton
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Chia-Wen Hsu
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Washington, DC, USA
| | - Srilatha Sakamuru
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Diana A Stavreva
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Vikas Soni
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Lyuba Varticovski
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Razi Raziuddin
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Gordon L Hager
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Keith A Houck
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
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Paakinaho V, Johnson TA, Presman DM, Hager GL. Glucocorticoid receptor quaternary structure drives chromatin occupancy and transcriptional outcome. Genome Res 2019; 29:1223-1234. [PMID: 31337711 PMCID: PMC6673716 DOI: 10.1101/gr.244814.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/09/2019] [Indexed: 01/11/2023]
Abstract
Most transcription factors, including nuclear receptors, are widely modeled as binding regulatory elements as monomers, homodimers, or heterodimers. Recent findings in live cells show that the glucocorticoid receptor NR3C1 (also known as GR) forms tetramers on enhancers, owing to an allosteric alteration induced by DNA binding, and suggest that higher oligomerization states are important for the gene regulatory responses of GR. By using a variant (GRtetra) that mimics this allosteric transition, we performed genome-wide studies using a GR knockout cell line with reintroduced wild-type GR or reintroduced GRtetra. GRtetra acts as a super receptor by binding to response elements not accessible to the wild-type receptor and both induces and represses more genes than GRwt. These results argue that DNA binding induces a structural transition to the tetrameric state, forming a transient higher-order structure that drives both the activating and repressive actions of glucocorticoids.
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Affiliation(s)
- Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA.,Institute of Biomedicine, University of Eastern Finland, Kuopio, FI-70211 Kuopio, Finland
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA.,IFIBYNE, UBA-CONICET, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EGA, Argentina
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
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Johnson TA, Chereji RV, Stavreva DA, Morris SA, Hager GL, Clark DJ. Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo. Nucleic Acids Res 2019; 46:203-214. [PMID: 29126175 PMCID: PMC5758879 DOI: 10.1093/nar/gkx1044] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/23/2017] [Indexed: 11/14/2022] Open
Abstract
Glucocorticoid hormone plays a major role in metabolism and disease. The hormone-bound glucocorticoid receptor (GR) binds to a specific set of enhancers in different cell types, resulting in unique patterns of gene expression. We have addressed the role of chromatin structure in GR binding by mapping nucleosome positions in mouse adenocarcinoma cells. Before hormone treatment, GR-enhancers exist in one of three chromatin states: (i) Nucleosome-depleted enhancers that are DNase I-hypersensitive, associated with the Brg1 chromatin remodeler and flanked by nucleosomes incorporating histone H2A.Z. (ii) Nucleosomal enhancers that are DNase I-hypersensitive, marked by H2A.Z and associated with Brg1. (iii) Nucleosomal enhancers that are inaccessible to DNase I, incorporate little or no H2A.Z and lack Brg1. Hormone-induced GR binding results in nucleosome shifts at all types of GR-enhancer, coinciding with increased recruitment of Brg1. We propose that nucleosome-depleted GR-enhancers are formed and maintained by other transcription factors which recruit Brg1 whereas, at nucleosomal enhancers, GR behaves like a pioneer factor, interacting with nucleosomal sites and recruiting Brg1 to remodel the chromatin.
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Affiliation(s)
- Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Razvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Stephanie A Morris
- Office of Cancer Nanotechnology Research, Center for Strategic Scientific Initiatives, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Goelzer JA, Stavreva DA, Hager GL, Ferguson ML. Transcriptional Activation by Glucocorticoid Receptor Studied by 3D Orbital Tracking Fluorescence Cross Correlation Spectroscopy. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Fujiwara S, Baek S, Varticovski L, Kim S, Hager GL. High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue. Sci Rep 2019; 9:516. [PMID: 30679562 PMCID: PMC6345852 DOI: 10.1038/s41598-018-36927-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/28/2018] [Indexed: 02/07/2023] Open
Abstract
DNA accessibility to transcription regulators varies between cells and modulates gene expression patterns. Several “open” chromatin profiling methods that provide valuable insight into the activity of these regulatory regions have been developed. However, their application to clinical samples has been limited despite the discovery that the Analysis of Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) method can be performed using fewer cells than other techniques. Obtaining fresh rather than stored samples and a lack of adequate optimization and quality controls are major barriers to ATAC’s clinical implementation. Here, we describe an optimized ATAC protocol in which we varied nuclear preparation conditions and transposase concentrations and applied rigorous quality control measures before testing fresh, flash frozen, and cryopreserved breast cells and tissue. We obtained high quality data from small cell number. Furthermore, the genomic distribution of sequencing reads, their enrichment at transcription start sites, and transcription factor footprint analyses were similar between cryopreserved and fresh samples. This updated method is applicable to clinical samples, including cells from fine needle aspiration and tissues obtained via core needle biopsy or surgery. Chromatin accessibility analysis using patient samples will greatly expand the range of translational research and personalized medicine by identification of clinically-relevant epigenetic features.
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Affiliation(s)
- Saori Fujiwara
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lyuba Varticovski
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Saloura V, Vougiouklakis T, Burkitt K, Nakamura Y, Hager GL, van Waes C. Corrigendum to "The role of protein methyltransferases as potential novel therapeutic targets in squamous cell carcinoma of the head and neck" [Oral Oncol. 81 (2018) 100-108]. Oral Oncol 2018; 86:318. [PMID: 30201513 DOI: 10.1016/j.oraloncology.2018.08.022] [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: 10/28/2022]
Affiliation(s)
- Vassiliki Saloura
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, United States.
| | | | - Kyunghee Burkitt
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, United States
| | - Yusuke Nakamura
- Department of Medicine, University of Chicago, United States; Department of Surgery, University of Chicago, United States
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, United States
| | - Carter van Waes
- Head and Neck Surgery Branch, National Institutes of Deafness and Communication Disorders, United States
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Abstract
Reprogramming of the chromatin landscape is a critical component to the transcriptional response in breast cancer. Effects of sex hormones such as estrogens and progesterone have been well described to have a critical impact on breast cancer proliferation. However, the complex network of the chromatin landscape, enhancer regions and mode of function of steroid receptors (SRs) and other transcription factors (TFs), is an intricate web of signaling and functional processes that is still largely misunderstood at the mechanistic level. In this review, we describe what is currently known about the dynamic interplay between TFs with chromatin and the reprogramming of enhancer elements. Emphasis has been placed on characterizing the different modes of action of TFs in regulating enhancer activity, specifically, how different SRs target enhancer regions to reprogram chromatin in breast cancer cells. In addition, we discuss current techniques employed to study enhancer function at a genome-wide level. Further, we have noted recent advances in live cell imaging technology. These single-cell approaches enable the coupling of population-based assays with real-time studies to address many unsolved questions about SRs and chromatin dynamics in breast cancer.
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Affiliation(s)
- Erin E Swinstead
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
- Institute of BiomedicineUniversity of Eastern Finland, Kuopio, Finland
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, NIH, Bethesda, Maryland, USA
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Oh KS, Gottschalk RA, Lounsbury NW, Sun J, Dorrington MG, Baek S, Sun G, Wang Z, Krauss KS, Milner JD, Dutta B, Hager GL, Sung MH, Fraser IDC. Dual Roles for Ikaros in Regulation of Macrophage Chromatin State and Inflammatory Gene Expression. J Immunol 2018; 201:757-771. [PMID: 29898962 DOI: 10.4049/jimmunol.1800158] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/15/2018] [Indexed: 12/19/2022]
Abstract
Macrophage activation by bacterial LPS leads to induction of a complex inflammatory gene program dependent on numerous transcription factor families. The transcription factor Ikaros has been shown to play a critical role in lymphoid cell development and differentiation; however, its function in myeloid cells and innate immune responses is less appreciated. Using comprehensive genomic analysis of Ikaros-dependent transcription, DNA binding, and chromatin accessibility, we describe unexpected dual repressor and activator functions for Ikaros in the LPS response of murine macrophages. Consistent with the described function of Ikaros as transcriptional repressor, Ikzf1-/- macrophages showed enhanced induction for select responses. In contrast, we observed a dramatic defect in expression of many delayed LPS response genes, and chromatin immunoprecipitation sequencing analyses support a key role for Ikaros in sustained NF-κB chromatin binding. Decreased Ikaros expression in Ikzf1+/- mice and human cells dampens these Ikaros-enhanced inflammatory responses, highlighting the importance of quantitative control of Ikaros protein level for its activator function. In the absence of Ikaros, a constitutively open chromatin state was coincident with dysregulation of LPS-induced chromatin remodeling, gene expression, and cytokine responses. Together, our data suggest a central role for Ikaros in coordinating the complex macrophage transcriptional program in response to pathogen challenge.
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Affiliation(s)
- Kyu-Seon Oh
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.,Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Rachel A Gottschalk
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nicolas W Lounsbury
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jing Sun
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Michael G Dorrington
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Guangping Sun
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Ze Wang
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Kathleen S Krauss
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Joshua D Milner
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Bhaskar Dutta
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Iain D C Fraser
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
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Baek S, Goldstein I, Hager GL. Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity. Cell Rep 2018; 19:1710-1722. [PMID: 28538187 DOI: 10.1016/j.celrep.2017.05.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/04/2017] [Accepted: 04/26/2017] [Indexed: 02/06/2023] Open
Abstract
In response to activating signals, transcription factors (TFs) bind DNA and regulate gene expression. TF binding can be measured by protection of the bound sequence from DNase digestion (i.e., footprint). Here, we report that 80% of TF binding motifs do not show a measurable footprint, partly because of a variable cleavage pattern within the motif sequence. To more faithfully portray the effect of TFs on chromatin, we developed an algorithm that captures two TF-dependent effects on chromatin accessibility: footprinting and motif-flanking accessibility. The algorithm, termed bivariate genomic footprinting (BaGFoot), efficiently detects TF activity. BaGFoot is robust to different accessibility assays (DNase-seq, ATAC-seq), all examined peak-calling programs, and a variety of cut bias correction approaches. BaGFoot reliably predicts TF binding and provides valuable information regarding the TFs affecting chromatin accessibility in various biological systems and following various biological events, including in cases where an absolute footprint cannot be determined.
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Affiliation(s)
- Songjoon Baek
- Lab of Receptor Biology and Gene Expression, The National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ido Goldstein
- Lab of Receptor Biology and Gene Expression, The National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Gordon L Hager
- Lab of Receptor Biology and Gene Expression, The National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Abstract
Upon lowered blood glucose occurring during fasting, glucagon is secreted from pancreatic islets, exerting various metabolic effects to normalize glucose levels. A considerable portion of these effects is mediated by glucagon-activated transcription factors (TFs) in liver. Glucagon directly activates several TFs via immediate cyclic adenosine monophosphate (cAMP)- and calcium-dependent signaling events. Among these TFs, cAMP response element-binding protein (CREB) is a major factor. CREB recruits histone-modifying enzymes and cooperates with other TFs on the chromatin template to increase the rate of gene transcription. In addition to direct signal transduction, the transcriptional effects of glucagon are also influenced by dynamic TF cross talk. Specifically, assisted loading of one TF by a companion TF leads to increased binding and activity. Lastly, transcriptional regulation by glucagon is also exerted by TF cascades by which a primary TF induces the gene expression of secondary TFs that bring about their activity a few hours after the initial glucagon signal. This mechanism of a delayed response may be instrumental in establishing the temporal organization of the fasting response by which distinct metabolic events separate early from prolonged fasting. In this mini-review, we summarize recent advances and critical discoveries in glucagon-dependent gene regulation with a focus on direct TF activation, dynamic TF cross talk, and TF cascades.
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Affiliation(s)
- Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Correspondence: Gordon L. Hager, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B602, Bethesda, Maryland 20892. E-mail: ; or Ido Goldstein, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B307, Bethesda, Maryland 20892. E-mail:
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Correspondence: Gordon L. Hager, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B602, Bethesda, Maryland 20892. E-mail: ; or Ido Goldstein, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B307, Bethesda, Maryland 20892. E-mail:
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Goldstein I, Hager GL. Dynamic enhancer function in the chromatin context. Wiley Interdiscip Rev Syst Biol Med 2018; 10:10.1002/wsbm.1390. [PMID: 28544514 PMCID: PMC6638546 DOI: 10.1002/wsbm.1390] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 12/28/2022]
Abstract
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding. More recently, fluorescent microscopy techniques, including fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, and single molecule tracking (SMT), reveal a highly dynamic binding behavior for these factors in live cells. Furthermore, a refined analysis of genomic footprinting suggests that many transcription factors leave minimal or no footprints in chromatin, even when present and active in a given cell type. In this study, we review the implications of these new approaches for an accurate understanding of enhancer function in real time. In vivo SMT, in particular, has recently evolved as a promising methodology to probe enhancer function in live cells. Integration of findings from the many approaches now employed in the study of enhancer function suggest a highly dynamic view for the action of enhancer activating factors, viewed on a time scale of milliseconds to seconds, rather than minutes to hours. WIREs Syst Biol Med 2018, 10:e1390. doi: 10.1002/wsbm.1390 This article is categorized under: Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Genetic/Genomic Methods Laboratory Methods and Technologies > Imaging.
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Affiliation(s)
- Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Goldstein I, Paakinaho V, Baek S, Sung MH, Hager GL. Synergistic gene expression during the acute phase response is characterized by transcription factor assisted loading. Nat Commun 2017; 8:1849. [PMID: 29185442 PMCID: PMC5707366 DOI: 10.1038/s41467-017-02055-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 11/03/2017] [Indexed: 12/18/2022] Open
Abstract
The cytokines interleukin 1β and 6 (IL-1β, IL-6) mediate the acute phase response (APR). In liver, they regulate the secretion of acute phase proteins. Using RNA-seq in primary hepatocytes, we show that these cytokines regulate transcription in a bifurcated manner, leading to both synergistic and antagonistic gene expression. By mapping changes in enhancer landscape and transcription factor occupancy (using ChIP-seq), we show that synergistic gene induction is achieved by assisted loading of STAT3 on chromatin by NF-κB. With IL-6 treatment alone, STAT3 does not efficiently bind 20% of its coordinated binding sites. In the presence of IL-1β, NF-κB is activated, binds a subset of enhancers and primes their activity, as evidenced by increasing H3K27ac. This facilitates STAT3 binding and synergistic gene expression. Our findings reveal an enhancer-specific crosstalk whereby NF-κB enables STAT3 binding at some enhancers while perturbing it at others. This model reconciles seemingly contradictory reports of NF-κB-STAT3 crosstalk. The cytokines IL-1β and IL-6 mediate the systemic acute phase response (APR). Here, the authors provide evidence that these cytokines lead to both synergistic and antagonistic gene expression during APR; synergistic induction occurs by assisted loading of STAT3 on chromatin by NF-κB.
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Affiliation(s)
- Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, Bethesda, MD, 20892, USA.
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore, MD, 21224, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, Bethesda, MD, 20892, USA.
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Paakinaho V, Presman DM, Swinstead EE, Miranda TB, Ball DA, Karpova TS, Hager GL. Abstract 4991: Dynamic reprogramming of the chromatin landscape in cancer: Studies in real time. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4991] [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
Reprogramming of the chromatin landscape by sequence-specific transcription factors (TF) can influence in the prevalence and progression of several diseases, including cancers. Steroid receptors are a class of hormone-regulated TF that have a major impact on the progression of cancers. The link between the androgen receptor (AR) action in prostate cancer and the glucocorticoid (GR) and estrogen receptor (ER) action in breast cancer is well-known. Furthermore, other TFs such as the pioneer factor FoxA1 has been extensively linked to AR and ER action in these cancers. Although the action of these TF have been widely studied, the knowledge is almost exclusively based on population-based assays such as ChIP-seq and DHS-seq. Hence, the dynamic binding behavior of these factors in living cell remains unclear. For example, the classical pioneer factor model suggests long term static binding events between pioneer TFs, such as FoxA1, and chromatin. However, little is known on the dynamic action of FoxA1 in living cells.
We have examined the behavior of steroid receptors and cofactors, including FoxA1, at the single-molecule level in living cells. These factors were fused with HaloTag, and labeled with the bright and stable fluorophore JF549. Single-molecule tracking (SMT) of these proteins (using HILO microscopy) revealed a highly dynamic binding behavior of TFs. This supports transient rather than stable TF chromatin interactions. Specifically, two distinct binding populations have been observed for all factors tested; fast or slow stops. Fast stops represent genomic scanning of TF, while slow stops, with residence time of 6-14 sec, represent functional binding events at specific response elements. The vast majority of molecules at any given time are either diffusing or exhibit fast stops, while only a small percentage exhibit slow stops. However, hormone activation of AR, GR or ER results in an increase in the percentage of molecules with slow stops compared to the unstimulated state. Thus, our results indicate that on a single-molecule level, only a small proportion TFs are functionally bound at any given time.
In addition to affirming the general model that many TFs are highly dynamic in their chromatin binding activity, SMT experiments in live cells revealed a highly dynamic interaction of FoxA1 with chromatin in vivo. Unexpectedly, we also observed by ChIP-seq and DHS-seq analysis that at subset of genomic sites, the role of pioneer can be reversed, with the steroid receptors serving to enhance binding of FoxA1. We propose a general model, dynamic assisted loading, wherein interactions between TFs and pioneer factors are highly dynamic. Our findings show that the action of key TFs in cancer development are more complex and dynamic in real time than previously reported.
Citation Format: Ville Paakinaho, Diego M. Presman, Erin E. Swinstead, Tina B. Miranda, David A. Ball, Tatiana S. Karpova, Gordon L. Hager. Dynamic reprogramming of the chromatin landscape in cancer: Studies in real time [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 4991. doi:10.1158/1538-7445.AM2017-4991
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Veschi V, Liu Z, Voss TC, Ozbun L, Gryder B, Yan C, Hu Y, Ma A, Jin J, Mazur SJ, Lam N, Souza BK, Giannini G, Hager GL, Arrowsmith CH, Khan J, Appella E, Thiele C. Abstract 3867: Epigenetic siRNA and chemical screens identify SETD8 inhibition as a therapeutic strategy to reactivate p53 in high-risk neuroblastoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3867] [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
Neuroblastoma (NB) is considered a failure of sympathoadrenal differentiation. High-risk neuroblastoma (HR-NB) is an aggressive pediatric tumor accounting for 15% of all pediatric oncology deaths. Less than 50% of HR-NB patients have long-term survival, despite intense multimodality treatment. Given the paucity of druggable mutations and findings that epigenetic drivers contribute to NB tumorigenesis, we undertook a chromatin-focused siRNA screen to uncover epigenetic regulators critical for survival of high-risk NBs. Of the 400 genes analyzed, high-content Opera imaging identified 53 genes whose loss of expression led to significant decreases in NB cell number with 16 also inducing differentiation. A screen with 21 epigenetic compounds in 8 NB cell lines and 2 non-transformed cell lines prioritized those siRNA hits with active tool compounds in the drug development pipeline. This revealed UNC0379 (targets SETD8) inhibited NB cell growth and identified SETD8 as an important and druggable NB target. SETD8 is the H4K20me1 methyltransferase which regulates DNA replication, chromosome condensation and gene expression. Analysis of primary NB revealed that high expression of SETD8 is associated with poor prognosis in NB (R2 platform ex. Kocak; p=1.4e-07). Levels of SETD8 were not significantly different between Stage 4 MYCN-amp compared to MYCN-WT tumors but high SETD8 levels were only associated with poor prognosis in the Stage 4 MYCN-WT(p=0.03). To understand SETD8-mechanism of action, we performed RNA-seq transcriptome analyses after genetic or pharmacological inhibition of SETD8. Ingenuity Pathway Analysis revealed that SETD8 ablation rescued p53 pro-apoptotic and cell-cycle arrest functions by activating the canonical p53 pathway. Functional studies showed SETD8 methylates p53 (K382) leading to its inactivation. Levels of p53K382me1 are higher in MYCN-WT NB cell lines compared to those with MYCN-amp. Less than 2% of NB tumors have p53 mutations but multiple mechanisms have been identified in MYCN-amp NB that functionally inactivate p53. This study identified that SETD8 inactivates p53 in NB and may be an important mechanism to inactivate p53 in MYCN-WT HR-NB. This subgroup represents 60-70% of HR-NB tumors. SETD8 inhibition led to increases in caspase-dependent cell death only in p53-WT but not -mutant or -null NB cells. Genetic rescue experiments confirmed that SETD8-induced cell death is p53 dependent and p53K382 is important for this activity. Our in vivo xenograft NB models, showed that genetic or pharmacologic (UNC0379) inhibition of SETD8 confers a significant survival advantage. This work identifies that SETD8 is a novel therapeutic target and its inhibition may be especially relevant for the subset of high-risk NB tumors with wildtype MYCN. This is the first in vivo preclinical study showing that targeting SETD8 inhibits tumor growth.
Citation Format: Veronica Veschi, Zhihui Liu, Ty C. Voss, Laurent Ozbun, Berkley Gryder, Chunhua Yan, Ying Hu, Anqi Ma, Jian Jin, Sharlyn J. Mazur, Norris Lam, Barbara K. Souza, Giuseppe Giannini, Gordon L. Hager, Cheryl H. Arrowsmith, Javed Khan, Ettore Appella, Carol Thiele. Epigenetic siRNA and chemical screens identify SETD8 inhibition as a therapeutic strategy to reactivate p53 in high-risk neuroblastoma [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 3867. doi:10.1158/1538-7445.AM2017-3867
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Affiliation(s)
| | - Zhihui Liu
- 1National Institutes of Health, Bethesda, MD
| | - Ty C. Voss
- 1National Institutes of Health, Bethesda, MD
| | | | | | - Chunhua Yan
- 1National Institutes of Health, Bethesda, MD
| | - Ying Hu
- 1National Institutes of Health, Bethesda, MD
| | - Anqi Ma
- 2Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jian Jin
- 2Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Norris Lam
- 1National Institutes of Health, Bethesda, MD
| | | | | | | | | | - Javed Khan
- 1National Institutes of Health, Bethesda, MD
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Presman DM, Ball DA, Paakinaho V, Grimm JB, Lavis LD, Karpova TS, Hager GL. Quantifying transcription factor binding dynamics at the single-molecule level in live cells. Methods 2017; 123:76-88. [PMID: 28315485 PMCID: PMC5522764 DOI: 10.1016/j.ymeth.2017.03.014] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [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] [Received: 11/15/2016] [Revised: 01/30/2017] [Accepted: 03/10/2017] [Indexed: 11/25/2022] Open
Abstract
Progressive, technological achievements in the quantitative fluorescence microscopy field are allowing researches from many different areas to start unraveling the dynamic intricacies of biological processes inside living cells. From super-resolution microscopy techniques to tracking of individual proteins, fluorescence microscopy is changing our perspective on how the cell works. Fortunately, a growing number of research groups are exploring single-molecule studies in living cells. However, no clear consensus exists on several key aspects of the technique such as image acquisition conditions, or analysis of the obtained data. Here, we describe a detailed approach to perform single-molecule tracking (SMT) of transcription factors in living cells to obtain key binding characteristics, namely their residence time and bound fractions. We discuss different types of fluorophores, labeling density, microscope, cameras, data acquisition, and data analysis. Using the glucocorticoid receptor as a model transcription factor, we compared alternate tags (GFP, mEOS, HaloTag, SNAP-tag, CLIP-tag) for potential multicolor applications. We also examine different methods to extract the dissociation rates and compare them with simulated data. Finally, we discuss several challenges that this exciting technique still faces.
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Affiliation(s)
- Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Goldstein I, Baek S, Sung MH, Hager GL. Abstract 5510: Pro inflammatory cytokines induce synergistic gene expression by assisted loading of STAT3 at a subset of primed enhancers. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5510] [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
During inflammation, the liver responds to pro-inflammatory signals by producing and secreting acute phase reactants (APR) involved in the inflammatory process. The notable increase in the level of these proteins is due to transcriptional induction that is jointly mediated by the pro-inflammatory cytokines IL-1β, TNFα and IL-6. Although critical to restoring homeostasis during infection or trauma, the hepatic response to these cytokines can be deleterious in pathologies involving chronic inflammation such as cancer.
We set out to decipher how pro-inflammatory cytokines cooperate to elicit a transcriptional response in hepatocytes. We examined the transcriptome of primary mouse hepatocytes treated with different combinations of cytokines and found several gene expression patterns showing a complex cross-talk between cytokine signaling pathways. Specifically, we found that a dual treatment of IL-1β and IL-6 results in a synergistic expression of 164 genes, many of which are APR genes. TNFα had an effect similar to IL-1β, albeit weaker. A sequential rather than a combined treatment attenuated the synergistic effect, suggesting direct cooperation between the two cytokines in inducing transcription (as opposed to a cascade of transcription). Assaying enhancer activity by H3K27ac ChIP-seq revealed the dynamic nature of cytokine-responsive enhancers, with hundreds of enhancers changing their activity level following either treatment. Importantly, enhancers becoming more active upon dual IL-1/IL-6 treatment were enriched with binding sequences for STAT3, CEBP, AP1 and NFkB. Because IL-6 is the major pro-inflammatory cytokine and its transcriptional effects are mediated by the STAT3 transcription factor (TF), we assayed STAT3 binding patterns by ChIP-seq. As expected, STAT3 binding was elevated following IL-6 treatment genome-wide. Surprisingly, in 351 enhancers, STAT3 binding was markedly increased in the dual treatment compared to IL-6 treatment alone, suggesting a supporting role for IL-1β in assisting STAT3 loading at a subset of enhancers. This sub-population of enhancers had lower motif scores compared to unassisted STAT3 binding sites, indicating optimal STAT3 binding at these enhancers might require some facilitation by other factors. Accordingly, these enhancers were less active at the untreated state, but increased in activity following IL-1β treatment, an effect we termed ‘IL-1β priming’.
Our results are consistent with a scenario whereby IL-1β-activated TFs (C/EBPβ, AP1 and/or NFκB) assist STAT3 loading by binding a subset of enhancers, activating them thereby augmenting STAT3 binding. This unexplored mechanism of transcriptional regulation by cytokines may be targeted to alleviate the deleterious effects of pro-tumorigenic inflammatory programs.
Citation Format: Ido Goldstein, Songjoon Baek, Myong-Hee Sung, Gordon L. Hager. Pro inflammatory cytokines induce synergistic gene expression by assisted loading of STAT3 at a subset of primed enhancers [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 5510. doi:10.1158/1538-7445.AM2017-5510
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Paakinaho V, Presman DM, Ball DA, Johnson TA, Schiltz RL, Levitt P, Mazza D, Morisaki T, Karpova TS, Hager GL. Single-molecule analysis of steroid receptor and cofactor action in living cells. Nat Commun 2017. [PMID: 28635963 PMCID: PMC5482060 DOI: 10.1038/ncomms15896] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Population-based assays have been employed extensively to investigate the interactions of transcription factors (TFs) with chromatin and are often interpreted in terms of static and sequential binding. However, fluorescence microscopy techniques reveal a more dynamic binding behaviour of TFs in live cells. Here we analyse the strengths and limitations of in vivo single-molecule tracking and performed a comprehensive analysis on the intranuclear dwell times of four steroid receptors and a number of known cofactors. While the absolute residence times estimates can depend on imaging acquisition parameters due to sampling bias, our results indicate that only a small proportion of factors are specifically bound to chromatin at any given time. Interestingly, the glucocorticoid receptor and its cofactors affect each other’s dwell times in an asymmetric manner. Overall, our data indicate transient rather than stable TF-cofactors chromatin interactions at response elements at the single-molecule level. Transcription factors (TFs) are thought to regulate gene expression by stably binding to target DNA elements. Here, the authors use single-molecule tracking to analyse the dynamic behaviour of steroid receptors TFs and show that most specific interactions with chromatin are transient and dynamic.
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Affiliation(s)
- Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - R Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Peter Levitt
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Davide Mazza
- Istituto Scientifico Ospedale San Raffaele, Centro di Imaging Sperimentale e Università Vita-Salute San Raffaele, 20132 Milano, Italy
| | - Tatsuya Morisaki
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
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Lynch C, Sakamuru S, Huang R, Stavreva DA, Varticovski L, Hager GL, Judson RS, Houck KA, Kleinstreuer NC, Casey W, Paules RS, Simeonov A, Xia M. Identifying environmental chemicals as agonists of the androgen receptor by using a quantitative high-throughput screening platform. Toxicology 2017; 385:48-58. [PMID: 28478275 PMCID: PMC6135100 DOI: 10.1016/j.tox.2017.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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] [Received: 08/19/2016] [Revised: 03/27/2017] [Accepted: 05/03/2017] [Indexed: 01/08/2023]
Abstract
The androgen receptor (AR, NR3C4) is a nuclear receptor whose main function is acting as a transcription factor regulating gene expression for male sexual development and maintaining accessory sexual organ function. It is also a necessary component of female fertility by affecting the functionality of ovarian follicles and ovulation. Pathological processes involving AR include Kennedy's disease and Klinefelter's syndrome, as well as prostate, ovarian, and testicular cancer. Strict regulation of sex hormone signaling is required for normal reproductive organ development and function. Therefore, testing small molecules for their ability to modulate AR is a first step in identifying potential endocrine disruptors. We screened the Tox21 10K compound library in a quantitative high-throughput format to identify activators of AR using two reporter gene cell lines, AR β-lactamase (AR-bla) and AR-luciferase (AR-luc). Seventy-five compounds identified through the primary assay were characterized as potential agonists or inactives through confirmation screens and secondary assays. Biochemical binding and AR nuclear translocation assays were performed to confirm direct binding and activation of AR from these compounds. The top seventeen compounds identified were found to bind to AR, and sixteen of them translocated AR from the cytoplasm into the nucleus. Five potentially novel or not well-characterized AR agonists were discovered through primary and follow-up studies. We have identified multiple AR activators, including known AR agonists such as testosterone, as well as novel/not well-known compounds such as prulifloxacin. The information gained from the current study can be directly used to prioritize compounds for further in-depth toxicological evaluations, as well as their potential to disrupt the endocrine system via AR activation.
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Affiliation(s)
- Caitlin Lynch
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Srilatha Sakamuru
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lyuba Varticovski
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Richard S Judson
- National Center for Computational Toxicology, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Keith A Houck
- National Center for Computational Toxicology, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Nicole C Kleinstreuer
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health,Research Triangle Park, NC, USA
| | - Warren Casey
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health,Research Triangle Park, NC, USA
| | - Richard S Paules
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health,Research Triangle Park, NC, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
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49
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Abstract
The assembly of specialized sub-nuclear microenvironments known as nuclear bodies (NBs) is important for promoting efficient nuclear function. In particular, the Cajal body (CB), a prominent NB that facilitates spliceosomal snRNP biogenesis, assembles in response to genomic cues. Here, we detail the factors that regulate CB assembly and structural maintenance. These include the importance of transcription at nucleating gene loci, the grouping of these genes on human chromosomes 1, 6 and 17, as well as cell cycle and biochemical regulation of CB protein function. We also speculate on the correlation between CB formation and RNA splicing levels in neurons and cancer. The timing and location of these specific molecular events is critical to CB assembly and its contribution to genome function. However, further work is required to explore the emerging biophysical characteristics of CB assembly and the impact upon subsequent genome reorganization.
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Affiliation(s)
- Iain A. Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine & Science, Chicago Medical School, North Chicago, IL, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine & Science, Chicago Medical School, North Chicago, IL, USA
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50
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Pooley JR, Flynn BP, Grøntved L, Baek S, Guertin MJ, Kershaw YM, Birnie MT, Pellatt A, Rivers CA, Schiltz RL, Hager GL, Lightman SL, Conway-Campbell BL. Genome-Wide Identification of Basic Helix-Loop-Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus. Endocrinology 2017; 158:1486-1501. [PMID: 28200020 PMCID: PMC5460825 DOI: 10.1210/en.2016-1929] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/03/2017] [Indexed: 12/14/2022]
Abstract
Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites are dependent on the activity of additional signal-activated transcription factors that prime chromatin toward context-specific organization. We hypothesized a stress context dependency for GR binding in hippocampus as a consequence of rapidly induced stress mediators priming chromatin accessibility. Using chromatin immunoprecipitation sequencing to interrogate GR binding, we found no effect of restraint stress context on GR binding, although analysis of sequences underlying GR binding sites revealed mechanistic detail for hippocampal GR function. We note enrichment of GR binding sites proximal to genes linked to structural and organizational roles, an absence of major tethering partners for GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding sites and is proposed as a candidate lineage-determining transcription factor directing hippocampal chromatin access for GRs. Of our GR binding sites, 54% additionally contained half-sites for nuclear factor (NF)-1 that we propose as a collaborative or general transcription factor involved in hippocampal GR function. Our findings imply a dose-dependent and context-independent action of GRs in the hippocampus. Alterations in the expression or activity of NF-1/basic helix-loop-helix factors may play an as yet undetermined role in glucocorticoid-related disease susceptibility and outcome by altering GR access to hippocampal binding sites.
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Affiliation(s)
- John R. Pooley
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Ben P. Flynn
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Songjoon Baek
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael J. Guertin
- University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Yvonne M. Kershaw
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Matthew T. Birnie
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Annie Pellatt
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Caroline A. Rivers
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - R. Louis Schiltz
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Gordon L. Hager
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Stafford L. Lightman
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Becky L. Conway-Campbell
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
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