1
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Verdikt R, Thienpont B. Epigenetic remodelling under hypoxia. Semin Cancer Biol 2024; 98:1-10. [PMID: 38029868 DOI: 10.1016/j.semcancer.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Hypoxia is intrinsic to tumours and contributes to malignancy and metastasis while hindering the efficiency of existing treatments. Epigenetic mechanisms play a crucial role in the regulation of hypoxic cancer cell programs, both in the initial phases of sensing the decrease in oxygen levels and during adaptation to chronic lack of oxygen. During the latter, the epigenetic regulation of tumour biology intersects with hypoxia-sensitive transcription factors in a complex network of gene regulation that also involves metabolic reprogramming. Here, we review the current literature on the epigenetic control of gene programs in hypoxic cancer cells. We highlight common themes and features of such epigenetic remodelling and discuss their relevance for the development of therapeutic strategies.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium; KU Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
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2
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Hu Y, Zhao Y, Li P, Lu H, Li H, Ge J. Hypoxia and panvascular diseases: exploring the role of hypoxia-inducible factors in vascular smooth muscle cells under panvascular pathologies. Sci Bull (Beijing) 2023; 68:1954-1974. [PMID: 37541793 DOI: 10.1016/j.scib.2023.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/13/2023] [Accepted: 07/10/2023] [Indexed: 08/06/2023]
Abstract
As an emerging discipline, panvascular diseases are a set of vascular diseases with atherosclerosis as the common pathogenic hallmark, which mostly affect vital organs like the heart, brain, kidney, and limbs. As the major responser to the most common stressor in the vasculature (hypoxia)-hypoxia-inducible factors (HIFs), and the primary regulator of pressure and oxygen delivery in the vasculature-vascular smooth muscle cells (VSMCs), their own multifaceted nature and their interactions with each other are fascinating. Abnormally active VSMCs (e.g., atherosclerosis, pulmonary hypertension) or abnormally dysfunctional VSMCs (e.g., aneurysms, vascular calcification) are associated with HIFs. These widespread systemic diseases also reflect the interdisciplinary nature of panvascular medicine. Moreover, given the comparable proliferative characteristics exhibited by VSMCs and cancer cells, and the delicate equilibrium between angiogenesis and cancer progression, there is a pressing need for more accurate modulation targets or combination approaches to bolster the effectiveness of HIF targeting therapies. Based on the aforementioned content, this review primarily focused on the significance of integrating the overall and local perspectives, as well as temporal and spatial balance, in the context of the HIF signaling pathway in VSMC-related panvascular diseases. Furthermore, the review discussed the implications of HIF-targeting drugs on panvascular disorders, while considering the trade-offs involved.
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Affiliation(s)
- Yiqing Hu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Yongchao Zhao
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China; Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
| | - Peng Li
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Hao Lu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai 200032, China; Shanghai Clinical Research Center for Interventional Medicine, Shanghai 200032, China.
| | - Hua Li
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China.
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai 200032, China; Shanghai Clinical Research Center for Interventional Medicine, Shanghai 200032, China; Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai 200032, China; Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai 200032, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Department of Cardiology, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China.
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3
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Collier H, Albanese A, Kwok CS, Kou J, Rocha S. Functional crosstalk between chromatin and hypoxia signalling. Cell Signal 2023; 106:110660. [PMID: 36990334 DOI: 10.1016/j.cellsig.2023.110660] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Eukaryotic genomes are organised in a structure called chromatin, comprising of DNA and histone proteins. Chromatin is thus a fundamental regulator of gene expression, as it offers storage and protection but also controls accessibility to DNA. Sensing and responding to reductions in oxygen availability (hypoxia) have recognised importance in both physiological and pathological processes in multicellular organisms. One of the main mechanisms controlling these responses is control of gene expression. Recent findings in the field of hypoxia have highlighted how oxygen and chromatin are intricately linked. This review will focus on mechanisms controlling chromatin in hypoxia, including chromatin regulators such as histone modifications and chromatin remodellers. It will also highlight how these are integrated with hypoxia inducible factors and the knowledge gaps that persist.
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Affiliation(s)
- Harry Collier
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom
| | - Adam Albanese
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom
| | - Chun-Sui Kwok
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom
| | - Jiahua Kou
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom
| | - Sonia Rocha
- Institute of Systems Molecular and Integrative Biology, University of Liverpool, United Kingdom.
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4
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Koukoulas K, Giakountis A, Karagiota A, Samiotaki M, Panayotou G, Simos G, Mylonis I. ERK signalling controls productive HIF-1 binding to chromatin and cancer cell adaptation to hypoxia through HIF-1α interaction with NPM1. Mol Oncol 2021; 15:3468-3489. [PMID: 34388291 PMCID: PMC8637566 DOI: 10.1002/1878-0261.13080] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/13/2021] [Accepted: 08/12/2021] [Indexed: 11/08/2022] Open
Abstract
The hypoxia-inducible factor HIF-1 is essential for oxygen homeostasis. Despite its well-understood oxygen-dependent expression, regulation of its transcriptional activity remains unclear. We show that phosphorylation by ERK1/2, in addition to promoting HIF-1α nuclear accumulation, also enhances its interaction with chromatin and stimulates direct binding to nucleophosmin (NPM1), a histone chaperone and chromatin remodeler. NPM1 is required for phosphorylation-dependent recruitment of HIF-1 to hypoxia-response elements (HREs), its interaction with acetylated histones and high expression of HIF-1 target genes under hypoxia. Transcriptome analysis revealed a significant number of hypoxia-related genes commonly regulated by NPM1 and HIF-1. These NPM1/HIF-1α co-upregulated genes are enriched in three different cancer types and their expression correlates with hypoxic tumor status and worse patient prognosis. In concert, silencing of NPM1 expression or disruption of its association with HIF-1α inhibits metabolic adaptation of cancer cells and triggers apoptotic death upon hypoxia. We suggest that ERK-mediated phosphorylation of HIF-1α regulates its physical interaction with NPM1, which is essential for productive association of HIF-1 with hypoxia target genes and their optimal transcriptional activation, required for survival under low oxygen or tumor growth.
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Affiliation(s)
- Kreon Koukoulas
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis Larissa, 41500, Greece
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis Larissa, 41500, Greece.,Institute for Bio-innovation, BSRC "Alexander Fleming", Vari, 16672, Greece
| | - Angeliki Karagiota
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis Larissa, 41500, Greece
| | - Martina Samiotaki
- Institute for Bio-innovation, BSRC "Alexander Fleming", Vari, 16672, Greece
| | - George Panayotou
- Institute for Bio-innovation, BSRC "Alexander Fleming", Vari, 16672, Greece
| | - George Simos
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis Larissa, 41500, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis Larissa, 41500, Greece.,Gerald Bronfman Department of Oncology, Faculty of Medicine, McGill University, Montreal, H4A 3T2, Canada
| | - Ilias Mylonis
- Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Biopolis Larissa, 41500, Greece
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5
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Han D, Yang P, Qin B, Ji G, Wu Y, Yu L, Zhang H. Upregulation of Nogo-B by hypoxia inducible factor-1 and activator protein-1 in hepatocellular carcinoma. Cancer Sci 2021; 112:2728-2738. [PMID: 33963651 PMCID: PMC8253276 DOI: 10.1111/cas.14941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022] Open
Abstract
Nogo-B is an important regulator of tumor angiogenesis. Expression of Nogo-B is remarkably upregulated in multiple tumor types, especially hepatocellular carcinoma (HCC). Here, we show the transcriptional regulation mechanisms of Nogo-B in liver cancer. In response to hypoxia, expression of Nogo-B significantly increased in HCC tissues and cells. The distal hypoxia-responsive element in the promoter was essential for transcriptional activation of Nogo-B under hypoxic conditions, which is the specific site for hypoxia inducible factor-1α (HIF-1α) binding. In addition, Nogo-B expression was associated with c-Fos expression in HCC tissues. Nogo-B expression was induced by c-Fos, yet inhibited by a dominant negative mutant A-Fos. Deletion and mutation analysis of the predicted activator protein-1 binding sites revealed that functional element mediated the induction of Nogo-B promoter activity, which was confirmed by ChIP. These results indicate that HIF-1α and c-Fos induce the expression of Nogo-B depending on tumor microenvironments, such as hypoxia and low levels of nutrients, and play a role in upregulation of Nogo-B in tumor angiogenesis.
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Affiliation(s)
- Dingding Han
- Department of Clinical LaboratoryShanghai Children’s HospitalShanghai Jiaotong UniversityShanghaiChina
- State Key Laboratory of Genetic EngineeringInstitute of GeneticsSchool of Life SciencesFudan UniversityShanghaiChina
| | - Penggao Yang
- Department of Plastic and Reconstruction SurgeryShanghai Ninth People’s HospitalSchool of MedicineShanghai Jiaotong UniversityShanghaiChina
| | - Bo Qin
- State Key Laboratory of Genetic EngineeringInstitute of GeneticsSchool of Life SciencesFudan UniversityShanghaiChina
| | - Guoqing Ji
- State Key Laboratory of Genetic EngineeringInstitute of GeneticsSchool of Life SciencesFudan UniversityShanghaiChina
| | - Yanhua Wu
- State Key Laboratory of Genetic EngineeringInstitute of GeneticsSchool of Life SciencesFudan UniversityShanghaiChina
| | - Long Yu
- State Key Laboratory of Genetic EngineeringInstitute of GeneticsSchool of Life SciencesFudan UniversityShanghaiChina
| | - Hong Zhang
- Department of Clinical LaboratoryShanghai Children’s HospitalShanghai Jiaotong UniversityShanghaiChina
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6
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DeFrates KG, Franco D, Heber-Katz E, Messersmith PB. Unlocking mammalian regeneration through hypoxia inducible factor one alpha signaling. Biomaterials 2021; 269:120646. [PMID: 33493769 PMCID: PMC8279430 DOI: 10.1016/j.biomaterials.2020.120646] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/19/2020] [Accepted: 12/29/2020] [Indexed: 02/08/2023]
Abstract
Historically, the field of regenerative medicine has aimed to heal damaged tissue through the use of biomaterials scaffolds or delivery of foreign progenitor cells. Despite 30 years of research, however, translation and commercialization of these techniques has been limited. To enable mammalian regeneration, a more practical approach may instead be to develop therapies that evoke endogenous processes reminiscent of those seen in innate regenerators. Recently, investigations into tadpole tail regrowth, zebrafish limb restoration, and the super-healing Murphy Roths Large (MRL) mouse strain, have identified ancient oxygen-sensing pathways as a possible target to achieve this goal. Specifically, upregulation of the transcription factor, hypoxia-inducible factor one alpha (HIF-1α) has been shown to modulate cell metabolism and plasticity, as well as inflammation and tissue remodeling, possibly priming injuries for regeneration. Since HIF-1α signaling is conserved across species, environmental or pharmacological manipulation of oxygen-dependent pathways may elicit a regenerative response in non-healing mammals. In this review, we will explore the emerging role of HIF-1α in mammalian healing and regeneration, as well as attempts to modulate protein stability through hyperbaric oxygen treatment, intermittent hypoxia therapy, and pharmacological targeting. We believe that these therapies could breathe new life into the field of regenerative medicine.
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Affiliation(s)
- Kelsey G DeFrates
- Department of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA.
| | - Daniela Franco
- Department of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA.
| | - Ellen Heber-Katz
- Laboratory of Regenerative Medicine, Lankenau Institute for Medical Research, Wynnewood, PA, USA.
| | - Phillip B Messersmith
- Department of Bioengineering and Materials Science and Engineering, University of California, Berkeley, CA, USA; Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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7
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Riou R, Ladli M, Gerbal-Chaloin S, Bossard P, Gougelet A, Godard C, Loesch R, Lagoutte I, Lager F, Calderaro J, Dos Santos A, Wang Z, Verdier F, Colnot S. ARID1A loss in adult hepatocytes activates β-catenin-mediated erythropoietin transcription. eLife 2020; 9:53550. [PMID: 33084574 PMCID: PMC7641585 DOI: 10.7554/elife.53550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 10/20/2020] [Indexed: 12/13/2022] Open
Abstract
Erythropoietin (EPO) is a key regulator of erythropoiesis. The embryonic liver is the main site of erythropoietin synthesis, after which the kidney takes over. The adult liver retains the ability to express EPO, and we discovered here new players of this transcription, distinct from the classical hypoxia-inducible factor pathway. In mice, genetically invalidated in hepatocytes for the chromatin remodeler Arid1a, and for Apc, the major silencer of Wnt pathway, chromatin was more accessible and histone marks turned into active ones at the Epo downstream enhancer. Activating β-catenin signaling increased binding of Tcf4/β-catenin complex and upregulated its enhancer function. The loss of Arid1a together with β-catenin signaling, resulted in cell-autonomous EPO transcription in mouse and human hepatocytes. In mice with Apc-Arid1a gene invalidations in single hepatocytes, Epo de novo synthesis led to its secretion, to splenic erythropoiesis and to dramatic erythrocytosis. Thus, we identified new hepatic EPO regulation mechanism stimulating erythropoiesis.
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Affiliation(s)
- Rozenn Riou
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), Paris, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,INSERM, CNRS, Institut COCHIN, Paris, France
| | | | - Sabine Gerbal-Chaloin
- INSERM U1183, Université Montpellier, Institute for Regenerative Medicine & Biotherapy (IRMB), Montpellier, France
| | - Pascale Bossard
- Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,INSERM, CNRS, Institut COCHIN, Paris, France
| | - Angélique Gougelet
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), Paris, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,INSERM, CNRS, Institut COCHIN, Paris, France
| | - Cécile Godard
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), Paris, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,INSERM, CNRS, Institut COCHIN, Paris, France
| | - Robin Loesch
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), Paris, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,INSERM, CNRS, Institut COCHIN, Paris, France
| | - Isabelle Lagoutte
- INSERM, CNRS, Institut COCHIN, Paris, France.,Plateforme d'Imageries du Vivant de l'Université de Paris, Paris, France
| | - Franck Lager
- INSERM, CNRS, Institut COCHIN, Paris, France.,Plateforme d'Imageries du Vivant de l'Université de Paris, Paris, France
| | - Julien Calderaro
- INSERM, Université Paris-Est UPEC, Créteil, France.,Department of Pathology, Henri Mondor Hospital, Créteil, France
| | - Alexandre Dos Santos
- INSERM, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif, France
| | - Zhong Wang
- Department of Cardiac Surgery Cardiovascular Research Center, University of Michigan, Ann Arbor, United States
| | | | - Sabine Colnot
- INSERM, Sorbonne Université, Université de Paris, Centre de Recherche des Cordeliers (CRC), Paris, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France.,INSERM, CNRS, Institut COCHIN, Paris, France
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8
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Chen Y, Liu M, Niu Y, Wang Y. Romance of the three kingdoms in hypoxia: HIFs, epigenetic regulators, and chromatin reprogramming. Cancer Lett 2020; 495:211-223. [PMID: 32931886 DOI: 10.1016/j.canlet.2020.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023]
Abstract
Hypoxia is a hallmark of cancer. To cope with hypoxic conditions, tumor cells alter their transcriptional profiles mainly through hypoxia-inducible factors (HIFs) and epigenetic reprogramming. Hypoxia, in part through HIF-dependent mechanisms, influences the expression or activity of epigenetic regulators to control epigenetic reprogramming, including DNA methylation and histone modifications, which regulate hypoxia-responsive gene expression in cells. Conversely, epigenetic regulators and chromatin architecture can modulate the expression, stability, or transcriptional activity of HIF. Understanding the complex networks between HIFs, epigenetic regulators, and chromatin reprogramming in response to hypoxia will provide insight into the fundamental mechanism of transcriptional adaptation to hypoxia, and may help identify novel targets for future therapies. In this review, we will discuss the comprehensive relationship between HIFs, epigenetic regulators, and chromatin reprogramming under hypoxic conditions.
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Affiliation(s)
- Yan Chen
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Zhuhai, Guangdong, 519000, China; School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, China; Biomedical Translational Research Institute, Jinan University, Guangzhou, Guangdong, 510632, China.
| | - Min Liu
- Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Yanling Niu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yijie Wang
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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9
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Chowdhury AR, Zielonka J, Kalyanaraman B, Hartley RC, Murphy MP, Avadhani NG. Mitochondria-targeted paraquat and metformin mediate ROS production to induce multiple pathways of retrograde signaling: A dose-dependent phenomenon. Redox Biol 2020; 36:101606. [PMID: 32604037 PMCID: PMC7327929 DOI: 10.1016/j.redox.2020.101606] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/11/2020] [Indexed: 01/12/2023] Open
Abstract
The mitochondrial electron transport chain is a major source of reactive oxygen species (ROS) and is also a target of ROS, with an implied role in the stabilization of hypoxia-inducible factor (HIF) and induction of the AMPK pathway. Here we used varying doses of two agents, Mito-Paraquat and Mito-Metformin, that have been conjugated to cationic triphenylphosphonium (TPP+) moiety to selectively target them to the mitochondrial matrix compartment, thereby resulting in the site-specific generation of ROS within mitochondria. These agents primarily induce superoxide (O2•-) production by acting on complex I. In Raw264.7 macrophages, C2C12 skeletal myocytes, and HCT116 adenocarcinoma cells, we show that mitochondria-targeted oxidants can induce ROS (O2•- and H2O2). In all three cell lines tested, the mitochondria-targeted agents disrupted membrane potential and activated calcineurin and the Cn-dependent retrograde signaling pathway. Hypoxic culture conditions also induced Cn activation and HIF1α activation in a temporally regulated manner, with the former appearing at shorter exposure times. Together, our results indicate that mitochondrial oxidant-induced retrograde signaling is driven by disruption of membrane potential and activation of Ca2+/Cn pathway and is independent of ROS-induced HIF1α or AMPK pathways.
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Affiliation(s)
- Anindya Roy Chowdhury
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacek Zielonka
- Department of Biophysics and Free Radical Research Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Balaraman Kalyanaraman
- Department of Biophysics and Free Radical Research Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Michael P Murphy
- MRC-Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge, CB2 OXY, UK
| | - Narayan G Avadhani
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Jancewicz I, Siedlecki JA, Sarnowski TJ, Sarnowska E. BRM: the core ATPase subunit of SWI/SNF chromatin-remodelling complex-a tumour suppressor or tumour-promoting factor? Epigenetics Chromatin 2019; 12:68. [PMID: 31722744 PMCID: PMC6852734 DOI: 10.1186/s13072-019-0315-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/31/2019] [Indexed: 02/07/2023] Open
Abstract
BRM (BRAHMA) is a core, SWI2/SNF2-type ATPase subunit of SWI/SNF chromatin-remodelling complex (CRC) involved in various important regulatory processes including development. Mutations in SMARCA2, a BRM-encoding gene as well as overexpression or epigenetic silencing were found in various human diseases including cancer. Missense mutations in SMARCA2 gene were recently connected with occurrence of Nicolaides-Baraitser genetics syndrome. By contrast, SMARCA2 duplication rather than mutations is characteristic for Coffin-Siris syndrome. It is believed that BRM usually acts as a tumour suppressor or a tumour susceptibility gene. However, other studies provided evidence that BRM function may differ depending on the cancer type and the disease stage, where BRM may play a role in the disease progression. The existence of alternative splicing forms of SMARCA2 gene, leading to appearance of truncated functional, loss of function or gain-of-function forms of BRM protein suggest a far more complicated mode of BRM-containing SWI/SNF CRCs actions. Therefore, the summary of recent knowledge regarding BRM alteration in various types of cancer and highlighting of differences and commonalities between BRM and BRG1, another SWI2/SNF2 type ATPase, will lead to better understanding of SWI/SNF CRCs function in cancer development/progression. BRM has been recently proposed as an attractive target for various anticancer therapies including the use of small molecule inhibitors, synthetic lethality induction or proteolysis-targeting chimera (PROTAC). However, such attempts have some limitations and may lead to severe side effects given the homology of BRM ATPase domain to other ATPases, as well as due to the tissue-specific appearance of BRM- and BRG1-containing SWI/SNF CRC classes. Thus, a better insight into BRM-containing SWI/SNF CRCs function in human tissues and cancers is clearly required to provide a solid basis for establishment of new safe anticancer therapies.
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Affiliation(s)
- Iga Jancewicz
- Department of Molecular and Translational Oncology, The Maria Sklodowska-Curie Institute-Oncology Center in Warsaw, Wawelska 15B, 02-034, Warsaw, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, The Maria Sklodowska-Curie Institute-Oncology Center in Warsaw, Wawelska 15B, 02-034, Warsaw, Poland
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
| | - Elzbieta Sarnowska
- Department of Molecular and Translational Oncology, The Maria Sklodowska-Curie Institute-Oncology Center in Warsaw, Wawelska 15B, 02-034, Warsaw, Poland.
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11
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Luo W, Wang Y. Epigenetic regulators: multifunctional proteins modulating hypoxia-inducible factor-α protein stability and activity. Cell Mol Life Sci 2018; 75:1043-1056. [PMID: 29032501 PMCID: PMC5984203 DOI: 10.1007/s00018-017-2684-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/26/2017] [Accepted: 10/09/2017] [Indexed: 12/19/2022]
Abstract
The hypoxia-inducible factor (HIF) is a heterodimeric transcription factor governing a transcriptional program in response to reduced O2 availability in metazoans. It contributes to physiology and pathogenesis of many human diseases through its downstream target genes. Emerging studies have shown that the transcriptional activity of HIF is highly regulated at multiple levels and the epigenetic regulators are essential for HIF-mediated transactivation. In this review, we will discuss the comprehensive regulation of HIF transcriptional activity by different types of epigenetic regulators.
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Affiliation(s)
- Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
- Department of Pharmacology, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
| | - Yingfei Wang
- Department of Pathology, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
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12
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Labrecque MP, Takhar MK, Nason R, Santacruz S, Tam KJ, Massah S, Haegert A, Bell RH, Altamirano-Dimas M, Collins CC, Lee FJS, Prefontaine GG, Cox ME, Beischlag TV. The retinoblastoma protein regulates hypoxia-inducible genetic programs, tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. Oncotarget 2018; 7:24284-302. [PMID: 27015368 PMCID: PMC5029701 DOI: 10.18632/oncotarget.8301] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 03/04/2016] [Indexed: 12/14/2022] Open
Abstract
Loss of tumor suppressor proteins, such as the retinoblastoma protein (Rb), results in tumor progression and metastasis. Metastasis is facilitated by low oxygen availability within the tumor that is detected by hypoxia inducible factors (HIFs). The HIF1 complex, HIF1α and dimerization partner the aryl hydrocarbon receptor nuclear translocator (ARNT), is the master regulator of the hypoxic response. Previously, we demonstrated that Rb represses the transcriptional response to hypoxia by virtue of its association with HIF1. In this report, we further characterized the role Rb plays in mediating hypoxia-regulated genetic programs by stably ablating Rb expression with retrovirally-introduced short hairpin RNA in LNCaP and 22Rv1 human prostate cancer cells. DNA microarray analysis revealed that loss of Rb in conjunction with hypoxia leads to aberrant expression of hypoxia-regulated genetic programs that increase cell invasion and promote neuroendocrine differentiation. For the first time, we have established a direct link between hypoxic tumor environments, Rb inactivation and progression to late stage metastatic neuroendocrine prostate cancer. Understanding the molecular pathways responsible for progression of benign prostate tumors to metastasized and lethal forms will aid in the development of more effective prostate cancer therapies.
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Affiliation(s)
- Mark P Labrecque
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mandeep K Takhar
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Rebecca Nason
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Stephanie Santacruz
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kevin J Tam
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shabnam Massah
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anne Haegert
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert H Bell
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Manuel Altamirano-Dimas
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin C Collins
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Frank J S Lee
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gratien G Prefontaine
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael E Cox
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Timothy V Beischlag
- The Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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13
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Khakshour S, Labrecque MP, Esmaeilsabzali H, Lee FJS, Cox ME, Park EJ, Beischlag TV. Retinoblastoma protein (Rb) links hypoxia to altered mechanical properties in cancer cells as measured by an optical tweezer. Sci Rep 2017; 7:7833. [PMID: 28798482 PMCID: PMC5552853 DOI: 10.1038/s41598-017-07947-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/06/2017] [Indexed: 12/18/2022] Open
Abstract
Hypoxia modulates actin organization via multiple pathways. Analyzing the effect of hypoxia on the biophysical properties of cancer cells is beneficial for studying modulatory signalling pathways by quantifying cytoskeleton rearrangements. We have characterized the biophysical properties of human LNCaP prostate cancer cells that occur in response to loss of the retinoblastoma protein (Rb) under hypoxic stress using an oscillating optical tweezer. Hypoxia and Rb-loss increased cell stiffness in a fashion that was dependent on activation of the extracellular signal-regulated kinase (ERK) and the protein kinase B (AKT)- mammalian target of rapamycin (MTOR) pathways. Pharmacological inhibition of MEK1/2, AKT or MTOR impeded hypoxia-inducible changes in the actin cytoskeleton and inhibited cell migration in Rb-deficient cells conditioned with hypoxia. These results suggest that loss of Rb in transformed hypoxic cancer cells affects MEK1/2-ERK/AKT-MTOR signalling and promotes motility. Thus, the mechanical characterization of cancer cells using an optical tweezer provides an additional technique for cancer diagnosis/prognosis and evaluating therapeutic performance.
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Affiliation(s)
- S Khakshour
- School of Mechatronic Systems Engineering, Faculty of Applied Sciences, Simon Fraser University, Surrey, BC, Canada
| | - M P Labrecque
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - H Esmaeilsabzali
- School of Mechatronic Systems Engineering, Faculty of Applied Sciences, Simon Fraser University, Surrey, BC, Canada
| | - F J S Lee
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - M E Cox
- Department of Urologic Sciences, The Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - E J Park
- School of Mechatronic Systems Engineering, Faculty of Applied Sciences, Simon Fraser University, Surrey, BC, Canada. .,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.
| | - T V Beischlag
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.
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14
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da Motta LL, Ledaki I, Purshouse K, Haider S, De Bastiani MA, Baban D, Morotti M, Steers G, Wigfield S, Bridges E, Li JL, Knapp S, Ebner D, Klamt F, Harris AL, McIntyre A. The BET inhibitor JQ1 selectively impairs tumour response to hypoxia and downregulates CA9 and angiogenesis in triple negative breast cancer. Oncogene 2017; 36:122-132. [PMID: 27292261 PMCID: PMC5061082 DOI: 10.1038/onc.2016.184] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/22/2016] [Accepted: 04/15/2016] [Indexed: 12/16/2022]
Abstract
The availability of bromodomain and extra-terminal inhibitors (BETi) has enabled translational epigenetic studies in cancer. BET proteins regulate transcription by selectively recognizing acetylated lysine residues on chromatin. BETi compete with this process leading to both downregulation and upregulation of gene expression. Hypoxia enables progression of triple negative breast cancer (TNBC), the most aggressive form of breast cancer, partly by driving metabolic adaptation, angiogenesis and metastasis through upregulation of hypoxia-regulated genes (for example, carbonic anhydrase 9 (CA9) and vascular endothelial growth factor A (VEGF-A). Responses to hypoxia can be mediated epigenetically, thus we investigated whether BETi JQ1 could impair the TNBC response induced by hypoxia and exert anti-tumour effects. JQ1 significantly modulated 44% of hypoxia-induced genes, of which two-thirds were downregulated including CA9 and VEGF-A. JQ1 prevented HIF binding to the hypoxia response element in CA9 promoter, but did not alter HIF expression or activity, suggesting some HIF targets are BET-dependent. JQ1 reduced TNBC growth in vitro and in vivo and inhibited xenograft vascularization. These findings identify that BETi dually targets angiogenesis and the hypoxic response, an effective combination at reducing tumour growth in preclinical studies.
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Affiliation(s)
- L L da Motta
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Biochemistry/UFRGS, Porto Alegre, Brazil
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil
| | - I Ledaki
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - K Purshouse
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - S Haider
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - D Baban
- High Throughput Genomics, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M Morotti
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - G Steers
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - S Wigfield
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - E Bridges
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - J-L Li
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute of Translational and Stratified Medicine, Plymouth University, Peninsula Schools of Medicine and Dentistry, Plymouth, UK
| | - S Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Oxford, UK
- Goethe University Frankfurt, Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Campus Riedberg, Frankfurt, Germany
| | - D Ebner
- Nuffield Department of Medicine, Target Discovery Institute (TDI), University of Oxford, Oxford, UK
| | - F Klamt
- Department of Biochemistry/UFRGS, Porto Alegre, Brazil
| | - A L Harris
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - A McIntyre
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Cancer Biology, Division of Cancer and Stem Cells, The University of Nottingham, Nottingham, UK
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15
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Cummins EP, Keogh CE. Respiratory gases and the regulation of transcription. Exp Physiol 2016; 101:986-1002. [DOI: 10.1113/ep085715] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/23/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Eoin P. Cummins
- School of Medicine; University College Dublin; Belfield 4 Dublin Ireland
| | - Ciara E. Keogh
- School of Medicine; University College Dublin; Belfield 4 Dublin Ireland
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16
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Samoilov M, Churilova A, Gluschenko T, Vetrovoy O, Dyuzhikova N, Rybnikova E. Acetylation of histones in neocortex and hippocampus of rats exposed to different modes of hypobaric hypoxia: Implications for brain hypoxic injury and tolerance. Acta Histochem 2016; 118:80-9. [PMID: 26643215 DOI: 10.1016/j.acthis.2015.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/14/2015] [Accepted: 11/16/2015] [Indexed: 12/26/2022]
Abstract
Acetylation of nucleosome histones results in relaxation of DNA and its availability for the transcriptional regulators, and is generally associated with the enhancement of gene expression. Although it is well known that activation of a variety of pro-adaptive genes represents a key event in the development of brain hypoxic/ischemic tolerance, the role of epigenetic mechanisms, in particular histone acetylation, in this process is still unexplored. The aim of the present study was to investigate changes in acetylation of histones in vulnerable brain neurons using original well-standardized model of hypobaric hypoxia and preconditioning-induced tolerance of the brain. Using quantitative immunohistochemistry and Western blot, effects of severe injurious hypobaric hypoxia (SH, 180mm Hg, 3h) and neuroprotective preconditioning mode (three episodes of 360mm Hg for 2h spaced at 24h) on the levels of the acetylated proteins and acetylated H3 Lys24 (H3K24ac) in the neocortex and hippocampus of rats were studied. SH caused global repression of the acetylation processes in the neocortex (layers II-III, V) and hippocampus (CA1, CA3) by 3-24h, and this effect was prevented by the preconditioning. Moreover, hypoxic preconditioning remarkably increased the acetylation of H3K24 in response to SH in the brain areas examined. The preconditioning hypoxia without subsequent SH also stimulated acetylation processes in the neocortex and hippocampus. The moderately enhanced expression of the acetylated proteins in the preconditioned rats was maintained for 24h, whereas acetylation of H3K24 was intense but transient, peaked at 3h. The novel data obtained in the present study indicate that large activation of the acetylation processes, in particular acetylation of histones might be essential for the development of brain hypoxic tolerance.
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Affiliation(s)
- Mikhail Samoilov
- Laboratory of Regulation of Brain Neuron Functions, Pavlov Institute of Physiology, Russian Academy of Sciences, Makarova nab. 6, 199034 St. Petersburg, Russian Federation
| | - Anna Churilova
- Laboratory of Regulation of Brain Neuron Functions, Pavlov Institute of Physiology, Russian Academy of Sciences, Makarova nab. 6, 199034 St. Petersburg, Russian Federation
| | - Tatjana Gluschenko
- Laboratory of Regulation of Brain Neuron Functions, Pavlov Institute of Physiology, Russian Academy of Sciences, Makarova nab. 6, 199034 St. Petersburg, Russian Federation
| | - Oleg Vetrovoy
- Laboratory of Regulation of Brain Neuron Functions, Pavlov Institute of Physiology, Russian Academy of Sciences, Makarova nab. 6, 199034 St. Petersburg, Russian Federation; Department of Biochemistry, Faculty of Biology, St. Petersburg State University, 7-9, Universitetskaya nab., 199034 St. Petersburg, Russian Federation
| | - Natalia Dyuzhikova
- Laboratory of Genetics of High Nervous Activity, Pavlov Institute of Physiology, Russian Academy of Sciences, Makarova nab. 6, 199034 St. Petersburg, Russian Federation
| | - Elena Rybnikova
- Laboratory of Neuroendocrinology, Pavlov Institute of Physiology, Russian Academy of Sciences, Makarova nab. 6, 199034 St. Petersburg, Russian Federation.
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17
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Rybnikova E, Samoilov M. Current insights into the molecular mechanisms of hypoxic pre- and postconditioning using hypobaric hypoxia. Front Neurosci 2015; 9:388. [PMID: 26557049 PMCID: PMC4615940 DOI: 10.3389/fnins.2015.00388] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/05/2015] [Indexed: 12/16/2022] Open
Abstract
Exposure of organisms to repetitive mild hypoxia results in development of brain hypoxic/ischemic tolerance and cross-tolerance to injurious factors of a psycho-emotional nature. Such preconditioning by mild hypobaric hypoxia functions as a “warning” signal which prepares an organism, and in particular the brain, to subsequent more harmful conditions. The endogenous defense processes which are mobilized by hypoxic preconditioning and result in development of brain tolerance are based on evolutionarily acquired gene-determined mechanisms of adaptation and neuroprotection. They involve an activation of intracellular cascades including kinases, transcription factors and changes in expression of multiple regulatory proteins in susceptible areas of the brain. On the other hand they lead to multilevel modifications of the hypothalamic-pituitary-adrenal endocrine axis regulating various functions in the organism. All these components are engaged sequentially in the initiation, induction and expression of hypoxia-induced tolerance. A special role belongs to the epigenetic regulation of gene expression, in particular of histone acetylation leading to changes in chromatin structure which ensure access of pro-adaptive transcription factors activated by preconditioning to the promoters of target genes. Mechanisms of another, relatively novel, neuroprotective phenomenon termed hypoxic postconditioning (an application of mild hypoxic episodes after severe insults) are still largely unknown but according to recent data they involve apoptosis-related proteins, hypoxia-inducible factor and neurotrophins. The fundamental data accumulated to date and discussed in this review open new avenues for elaboration of the effective therapeutic applications of hypoxic pre- and postconditioning.
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Affiliation(s)
- Elena Rybnikova
- Laboratory of Neuroendocrinology, and Laboratory of Regulation of Brain Neuron Functions, Pavlov Institute of Physiology, Russian Academy of Sciences St. Petersburg, Russia
| | - Mikhail Samoilov
- Laboratory of Neuroendocrinology, and Laboratory of Regulation of Brain Neuron Functions, Pavlov Institute of Physiology, Russian Academy of Sciences St. Petersburg, Russia
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18
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Abstract
Oxygen is the basic molecule which supports life and it truly is "god's gift to life." Despite its immense importance, research on "oxygen biology" has never received the light of the day and has been limited to physiological and biochemical studies. It seems that in modern day biology, oxygen research is summarized in one word "hypoxia." Scientists have focused on hypoxia-induced transcriptomics and molecular-cellular alterations exclusively in disease models. Interestingly, the potential of oxygen to control the basic principles of biology like homeostatic maintenance, transcription, replication, and protein folding among many others, at the molecular level, has been completely ignored. Here, we present a perspective on the crucial role played by oxygen in regulation of basic biological phenomena. Our conclusion highlights the importance of establishing novel research areas like oxygen biology, as there is great potential in this field for basic science discoveries and clinical benefits to the society.
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19
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Hypoxia Signaling Cascade for Erythropoietin Production in Hepatocytes. Mol Cell Biol 2015; 35:2658-72. [PMID: 26012551 DOI: 10.1128/mcb.00161-15] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/22/2015] [Indexed: 01/01/2023] Open
Abstract
Erythropoietin (Epo) is produced in the kidney and liver in a hypoxia-inducible manner via the activation of hypoxia-inducible transcription factors (HIFs) to maintain oxygen homeostasis. Accelerating Epo production in hepatocytes is one plausible therapeutic strategy for treating anemia caused by kidney diseases. To elucidate the regulatory mechanisms of hepatic Epo production, we analyzed mouse lines harboring liver-specific deletions of genes encoding HIF-prolyl-hydroxylase isoforms (PHD1, PHD2, and PHD3) that mediate the inactivation of HIF1α and HIF2α under normal oxygen conditions. The loss of all PHD isoforms results in both polycythemia, which is caused by Epo overproduction, and fatty livers. We found that deleting any combination of two PHD isoforms induces polycythemia without steatosis complications, whereas the deletion of a single isoform induces no apparent phenotype. Polycythemia is prevented by the loss of either HIF2α or the hepatocyte-specific Epo gene enhancer (EpoHE). Chromatin analyses show that the histones around EpoHE dissociate from the nucleosome structure after HIF2α activation. HIF2α also induces the expression of HIF3α, which is involved in the attenuation of Epo production. These results demonstrate that the total amount of PHD activity is more important than the specific function of each isoform for hepatic Epo expression regulated by a PHD-HIF2α-EpoHE cascade in vivo.
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20
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Dutta B, Yan R, Lim SK, Tam JP, Sze SK. Quantitative profiling of chromatome dynamics reveals a novel role for HP1BP3 in hypoxia-induced oncogenesis. Mol Cell Proteomics 2014; 13:3236-49. [PMID: 25100860 DOI: 10.1074/mcp.m114.038232] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In contrast to the intensely studied genetic and epigenetic changes that induce host cell transformation to initiate tumor development, those that promote the malignant progression of cancer remain poorly defined. As emerging evidence suggests that the hypoxic tumor microenvironment could re-model the chromatin-associated proteome (chromatome) to induce epigenetic changes and alter gene expression in cancer cells, we hypothesized that hypoxia-driven evolution of the chromatome promotes malignant changes and the development of therapy resistance in tumor cells. To test this hypothesis, we isolated chromatins from tumor cells treated with varying conditions of normoxia, hypoxia, and re-oxygenation and then partially digested them with DNase I and analyzed them for changes in euchromatin- and heterochromatin-associated proteins using an iTRAQ-based quantitative proteomic approach. We identified a total of 1446 proteins with a high level of confidence, including 819 proteins that were observed to change their chromatin association topology under hypoxic conditions. These hypoxia-sensitive proteins included key mediators of chromatin organization, transcriptional regulation, and DNA repair. Furthermore, our proteomic and functional experiments revealed a novel role for the chromatin organizer protein HP1BP3 in mediating chromatin condensation during hypoxia, leading to increased tumor cell viability, radio-resistance, chemo-resistance, and self-renewal. Taken together, our findings indicate that HP1BP3 is a key mediator of tumor progression and cancer cell acquisition of therapy-resistant traits, and thus might represent a novel therapeutic target in a range of human malignancies.
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Affiliation(s)
- Bamaprasad Dutta
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551
| | - Ren Yan
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551
| | - Sai Kiang Lim
- §Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, Singapore 138648
| | - James P Tam
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551
| | - Siu Kwan Sze
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551;
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21
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A TRIP230-retinoblastoma protein complex regulates hypoxia-inducible factor-1α-mediated transcription and cancer cell invasion. PLoS One 2014; 9:e99214. [PMID: 24919196 PMCID: PMC4053355 DOI: 10.1371/journal.pone.0099214] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/12/2014] [Indexed: 12/15/2022] Open
Abstract
Localized hypoxia in solid tumors activates transcriptional programs that promote the metastatic transformation of cells. Like hypoxia-inducible hyper-vascularization, loss of the retinoblastoma protein (Rb) is a trait common to advanced stages of tumor progression in many metastatic cancers. However, no link between the role of Rb and hypoxia-driven metastatic processes has been established. We demonstrated that Rb is a key mediator of the hypoxic response mediated by HIF1α/β, the master regulator of the hypoxia response, and its essential co-activator, the thyroid hormone receptor/retinoblastoma-interacting protein (TRIP230). Furthermore, loss of Rb unmasks the full co-activation potential of TRIP230. Using small inhibitory RNA approaches in vivo, we established that Rb attenuates the normal physiological response to hypoxia by HIF1α. Notably, loss of Rb results in hypoxia-dependent biochemical changes that promote acquisition of an invasive phenotype in MCF7 breast cancer cells. In addition, Rb is present in HIF1α-ARNT/HIF1β transcriptional complexes associated with TRIP230 as determined by co-immuno-precipitation, GST-pull-down and ChIP assays. These results demonstrate that Rb is a negative modulator of hypoxia-regulated transcription by virtue of its direct effects on the HIF1 complex. This work represents the first link between the functional ablation of Rb in tumor cells and HIF1α-dependent transcriptional activation and invasion.
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22
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Chromatin-modifying agents for epigenetic reprogramming and endogenous neural stem cell-mediated repair in stroke. Transl Stroke Res 2013; 2:7-16. [PMID: 24014083 DOI: 10.1007/s12975-010-0051-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The recent explosion of interest in epigenetics and chromatin biology has made a significant impact on our understanding of the pathophysiology of cerebral ischemia and led to the identification of new treatment strategies for stroke, such as those that employ histone deacetylase inhibitors. These are key advances; however, the rapid pace of discovery in chromatin biology and innovation in the development of chromatin-modifying agents implies there are emerging classes of drugs that may also have potential benefits in stroke. Herein, we discuss how various chromatin regulatory factors and their recently identified inhibitors may serve as drug targets and therapeutic agents for stroke, respectively. These factors primarily include members of the repressor element-1 silencing transcription factor (REST)/neuron-restrictive silencer factor macromolecular complex, polycomb group (PcG) proteins, and associated chromatin remodeling factors, which have been linked to the pathophysiology of cerebral ischemia. Further, we suggest that, because of the key roles played by REST, PcG proteins and other chromatin remodeling factors in neural stem and progenitor cell (NSPC) biology, chromatin-modifying agents can be utilized not only to mitigate ischemic injury directly but also potentially to promote endogenous NSPC-mediated brain repair mechanisms.
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23
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Holik AZ, Krzystyniak J, Young M, Richardson K, Jardé T, Chambon P, Shorning BY, Clarke AR. Brg1 is required for stem cell maintenance in the murine intestinal epithelium in a tissue-specific manner. Stem Cells 2013; 31:2457-66. [PMID: 23922304 DOI: 10.1002/stem.1498] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Accepted: 07/07/2013] [Indexed: 01/08/2023]
Abstract
Brg1 is a chromatin remodeling factor involved in mediation of a plethora of signaling pathways leading to its participation in various physiological processes both during development and in adult tissues. Among other signaling pathways, the Wnt pathway has been proposed to require Brg1 for transactivation of its target genes. Given the pivotal role of the Wnt pathway in the maintenance of normal intestinal homeostasis, we aimed to investigate the effects of Brg1 loss on the intestinal physiology. To this end, we deleted Brg1 in the murine small and large intestinal epithelia using a range of transgenic approaches. Pan-epithelial loss of Brg1 in the small intestine resulted in crypt ablation, while partial Brg1 deficiency led to gradual repopulation of the intestinal mucosa with wild-type cells. In contrast, Brg1 loss in the large intestinal epithelium was compensated by upregulation of Brm. We propose that while Brg1 is dispensable for the survival and function of the progenitor and differentiated cells in the murine intestinal epithelium, it is essential for the maintenance of the stem cell population in a tissue-specific manner.
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Affiliation(s)
- Aliaksei Z Holik
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom; Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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24
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Dengler VL, Galbraith M, Espinosa JM. Transcriptional regulation by hypoxia inducible factors. Crit Rev Biochem Mol Biol 2013; 49:1-15. [PMID: 24099156 DOI: 10.3109/10409238.2013.838205] [Citation(s) in RCA: 518] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The cellular response to oxygen deprivation is governed largely by a family of transcription factors known as Hypoxia Inducible Factors (HIFs). This review focuses on the molecular mechanisms by which HIFs regulate the transcriptional apparatus to enable the cellular and organismal response to hypoxia. We discuss here how the various HIF polypeptides, their posttranslational modifications, binding partners and transcriptional cofactors affect RNA polymerase II activity to drive context-dependent transcriptional programs during hypoxia.
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Affiliation(s)
- Veronica L Dengler
- Howard Hughes Medical Institute & Department of Molecular, Cellular and Developmental Biology, The University of Colorado at Boulder, Boulder, CO 80309-0347, U.S.A
| | - Matthew Galbraith
- Howard Hughes Medical Institute & Department of Molecular, Cellular and Developmental Biology, The University of Colorado at Boulder, Boulder, CO 80309-0347, U.S.A
| | - Joaquín M Espinosa
- Howard Hughes Medical Institute & Department of Molecular, Cellular and Developmental Biology, The University of Colorado at Boulder, Boulder, CO 80309-0347, U.S.A
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25
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Muscari C, Giordano E, Bonafè F, Govoni M, Pasini A, Guarnieri C. Priming adult stem cells by hypoxic pretreatments for applications in regenerative medicine. J Biomed Sci 2013; 20:63. [PMID: 23985033 PMCID: PMC3765890 DOI: 10.1186/1423-0127-20-63] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 08/24/2013] [Indexed: 12/16/2022] Open
Abstract
The efficiency of regenerative medicine can be ameliorated by improving the biological performances of stem cells before their transplantation. Several ex-vivo protocols of non-damaging cell hypoxia have been demonstrated to significantly increase survival, proliferation and post-engraftment differentiation potential of stem cells. The best results for priming cultured stem cells against a following, otherwise lethal, ischemic stress have been obtained with brief intermittent episodes of hypoxia, or anoxia, and reoxygenation in accordance with the extraordinary protection afforded by the conventional maneuver of ischemic preconditioning in severely ischemic organs. These protocols of hypoxic preconditioning can be rather easily reproduced in a laboratory; however, more suitable pharmacological interventions inducing stem cell responses similar to those activated in hypoxia are considered among the most promising solutions for future applications in cell therapy. Here we want to offer an up-to-date review of the molecular mechanisms translating hypoxia into beneficial events for regenerative medicine. To this aim the involvement of epigenetic modifications, microRNAs, and oxidative stress, mainly activated by hypoxia inducible factors, will be discussed. Stem cell adaptation to their natural hypoxic microenvironments (niche) in healthy and neoplastic tissues will be also considered.
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Affiliation(s)
- Claudio Muscari
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126, Bologna, Italy.
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Fang F, Chen D, Yu L, Dai X, Yang Y, Tian W, Cheng X, Xu H, Weng X, Fang M, Zhou J, Gao Y, Chen Q, Xu Y. Proinflammatory stimuli engage Brahma related gene 1 and Brahma in endothelial injury. Circ Res 2013; 113:986-96. [PMID: 23963727 DOI: 10.1161/circresaha.113.301296] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RATIONALE Endothelial dysfunction inflicted by inflammation is found in a host of cardiovascular pathologies. One hallmark event in this process is the aggregation and adhesion of leukocyte to the vessel wall mediated by the upregulation of adhesion molecules (CAM) in endothelial cells at the transcriptional level. The epigenetic modulator(s) of CAM transactivation and its underlying pathophysiological relevance remain poorly defined. OBJECTIVE Our goal was to determine the involvement of Brahma related gene 1 (Brg1) and Brahma (Brm) in CAM transactivation and its relevance in the pathogenesis of atherosclerosis. METHODS AND RESULTS In the present study, we report that proinflammatory stimuli augmented the expression of Brg1 and Brm in vitro in cultured endothelial cells and in vivo in arteries isolated from rodents. Overexpression of Brg1 and Brm promoted while knockdown of Brg1 and Brm abrogated transactivation of adhesion molecules and leukocyte adhesion induced by inflammatory signals. Brg1 and Brm interacted with and were recruited to the CAM promoters by nuclear factor κB/p65. Conversely, depletion of Brg1 and Brm disrupted the kinetics of p65 binding on CAM promoters and crippled CAM activation. Silencing of Brg1 and Brm also altered key epigenetic changes associated with CAM transactivation. Of intrigue, 17β-estradiol antagonized both the expression and activity of Brg1/Brm. Most importantly, endothelial-targeted elimination of Brg1/Brm conferred atheroprotective effects to Apoe(-/-) mice on a Western diet. CONCLUSIONS Our data suggest that Brg1 and Brm integrate various proinflammatory cues into CAM transactivation and endothelial malfunction and, as such, may serve as potential therapeutic targets in treating inflammation-related cardiovascular diseases.
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Affiliation(s)
- Fei Fang
- From the State Key Laboratory of Reproductive Medicine, and Atherosclerosis Research Center, Provincial Key Laboratory of Cardiovascular Disease; and Department of Pathophysiology, Nanjing Medical University, Nanjing, China
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BRG1 and BRM chromatin-remodeling complexes regulate the hypoxia response by acting as coactivators for a subset of hypoxia-inducible transcription factor target genes. Mol Cell Biol 2013; 33:3849-63. [PMID: 23897427 DOI: 10.1128/mcb.00731-13] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Chromatin remodeling is an active process, which represses or enables the access of transcription machinery to genes in response to external stimuli, including hypoxia. However, in hypoxia, the specific requirement, as well as the molecular mechanism by which the chromatin-remodeling complexes regulate gene expression, remains unclear. In this study, we report that the Brahma (BRM) and Brahma-related gene 1 (BRG1) ATPase-containing SWI/SNF chromatin-remodeling complexes promote the expression of the hypoxia-inducible transcription factor 1α (HIF1α) and HIF2α genes and also promote hypoxic induction of a subset of HIF1 and HIF2 target genes. We show that BRG1 or BRM knockdown in Hep3B and RCC4T cells reduces hypoxic induction of HIF target genes, while reexpression of BRG1 or BRM in BRG1/BRM-deficient SW13 cells increases HIF target gene activation. Mechanistically, HIF1 and HIF2 increase the hypoxic induction of HIF target genes by recruiting BRG1 complexes to HIF target gene promoters, which promotes nucleosome remodeling of HIF target gene promoters in a BRG1 ATPase-dependent manner. Importantly, we found that the function of BRG1 complexes in hypoxic SW13 and RCC4T cells is dictated by the HIF-mediated hypoxia response and could be opposite from their function in normoxic SW13 and RCC4T cells.
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Tumor necrosis factor α-induced hypoxia-inducible factor 1α-β-catenin axis regulates major histocompatibility complex class I gene activation through chromatin remodeling. Mol Cell Biol 2013; 33:2718-31. [PMID: 23671189 DOI: 10.1128/mcb.01254-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Hypoxia-inducible factor 1α (HIF-1α) plays a crucial role in the progression of glioblastoma multiforme tumors, which are characterized by their effective immune escape mechanisms. As major histocompatibility complex class I (MHC-I) is involved in glioma immune evasion and since HIF-1α is a pivotal link between inflammation and glioma progression, the role of tumor necrosis factor alpha (TNF-α)-induced inflammation in MHC-I gene regulation was investigated. A TNF-α-induced increase in MHC-I expression and transcriptional activation was concurrent with increased HIF-1α, ΝF-κΒ, and β-catenin activities. While knockdown of HIF-1α and β-catenin abrogated TNF-α-induced MHC-I activation, NF-κB had no effect. β-Catenin inhibition abrogated HIF-1α activation and vice versa, and this HIF-1α-β-catenin axis positively regulated CREB phosphorylation. Increased CREB activation was accompanied by its increased association with β-catenin and CBP. Chromatin immunoprecipitation revealed increased CREB enrichment at CRE/site α on the MHC-I promoter in a β-catenin-dependent manner. β-Catenin replaced human Brahma (hBrm) with Brg1 as the binding partner for CREB at the CRE site. The hBrm-to-Brg1 switch is crucial for MHC-I regulation, as ATPase-deficient Brg1 abolished TNF-α-induced MHC-I expression. β-Catenin also increased the association of MHC-I enhanceosome components RFX5 and NF-YB at the SXY module. CREB acts as a platform for assembling coactivators and chromatin remodelers required for MHC-I activation in a HIF-1α/β-catenin-dependent manner.
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Guo S, Zhou Y, Xing C, Lok J, Som AT, Ning M, Ji X, Lo EH. The vasculome of the mouse brain. PLoS One 2012; 7:e52665. [PMID: 23285140 PMCID: PMC3527566 DOI: 10.1371/journal.pone.0052665] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/20/2012] [Indexed: 01/08/2023] Open
Abstract
The blood vessel is no longer viewed as passive plumbing for the brain. Increasingly, experimental and clinical findings suggest that cerebral endothelium may possess endocrine and paracrine properties – actively releasing signals into and receiving signals from the neuronal parenchyma. Hence, metabolically perturbed microvessels may contribute to central nervous system (CNS) injury and disease. Furthermore, cerebral endothelium can serve as sensors and integrators of CNS dysfunction, releasing measurable biomarkers into the circulating bloodstream. Here, we define and analyze the concept of a brain vasculome, i.e. a database of gene expression patterns in cerebral endothelium that can be linked to other databases and systems of CNS mediators and markers. Endothelial cells were purified from mouse brain, heart and kidney glomeruli. Total RNA were extracted and profiled on Affymetrix mouse 430 2.0 micro-arrays. Gene expression analysis confirmed that these brain, heart and glomerular preparations were not contaminated by brain cells (astrocytes, oligodendrocytes, or neurons), cardiomyocytes or kidney tubular cells respectively. Comparison of the vasculome between brain, heart and kidney glomeruli showed that endothelial gene expression patterns were highly organ-dependent. Analysis of the brain vasculome demonstrated that many functionally active networks were present, including cell adhesion, transporter activity, plasma membrane, leukocyte transmigration, Wnt signaling pathways and angiogenesis. Analysis of representative genome-wide-association-studies showed that genes linked with Alzheimer’s disease, Parkinson’s disease and stroke were detected in the brain vasculome. Finally, comparison of our mouse brain vasculome with representative plasma protein databases demonstrated significant overlap, suggesting that the vasculome may be an important source of circulating signals in blood. Perturbations in cerebral endothelial function may profoundly affect CNS homeostasis. Mapping and dissecting the vasculome of the brain in health and disease may provide a novel database for investigating disease mechanisms, assessing therapeutic targets and exploring new biomarkers for the CNS.
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Affiliation(s)
- Shuzhen Guo
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (SG); (EHL)
| | - Yiming Zhou
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Massachusetts Institute of Technology and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Changhong Xing
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Josephine Lok
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Angel T. Som
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - MingMing Ning
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Clinical Proteomics Research Center, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xunming Ji
- Cerebrovascular Research Center, XuanWu Hospital, Capital Medical University, Beijing, Peoples Republic of China
| | - Eng H. Lo
- Neuroprotection Research Laboratory, Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Clinical Proteomics Research Center, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (SG); (EHL)
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Melvin A, Rocha S. Chromatin as an oxygen sensor and active player in the hypoxia response. Cell Signal 2012; 24:35-43. [PMID: 21924352 PMCID: PMC3476533 DOI: 10.1016/j.cellsig.2011.08.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 08/29/2011] [Indexed: 12/28/2022]
Abstract
Changes in the availability or demand for oxygen induce dramatic changes at the cellular level. Primarily, activation of a family of oxygen labile transcription factors, Hypoxia Inducible Factor (HIF), initiates a variety of cellular processes required to re-instate oxygen homeostasis. Oxygen is sensed by molecular dioxygenases in cells, such as the prolyl-hydroxylases (PHDs), enzymes which are responsible for the oxygen-dependent regulation of HIF. As HIF is a transcription factor it must bind DNA sequences of its target genes possibly in the context of a complex chromatin structure. How chromatin structure changes in response to hypoxia is currently unknown. However, the identification of a novel class of histone demethylases as true dioxygenases suggests that chromatin can act as an oxygen sensor and plays an active role in the coordination of the cellular response to hypoxia. This review will discuss the current knowledge on how hypoxia engages with different proteins involved in chromatin organisation and dynamics.
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Key Words
- hif, hypoxia inducible factor
- arnt, aryl hydrocarbon nuclear translocator
- vhl, von hippel lindau
- phd, prolyl-hydroxylase
- fih, factor inhibiting hif
- chip, chromatin immunoprecipitation
- swi/snf, switch/sucrose nonfermentable
- iswi, imitation switch
- chd, chromodomain helicase dna-binding
- nurf, nucleosome remodelling factor
- chrac, chromatin remodelling and assembly complex
- acf, atp-utilising chromatin remodelling and assembly factor
- norc, nucleolar remodelling complex
- rsf, remodelling and spacing factor
- wich, wstf–iswi chromatin remodelling complex
- nurd, nucleosome remodelling and histone deacetylase
- srcap, snf2-related cbp activator protein
- trrap, transformation/transcription domain-associated protein/tip60
- hat, histone acetyl transferase
- hdac, histone deacetylase
- lsd1, lysine-specific demethylase-1
- jmjc, jumonji c domain
- hypoxia
- chromatin
- hif
- transcription
- chromatin remodellers
- jmjc demethylases
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Affiliation(s)
| | - Sonia Rocha
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom
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Perez-Perri JI, Acevedo JM, Wappner P. Epigenetics: new questions on the response to hypoxia. Int J Mol Sci 2011; 12:4705-21. [PMID: 21845106 PMCID: PMC3155379 DOI: 10.3390/ijms12074705] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 07/08/2011] [Accepted: 07/08/2011] [Indexed: 12/16/2022] Open
Abstract
Reduction in oxygen levels below normal concentrations plays important roles in different normal and pathological conditions, such as development, tumorigenesis, chronic kidney disease and stroke. Organisms exposed to hypoxia trigger changes at both cellular and systemic levels to recover oxygen homeostasis. Most of these processes are mediated by Hypoxia Inducible Factors, HIFs, a family of transcription factors that directly induce the expression of several hundred genes in mammalian cells. Although different aspects of HIF regulation are well known, it is still unclear by which precise mechanism HIFs activate transcription of their target genes. Concomitantly, hypoxia provokes a dramatic decrease of general transcription that seems to rely in part on epigenetic changes through a poorly understood mechanism. In this review we discuss the current knowledge on chromatin changes involved in HIF dependent gene activation, as well as on other epigenetic changes, not necessarily linked to HIF that take place under hypoxic conditions.
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Affiliation(s)
- Joel I. Perez-Perri
- Instituto Leloir, Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina; E-Mails: (J.I.P.-P.); (J.M.A.)
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires C1033AAJ, Argentina
| | - Julieta M. Acevedo
- Instituto Leloir, Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina; E-Mails: (J.I.P.-P.); (J.M.A.)
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires C1033AAJ, Argentina
| | - Pablo Wappner
- Instituto Leloir, Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina; E-Mails: (J.I.P.-P.); (J.M.A.)
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires C1033AAJ, Argentina
- Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +54-11-5238-7500 ext.3112; Fax: +54-11-5238-7501
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Specific contribution of the erythropoietin gene 3' enhancer to hepatic erythropoiesis after late embryonic stages. Mol Cell Biol 2011; 31:3896-905. [PMID: 21746884 DOI: 10.1128/mcb.05463-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Erythropoietin (Epo) is secreted from the liver and kidney, where Epo production is strictly regulated at the transcriptional level in a hypoxia- and/or anemia-inducible manner. Here, we examined the in vivo function of the enhancer located 3' to the Epo gene (EpoE-3'). Reporter transgenic-mouse analyses revealed that the EpoE-3' enhancer is necessary and sufficient for the liver-specific and hypoxia-responsive expression of the gene after embryonic day 14.5 (E14.5). However, the enhancer is dispensable for Epo gene expression in the kidney and early-stage embryonic liver. Genetic removal of EpoE-3' from the endogenous Epo gene resulted in mice with severe anemia at late embryonic and neonatal stages due to defects in hepatic erythropoiesis, but early hepatic and splenic erythropoiesis was not affected. The mutant mice recover from the anemia in the juvenile period when major Epo production switches from the liver to the kidney. These results demonstrate that EpoE-3' is necessary for late hepatic erythropoiesis by specifically supporting paracrine production of Epo in the liver. In contrast, Epo production in the kidney utilizes distinct regulatory machinery and supports erythropoiesis in the bone marrow and spleen in adult animals.
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33
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Dekanty A, Romero NM, Bertolin AP, Thomas MG, Leishman CC, Perez-Perri JI, Boccaccio GL, Wappner P. Drosophila genome-wide RNAi screen identifies multiple regulators of HIF-dependent transcription in hypoxia. PLoS Genet 2010; 6:e1000994. [PMID: 20585616 PMCID: PMC2891703 DOI: 10.1371/journal.pgen.1000994] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 05/19/2010] [Indexed: 01/08/2023] Open
Abstract
Hypoxia-inducible factors (HIFs) are a family of evolutionary conserved alpha-beta heterodimeric transcription factors that induce a wide range of genes in response to low oxygen tension. Molecular mechanisms that mediate oxygen-dependent HIF regulation operate at the level of the alpha subunit, controlling protein stability, subcellular localization, and transcriptional coactivator recruitment. We have conducted an unbiased genome-wide RNA interference (RNAi) screen in Drosophila cells aimed to the identification of genes required for HIF activity. After 3 rounds of selection, 30 genes emerged as critical HIF regulators in hypoxia, most of which had not been previously associated with HIF biology. The list of genes includes components of chromatin remodeling complexes, transcription elongation factors, and translational regulators. One remarkable hit was the argonaute 1 (ago1) gene, a central element of the microRNA (miRNA) translational silencing machinery. Further studies confirmed the physiological role of the miRNA machinery in HIF–dependent transcription. This study reveals the occurrence of novel mechanisms of HIF regulation, which might contribute to developing novel strategies for therapeutic intervention of HIF–related pathologies, including heart attack, cancer, and stroke. Adaptation of cells to low oxygen (hypoxia) is a physiological response related to important diseases, including heart attacks, stroke, cancer, and diabetes. The mechanisms that mediate adaptation to hypoxia in humans are almost identical to those operating in diverse animal species, including mice, worms, and insects. The master regulator of cellular responses to hypoxia is a transcription factor named HIF, which induces a set of genes that mediate adaptation to oxygen starvation. Although it is known that regulation of HIF occurs mainly at the level of protein degradation and transcriptional coactivator recruitment, a comprehensive screen for HIF regulators has not been performed before. In this work, we have conducted an RNAi-based screen of the genome of the fruit fly Drosophila melanogaster, searching for genes that are required for HIF activity. This screen carried out in a cell culture system led to the definition of 30 critical regulators of HIF, most of which have not been associated with hypoxia biology before. The hits of the screen included components of chromatin remodeling complexes, transcription elongation factors, and translational regulators. Our results open the possibility of performing detailed studies on HIF regulation that may lead to novel therapeutic strategies for important human diseases.
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Affiliation(s)
- Andrés Dekanty
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nuria M. Romero
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular, y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Agustina P. Bertolin
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - María G. Thomas
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | | | | | - Graciela L. Boccaccio
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Pablo Wappner
- Instituto Leloir, Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular, y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- * E-mail:
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Zhou X, Sun H, Chen H, Zavadil J, Kluz T, Arita A, Costa M. Hypoxia induces trimethylated H3 lysine 4 by inhibition of JARID1A demethylase. Cancer Res 2010; 70:4214-21. [PMID: 20406991 DOI: 10.1158/0008-5472.can-09-2942] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Histone H3 lysine 4 (H3K4) trimethylation (H3K4me3) at the promoter region of genes has been linked to transcriptional activation. In the present study, we found that hypoxia (1% oxygen) increased H3K4me3 in both normal human bronchial epithelial Beas-2B cells and human lung carcinoma A549 cells. The increase of H3K4me3 from hypoxia was likely caused by the inhibition of H3K4 demethylating activity, as hypoxia still increased H3K4me3 in methionine-deficient medium. Furthermore, an in vitro histone demethylation assay showed that 1% oxygen decreased the activity of H3K4 demethylases in Beas-2B nuclear extracts because ambient oxygen tensions were required for the demethylation reaction to proceed. Hypoxia only minimally increased H3K4me3 in the BEAS-2B cells with knockdown of JARID1A, which is the major histone H3K4 demethylase in this cell line. However, the mRNA and protein levels of JARID1A were not affected by hypoxia. GeneChip and pathway analysis in JARID1A knockdown Beas-2B cells revealed that JARID1A regulates the expression of hundreds of genes involved in different cellular functions, including tumorigenesis. Knocking down of JARID1A increased H3K4me3 at the promoters of HMOX1 and DAF genes. Thus, these results indicate that hypoxia might target JARID1A activity, which in turn increases H3K4me3 at both the global and gene-specific levels, leading to the altered programs of gene expression and tumor progression.
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Affiliation(s)
- Xue Zhou
- Nelson Institute of Environmental Medicine, New York University School of Medicine, Tuxedo, New York 10987, USA
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Wang F, Zhang R, Wu X, Hankinson O. Roles of coactivators in hypoxic induction of the erythropoietin gene. PLoS One 2010; 5:e10002. [PMID: 20368990 PMCID: PMC2848849 DOI: 10.1371/journal.pone.0010002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 03/09/2010] [Indexed: 11/24/2022] Open
Abstract
Background Hypoxia-inducible expression of the erythropoietin (EPO) gene is mediated principally by hypoxia-inducible factor 2α (HIF-2α) in Hep3B cells under physiologic conditions. How/whether p300/CBP and the members of p160 coactivator family potentiate hypoxic induction of endogenous EPO and other HIF-2α and hypoxia-inducible factor 1α (HIF-1α) target genes remains unclear. Methodology/Principal Findings We demonstrate, using chromatin immunoprecipitation (ChIP) analysis, that the histone acetyl transferase (HAT) coactivators p300, SRC-1 and SRC-3 are recruited to the 3′ enhancer of the EPO gene upon hypoxic stimulation, and that each associates with the enhancer in a periodic fashion. Hypoxia induced acetylation of the EPO gene 5′ promoter at histone 4 and lysine 23 of histone 3. Knocking down SRC-3, but not SRC-1 or SRC-2, using short interfering RNAs (siRNAs), reduced EPO transcriptional activity. Knocking down p300 resulted in dramatic down-regulation of hypoxic stimulation of EPO gene transcription, negated recruitment of RNA polymerase II to the gene's promoter, and eliminated hypoxia-stimulated acetylation at the promoter and recruitments of SRC-1 and SRC-3 to the enhancer. The inhibitory effects of knocking down p300 and the chromatin remodeling coactivator, Brm/Brg-1, on EPO transcription were additive, suggesting that p300 and Brm/Brg-1 act independently. p300 was also required for hypoxia induced transcription of the HIF-1α target gene, VEGF, but was dispensable for induction of two other HIF-1α target genes, PGK and LDHA. Knocking down CBP, a homolog of p300, augmented hypoxic induction of VEGF, LDHA and PGK. Different HIF target genes also exhibited different requirements for members of the p160 coactivator family. Conclusions/Significance p300 plays a central coactivator role in hypoxic induction of EPO. The coactivators exhibit different specificities for different HIF target genes and each can behave differently in transcriptional regulation of different target genes mediated by the same transcription factor.
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Affiliation(s)
- Feng Wang
- Department of Pathology and Laboratory Medicine, and Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ruixue Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Xiaomeng Wu
- Department of Pathology and Laboratory Medicine, and Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
| | - Oliver Hankinson
- Department of Pathology and Laboratory Medicine, and Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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36
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Abstract
Hypoxia is an integral component of the inflamed tissue microenvironment. Today, the influence of hypoxia on the natural evolution of inflammatory responses is widely accepted; however, many molecular and cellular mechanisms mediating this relationship remain to be clarified. Hypoxic stress affects several independent transcriptional regulators related to inflammation in which HIF-1 and NF-kappaB play central roles. Transcription factors interact with both HATs and HDACs, which are components of large multiprotein co-regulatory complexes. This review summarizes the current knowledge on hypoxia-responsive transcriptional pathways in inflammation and their importance in the etiology of chronic inflammatory diseases, with the primary focus on transcriptional co-regulators and histone modifications in defining gene-specific transcriptional responses in hypoxia, and on the recent progress in the understanding of hypoxia-mediated epigenetic reprogramming. Furthermore, this review discusses the molecular cross-talk between glucocorticoid anti-inflammatory pathways and hypoxia.
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Affiliation(s)
- O Safronova
- Department of Cellular Physiological Chemistry, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
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Sunagawa Y, Morimoto T, Takaya T, Kaichi S, Wada H, Kawamura T, Fujita M, Shimatsu A, Kita T, Hasegawa K. Cyclin-dependent kinase-9 is a component of the p300/GATA4 complex required for phenylephrine-induced hypertrophy in cardiomyocytes. J Biol Chem 2010; 285:9556-9568. [PMID: 20081228 DOI: 10.1074/jbc.m109.070458] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A zinc finger protein GATA4 is one of the hypertrophy-responsive transcription factors and forms a complex with an intrinsic histone acetyltransferase, p300. Disruption of this complex results in the inhibition of cardiomyocyte hypertrophy and heart failure in vivo. By tandem affinity purification and mass spectrometric analyses, we identified cyclin-dependent kinase-9 (Cdk9) as a novel GATA4-binding partner. Cdk9 also formed a complex with p300 as well as GATA4 and cyclin T1. We showed that p300 was required for the interaction of GATA4 with Cdk9 and for the kinase activity of Cdk9. Conversely, Cdk9 kinase activity was required for the p300-induced transcriptional activities, DNA binding, and acetylation of GATA4. Furthermore, the kinase activity of Cdk9 was required for the phosphorylation of p300 as well as for cardiomyocyte hypertrophy. These findings demonstrate that Cdk9 forms a functional complex with the p300/GATA4 and is required for p300/GATA4- transcriptional pathway during cardiomyocyte hypertrophy.
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Affiliation(s)
- Yoichi Sunagawa
- Division of Translational Research, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto 612-8555
| | - Tatsuya Morimoto
- Division of Translational Research, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto 612-8555.
| | - Tomohide Takaya
- Division of Translational Research, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto 612-8555; Department of Cardiovascular Medicine, 54 Kawara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shinji Kaichi
- Division of Translational Research, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto 612-8555; Department of Pediatrics, 54 Kawara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiromichi Wada
- Division of Translational Research, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto 612-8555
| | - Teruhisa Kawamura
- Division of Translational Research, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto 612-8555
| | - Masatoshi Fujita
- Human Health Sciences, Graduate School of Medicine, Kyoto University, 54 Kawara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Akira Shimatsu
- Clinical Research Institute, Kyoto Medical Center, National Hospital Organization, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto 612-8555
| | - Toru Kita
- Department of Cardiovascular Medicine, 54 Kawara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Koji Hasegawa
- Division of Translational Research, 1-1 Mukaihata-cho, Fukakusa, Fushimi-ku, Kyoto 612-8555
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Vicent GP, Zaurin R, Nacht AS, Li A, Font-Mateu J, Le Dily F, Vermeulen M, Mann M, Beato M. Two chromatin remodeling activities cooperate during activation of hormone responsive promoters. PLoS Genet 2009; 5:e1000567. [PMID: 19609353 PMCID: PMC2704372 DOI: 10.1371/journal.pgen.1000567] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 06/18/2009] [Indexed: 12/22/2022] Open
Abstract
Steroid hormones regulate gene expression by interaction of their receptors with hormone responsive elements (HREs) and recruitment of kinases, chromatin remodeling complexes, and coregulators to their target promoters. Here we show that in breast cancer cells the BAF, but not the closely related PBAF complex, is required for progesterone induction of several target genes including MMTV, where it catalyzes localized displacement of histones H2A and H2B and subsequent NF1 binding. PCAF is also needed for induction of progesterone target genes and acetylates histone H3 at K14, an epigenetic mark that interacts with the BAF subunits by anchoring the complex to chromatin. In the absence of PCAF, full loading of target promoters with hormone receptors and BAF is precluded, and induction is compromised. Thus, activation of hormone-responsive promoters requires cooperation of at least two chromatin remodeling activities, BAF and PCAF. In order to adapt its gene expression program to the needs of the environment, the cell must access the information stored in the DNA sequence that is tightly packaged into chromatin in the cell nucleus. How the cell manages to do it in a selective maner is still unclear. Here we show that, in breast cancer cells treated with the ovarian hormone progesterone, the hormone receptor recruits to the regulated genes two chromatin remodeling complexes that cooperate in opening the chromatin structure. One of the complexes puts a mark in a chromatin protein that anchors the other complex, enabling full gene activation. The present discovery highlights the importance of the concerted order of events for access to genomic information during activation of gene expression and reveals the intricacies of hormonal gene regulation.
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Affiliation(s)
- Guillermo Pablo Vicent
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Barcelona, Spain
| | - Roser Zaurin
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Barcelona, Spain
| | - A. Silvina Nacht
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Barcelona, Spain
| | - Ang Li
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Barcelona, Spain
| | - Jofre Font-Mateu
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Barcelona, Spain
| | - Francois Le Dily
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Barcelona, Spain
| | - Michiel Vermeulen
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
- Department of Physiological Chemistry and Cancer Genomics Centre, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Miguel Beato
- Centre de Regulació Genòmica (CRG), Universitat Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Barcelona, Spain
- * E-mail:
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39
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Naito M, Zager RA, Bomsztyk K. BRG1 increases transcription of proinflammatory genes in renal ischemia. J Am Soc Nephrol 2009; 20:1787-96. [PMID: 19556365 DOI: 10.1681/asn.2009010118] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Acute kidney injury stimulates renal production of inflammatory mediators, including TNF-alpha and monocyte chemoattractant protein 1 (MCP-1). These responses reflect, in part, injury-induced transcription of proinflammatory genes by proximal tubule cells. Because of the compact structure of chromatin, a series of events at specified loci remodel chromatin to provide access for transcription factors and RNA polymerase II (Pol II). Here, we examined the role of Brahma-related gene-1 (BRG1), a chromatin remodeling enzyme, in the transcription of TNF-alpha and MCP-1 in response to renal ischemia. Two hours after renal ischemic injury in mice, renal TNF-alpha and MCP-1 mRNA increased and remained elevated for at least 1 wk. Matrix chromatin immunoprecipitation assays revealed sustained increases in Pol II at these genes, suggesting that the elevated mRNA levels were, at least in part, transcriptionally mediated. The profile of BGR1 binding to the genes encoding TNF-alpha and MCP-1 resembled Pol II recruitment. Knockdown of BRG1 by small interfering RNA blocked an ATP depletion-induced increase in TNF-alpha and MCP-1 transcription in a human proximal tubule cell line; this effect was associated with decreased recruitment of BRG1 and Pol II to these genes. In conclusion, BRG1 promotes increased transcription of TNF-alpha and MCP-1 by the proximal tubule in response to renal ischemia.
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Affiliation(s)
- Masayo Naito
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
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40
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Flowers S, Nagl NG, Beck GR, Moran E. Antagonistic roles for BRM and BRG1 SWI/SNF complexes in differentiation. J Biol Chem 2009; 284:10067-75. [PMID: 19144648 PMCID: PMC2665061 DOI: 10.1074/jbc.m808782200] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 01/13/2009] [Indexed: 11/06/2022] Open
Abstract
The mammalian SWI/SNF chromatin-remodeling complex is essential for the multiple changes in gene expression that occur during differentiation. However, the basis within the complex for specificity in effecting positive versus negative changes in gene expression has only begun to be elucidated. The catalytic core of the complex can be either of two closely related ATPases, BRM or BRG1, with the potential that the choice of alternative subunits is a key determinant of specificity. Short hairpin RNA-mediated depletion of the ATPases was used to explore their respective roles in the well characterized multistage process of osteoblast differentiation. The results reveal an unexpected role for BRM-specific complexes. Instead of impeding differentiation as was seen with BRG1 depletion, depletion of BRM caused accelerated progression to the differentiation phenotype. Multiple tissue-specific differentiation markers, including the tightly regulated late stage marker osteocalcin, become constitutively up-regulated in BRM-depleted cells. Chromatin immunoprecipitation analysis of the osteocalcin promoter as a model for the behavior of the complexes indicates that the promoter is a direct target of both BRM- and BRG1-containing complexes. BRG1 complexes, which are required for activation, are associated with the promoter well before induction, but the concurrent presence of BRM-specific complexes overrides their activation function. BRM-specific complexes are present only on the repressed promoter and are required for association of the co-repressor HDAC1. These findings reveal an unanticipated degree of specialization of function linked with the choice of ATPase and suggest a new paradigm for the roles of the alternative subunits during differentiation.
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Affiliation(s)
- Stephen Flowers
- Department of Orthopaedics, New Jersey Medical School-University Hospital Cancer Center, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
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41
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Kenneth NS, Mudie S, van Uden P, Rocha S. SWI/SNF regulates the cellular response to hypoxia. J Biol Chem 2008; 284:4123-31. [PMID: 19097995 DOI: 10.1074/jbc.m808491200] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hypoxia induces a variety of cellular responses such as cell cycle arrest, apoptosis, and autophagy. Most of these responses are mediated by the hypoxia-inducible factor-1alpha. To induce target genes, hypoxia-inducible factor-1alpha requires a chromatin environment conducive to allow binding to specific sequences. Here, we have studied the role of the chromatin-remodeling complex SWI/SNF in the cellular response to hypoxia. We find that SWI/SNF is required for several of the cellular responses induced by hypoxia. Surprisingly, hypoxia-inducible factor-1alpha is a direct target of the SWI/SNF chromatin-remodeling complex. SWI/SNF components are found associated with the hypoxia-inducible factor-1alpha promoter and modulation of SWI/SNF levels results in pronounced changes in hypoxia-inducible factor-1alpha expression and its ability to transactivate target genes. Furthermore, impairment of SWI/SNF function renders cells resistant to hypoxia-induced cell cycle arrest. These results reveal a previously uncharacterized dependence of hypoxia signaling on the SWI/SNF complex and demonstrate a new level of control over the hypoxia-inducible factor-1alpha system.
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Affiliation(s)
- Niall S Kenneth
- College of Life Sciences, Wellcome Trust Centre for Gene Regulation and Expression, MSI/WTB/JBC Complex, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
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42
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Abstract
The sensitivity of an organism to hypoxic injury varies widely across species and among cell types. However, a systematic description of the determinants of metazoan hypoxic sensitivity is lacking. Toward this end, we screened a whole-genome RNAi library for genes that promote hypoxic sensitivity in Caenorhabditis elegans. RNAi knockdown of 198 genes conferred an invariant hypoxia-resistant phenotype (Hyp-r). Eighty-six per cent of these hyp genes had strong homologs in other organisms, 73 with human reciprocal orthologs. The hyp genes were distributed among multiple functional categories. Transcription factors, chromatin modifying enzymes, and intracellular signaling proteins were highly represented. RNAi knockdown of about half of the genes produced no apparent deleterious phenotypes. The hyp genes had significant overlap with previously identified life span extending genes. Testing of the RNAi's in a mutant background defective in somatic RNAi machinery showed that most genes function in somatic cells to control hypoxic sensitivity. DNA microarray analysis identified a subset of the hyp genes that may be hypoxia regulated. siRNA knockdown of human orthologs of the hyp genes conferred hypoxia resistance to transformed human cells for 40% of the genes tested, indicating extensive evolutionary conservation of the hypoxic regulatory activities. The results of the screen provide the first systematic picture of the genetic determinants of hypoxic sensitivity. The number and diversity of genes indicates a surprisingly nonredundant genetic network promoting hypoxic sensitivity.
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43
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Tian Y. Ah receptor and NF-kappaB interplay on the stage of epigenome. Biochem Pharmacol 2008; 77:670-80. [PMID: 19014911 DOI: 10.1016/j.bcp.2008.10.023] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 10/16/2008] [Accepted: 10/21/2008] [Indexed: 12/15/2022]
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that belongs to the basic helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) family. Its ligands include many natural and synthetic compounds, some of which, such as polyhalogenated aromatic hydrocarbons and polycyclic aromatic hydrocarbons, are important environmental contaminants. NF-kappaB is a pleiotropic factor that regulates many physiological and pathophysiological processes including the immune and inflammatory responses. In the past decade, accumulating evidence suggests close interactions between AhR and NF-kappaB pathways, and these interactions are potentially important mechanisms for many pathological processes such as the chemical-induced immune dysfunctions, carcinogenesis and alteration of xenobiotic metabolism and disposition. AhR-NF-kappaB interaction has become a mechanistic linchpin linking certain pathological responses induced by environmental insults. Furthermore, the AhR-NF-kappaB interaction provides basis for therapeutic applications of certain AhR ligands to treat human diseases. The effects of AhR-NF-kappaB on the epigenome are an important area that is not well understood. In this review, I highlight current research regarding the AhR-NF-kappaB(RelA) interactions with emphasis on the epigenetic impacts of these interactions on chromatin modifications and transcription elongation control.
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Affiliation(s)
- Yanan Tian
- Interdisciplinary Graduate Program of Toxicology, Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX 77843-4466, USA.
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44
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Taylor RT, Wang F, Hsu EL, Hankinson O. Roles of coactivator proteins in dioxin induction of CYP1A1 and CYP1B1 in human breast cancer cells. Toxicol Sci 2008; 107:1-8. [PMID: 18842620 DOI: 10.1093/toxsci/kfn217] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cytochrome P450 (CYP) 1A1 and CYP1B1 are inducible by 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) in the human breast cancer cell line, MCF-7. Since CYP1A1 was inducible to a much greater degree than CYP1B1, we hypothesized that there may be differences in coactivator recruitment to the promoter and/or enhancer regions of these genes. Dioxin treatment leads to recruitment of the aryl hydrocarbon receptor to the enhancer regions but not to the proximal promoter regions of both the CYP1A1 and CYP1B1 genes. On the other hand, dioxin treatment facilitated recruitment of RNA polymerase II to the promoters but not the enhancer regions. Dioxin treatment also elicited recruitment of the transcriptional coactivators, steroid receptor coactivator 1 (SRC-1) and steroid receptor coactivator 2 (SRC-2) and p300, which possess intrinsic histone acetyltranferase activities, to both genes, whereas Brahma (BRM)/Switch 2-related gene 1 (BRG-1), a subunit of nucleosomal remodeling factors, was recruited more robustly to CYP1A1 relative to CYP1B1. Small inhibitory RNA-mediated knockdown of p300 and SRC-2 adversely affected dioxin induction of both genes, whereas knockdown of BRM/BRG-1 reduced CYP1A1 induction but had little, if any, effect on CYP1B1 induction. These results suggest that nucleosomal remodeling is less significant for dioxin-mediated induction of CYP1B1 than that of CYP1A1 and may be related to the more modest inducibility of the former. Interestingly, simultaneous knockdown of SRC-2 and BRM/BRG-1 had no greater effect on CYP1A1 induction than knockdown of each coactivator individually, while simultaneous knockdown of p300 and BRM/BRG-1 had a much greater effect than knockdown of each individual gene, suggesting that the recruitment of SRC-2 to CYP1A1 depends upon BRM/BRG-1, while the recruitments of p300 and BRM/BRG-1 are independent of each other. These observations provide novel insights into the functional roles of the endogenous coactivators in dioxin induction of the human CYP1A1 and CYP1B1 genes in their natural chromosomal configurations.
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Affiliation(s)
- Robert T Taylor
- Molecular Toxicology Program, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California 90095, USA
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45
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Abstract
Hypoxia induces profound changes in the cellular gene expression profile. The discovery of a major transcription factor family activated by hypoxia, HIF (hypoxia-inducible factor), and the factors that contribute to HIF regulation have greatly enhanced our knowledge of the molecular aspects of the hypoxic response. However, in addition to HIF, other transcription factors and cellular pathways are activated by exposure to reduced oxygen. In the present review, we summarize the current knowledge of how additional hypoxia-responsive transcription factors integrate with HIF and how other cellular pathways such as chromatin remodelling, translation regulation and microRNA induction, contribute to the co-ordinated cellular response observed following hypoxic stress.
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46
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Magnani L, Lee K, Fodor WL, Machaty Z, Cabot RA. Developmental capacity of porcine nuclear transfer embryos correlate with levels of chromatin-remodeling transcripts in donor cells. Mol Reprod Dev 2008; 75:766-76. [PMID: 18246531 DOI: 10.1002/mrd.20818] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Somatic cell nuclear transfer (SCNT) still retains important limitations. Impaired epigenetic reprogramming is considered responsible for altered gene expression and developmental failure in SCNT-derived embryos. After nuclear transfer the donor cell nucleus undergoes extensive changes in gene expression that involve epigenetic modifications and chromatin remodeling. We hypothesized that SNF2-type ATP-dependent chromatin factors contribute to epigenetic reprogramming and the relative amount of these factors in the donor cell affects developmental potential of the reconstructed embryos. In order to test this hypothesis, we assessed the relative amount of SNF2-type ATPases (Brahma, Brg1, SNF2H, SNF2L, CHD3, and CHD5) in three different donor cells as well as in porcine metaphase II oocytes. We performed SCNT with fetal fibroblast cells, olfactory bulb (OB) progenitor cells, and porcine skin originating sphere stem cells (PSOS). We found that OB-NT embryos and PSOS-NT embryos resulted in a higher morulae/blastocysts ratio as compared to fibroblast-NT embryos (23.53%, 16.98%, and 11.63%, respectively; P < 0.05). Fibroblast cells contained a significantly higher amount of SNF2L and CHD3 transcripts while Brg1 and SNF2H were the most expressed transcripts in all the cell lines analyzed. Metaphase II oocyte expression profile appeared to be unique compared to the cell lines analyzed. This work supports our hypothesis that an array of chromatin-remodeling proteins on donor cells may influence the chromatin structure, effect epigenetic reprogramming, and developmental potential.
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Affiliation(s)
- Luca Magnani
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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47
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Koizume S, Yokota N, Miyagi E, Hirahara F, Tsuchiya E, Miyagi Y. Heterogeneity in binding and gene-expression regulation by HIF-2alpha. Biochem Biophys Res Commun 2008; 371:251-5. [PMID: 18423372 DOI: 10.1016/j.bbrc.2008.04.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 04/09/2008] [Indexed: 11/29/2022]
Abstract
Here, we demonstrate by chromatin immunoprecipitation that the binding of hypoxia-inducible factors to gene regulatory regions is differentially influenced in cancer cells. Binding of HIF-2alpha varies depending on hypoxic conditions, although HIF-1alpha is constantly bound to these regions. We found by RNA interference experiments that HIF-2alpha plays a minor role in VEGF gene upregulation under hypoxia or CoCl(2) treatment, even when both HIFs are similarly bound to the promoter region. HIF-2alpha activated or suppressed the ENO1 gene under various conditions, irrespective of promoter binding. We additionally found that HIF dependence on EPO gene induction could be altered depending on the conditions, irrespective of the binding pattern of HIFs. These results demonstrate that, unlike HIF-1alpha, HIF-2alpha differentially binds and regulates transcription under hypoxia.
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Affiliation(s)
- Shiro Koizume
- Molecular Pathology & Genetics Division, Kanagawa Cancer Center Research Institute, 1-1-2 Nakao, Asahi-ku, Yokohama 241-0815, Japan
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48
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Lin MT, Kuo IH, Chang CC, Chu CY, Chen HY, Lin BR, Sureshbabu M, Shih HJ, Kuo ML. Involvement of hypoxia-inducing factor-1alpha-dependent plasminogen activator inhibitor-1 up-regulation in Cyr61/CCN1-induced gastric cancer cell invasion. J Biol Chem 2008; 283:15807-15. [PMID: 18381294 DOI: 10.1074/jbc.m708933200] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cysteine-rich 61 (Cyr61/CCN1), one of the members of CCN family, has been implicated in the progression of human malignancies. Previously, our studies have demonstrated that Cyr61/CCN1 has a role in promoting gastric cancer cell invasion, but the mechanism is not clear yet. Here, we found that hypoxia-inducing factor-1alpha (HIF-1alpha) protein, but not mRNA, expression was significantly elevated in gastric cancer cells overexpressing Cyr61. Supportively, a profound reduction of endogenous HIF-1alpha protein was noted in one highly invasive cell line, TSGH, when transfected with antisense Cyr61. By comparison, the induction kinetics of HIF-1alpha protein by recombinant Cyr61 (rCyr61) was distinct from that of insulin-like growth factor-1 and CoCl(2) treatment, both well known for induction of HIF-1alpha. Using cycloheximide and MG132, we demonstrated that the Cyr61-mediated HIF-1alpha up-regulation was through de novo protein synthesis, rather than increased protein stability. rCyr61 could also activate the PI3K/AKT/mTOR and ERK1/2 signaling pathways, both of which were essential for HIF-1alpha protein accumulation. Blockage of HIF-1alpha activity in Cyr61-expressing cells by transfecting with a dominant negative (DN)-HIF-1alpha strongly inhibited their invasion ability, suggesting that elevation in HIF-1alpha protein is vital for Cyr61-mediated gastric cancer cell invasion. In addition, several HIF-1alpha-regulated invasiveness genes were examined, and we found that only plasminogen activator inhibitor-1 (PAI-1) showed a significant increase in mRNA and protein levels in cells overexpressing Cyr61. Treatment with PAI-1-specific antisense oligonucleotides or function-neutralizing antibodies abolished the invasion ability of the Cyr61-overexpressing cells. Transfection with dominant negative-HIF-1alpha to block HIF-1alpha activity also effectively reduced the elevated PAI-1 level. In conclusion, our data provide a detailed mechanism by which Cyr61 promoted gastric cancer cell invasive ability via an HIF-1alpha-dependent up-regulation of PAI-1.
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Affiliation(s)
- Ming-Tsan Lin
- Department of Primary Care Medicine, National Taiwan University Hospital, Taipei, Taiwan
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49
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Xu Y, Zhang J, Chen X. The Activity of p53 Is Differentially Regulated by Brm- and Brg1-containing SWI/SNF Chromatin Remodeling Complexes. J Biol Chem 2007; 282:37429-35. [DOI: 10.1074/jbc.m706039200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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50
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Wang F, Zhang R, Xia T, Hsu E, Cai Y, Gu Z, Hankinson O. Inhibitory effects of nitric oxide on invasion of human cancer cells. Cancer Lett 2007; 257:274-82. [PMID: 17869411 PMCID: PMC2763642 DOI: 10.1016/j.canlet.2007.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2007] [Revised: 08/01/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
Hypoxia increased the ability of two human cancer cell lines, PC-3M and T24, to invade through Matrigel, while sodium nitroprusside (SNP), a nitric oxide (NO) donor, strongly inhibited this invasion, along with down-regulating HIF-1alpha. SNP also inhibited the function of mitochondria in PC-3M cells, and mitochondrion-specific inhibitors reduced the invasion of these cells. Furthermore, knocking down either Rieske iron-sulfur protein (Fe-S) of mitochondrial complex III or HIF-1beta in these cells decreased their invasive potential. Our findings suggest that NO inhibits invasion of cancer cells via both inhibition of HIF-1, and impairment of mitochondria.
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Affiliation(s)
- Feng Wang
- Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095, USA
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