1
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Deochand DK, Dacic M, Bale MJ, Daman AW, Josefowicz SZ, Oliver D, Chinenov Y, Rogatsky I. Mechanisms of Epigenomic and Functional Convergence Between Glucocorticoid- and IL4-Driven Macrophage Programming. bioRxiv 2024:2024.02.16.580560. [PMID: 38405750 PMCID: PMC10888924 DOI: 10.1101/2024.02.16.580560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Macrophages adopt distinct phenotypes in response to environmental cues, with type-2 cytokine interleukin-4 promoting a tissue-repair homeostatic state (M2IL4). Glucocorticoids, widely used anti-inflammatory therapeutics, reportedly impart a similar phenotype (M2GC), but how such disparate pathways may functionally converge is unknown. We show using integrative functional genomics that M2IL4 and M2GC transcriptomes share a striking overlap mirrored by a shift in chromatin landscape in both common and signal-specific gene subsets. This core homeostatic program is enacted by transcriptional effectors KLF4 and the GC receptor, whose genome-wide occupancy and actions are integrated in a stimulus-specific manner by the nuclear receptor cofactor GRIP1. Indeed, many of the M2IL4:M2GC-shared transcriptomic changes were GRIP1-dependent. Consistently, GRIP1 loss attenuated phagocytic activity of both populations in vitro and macrophage tissue-repair properties in the murine colitis model in vivo. These findings provide a mechanistic framework for homeostatic macrophage programming by distinct signals, to better inform anti-inflammatory drug design.
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Affiliation(s)
- Dinesh K Deochand
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
| | - Marija Dacic
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Michael J Bale
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Andrew W Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Steven Z Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - David Oliver
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
| | - Yurii Chinenov
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
| | - Inez Rogatsky
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
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2
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Turajane K, Ji G, Chinenov Y, Chao M, Ayturk U, Suhardi VJ, Greenblatt MB, Ivashkiv LB, Bostrom MPG, Yang X. RNA-seq Analysis of Peri-Implant Tissue Shows Differences in Immune, Notch, Wnt, and Angiogenesis Pathways in Aged Versus Young Mice. JBMR Plus 2021; 5:e10535. [PMID: 34761143 PMCID: PMC8567488 DOI: 10.1002/jbm4.10535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/19/2021] [Accepted: 07/27/2021] [Indexed: 12/16/2022] Open
Abstract
The number of total joint replacements (TJRs) in the United States is increasing annually. Cementless implants are intended to improve upon traditional cemented implants by allowing bone growth directly on the surface to improve implant longevity. One major complication of TJR is implant loosening, which is related to deficient osseointegration in cementless TJRs. Although poor osseointegration in aged patients is typically attributed to decreased basal bone mass, little is known about the molecular pathways that compromise the growth of bone onto porous titanium implants. To identify the pathways important for osseointegration that are compromised by aging, we developed an approach for transcriptomic profiling of peri-implant tissue in young and aged mice using our murine model of osseointegration. Based on previous findings of changes of bone quality associated with aging, we hypothesized that aged mice have impaired activation of bone anabolic pathways at the bone-implant interface. We found that pathways most significantly downregulated in aged mice relative to young mice are related to angiogenic, Notch, and Wnt signaling. Downregulation of these pathways is associated with markedly increased expression of inflammatory and immune genes at the bone-implant interface in aged mice. These results identify osseointegration pathways affected by aging and suggest that an increased inflammatory response in aged mice may compromise peri-implant bone healing. Targeting the Notch and Wnt pathways, promoting angiogenesis, or modulating the immune response at the peri-implant site may enhance osseointegration and improve the outcome of joint replacement in older patients. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
| | - Gang Ji
- Hospital for Special SurgeryNew YorkNYUSA
- The Third Hospital of Hebei Medical UniversityShijiazhuangChina
| | - Yurii Chinenov
- Hospital for Special SurgeryNew YorkNYUSA
- David Z. Rosensweig Genomics Research CenterHospital for Special SurgeryNew YorkNYUSA
| | - Max Chao
- Hospital for Special SurgeryNew YorkNYUSA
- David Z. Rosensweig Genomics Research CenterHospital for Special SurgeryNew YorkNYUSA
| | | | | | - Matthew B Greenblatt
- Hospital for Special SurgeryNew YorkNYUSA
- Department of Pathology and Laboratory MedicineWeill Cornell MedicineNew YorkNYUSA
| | - Lionel B Ivashkiv
- Hospital for Special SurgeryNew YorkNYUSA
- David Z. Rosensweig Genomics Research CenterHospital for Special SurgeryNew YorkNYUSA
| | | | - Xu Yang
- Hospital for Special SurgeryNew YorkNYUSA
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3
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Ricker E, Manni M, Flores-Castro D, Jenkins D, Gupta S, Rivera-Correa J, Meng W, Rosenfeld AM, Pannellini T, Bachu M, Chinenov Y, Sculco PK, Jessberger R, Prak ETL, Pernis AB. Altered function and differentiation of age-associated B cells contribute to the female bias in lupus mice. Nat Commun 2021; 12:4813. [PMID: 34376664 PMCID: PMC8355159 DOI: 10.1038/s41467-021-25102-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/15/2021] [Indexed: 12/11/2022] Open
Abstract
Differences in immune responses to viruses and autoimmune diseases such as systemic lupus erythematosus (SLE) can show sexual dimorphism. Age-associated B cells (ABC) are a population of CD11c+T-bet+ B cells critical for antiviral responses and autoimmune disorders. Absence of DEF6 and SWAP-70, two homologous guanine exchange factors, in double-knock-out (DKO) mice leads to a lupus-like syndrome in females marked by accumulation of ABCs. Here we demonstrate that DKO ABCs show sex-specific differences in cell number, upregulation of an ISG signature, and further differentiation. DKO ABCs undergo oligoclonal expansion and differentiate into both CD11c+ and CD11c- effector B cell populations with pathogenic and pro-inflammatory function as demonstrated by BCR sequencing and fate-mapping experiments. Tlr7 duplication in DKO males overrides the sex-bias and further augments the dissemination and pathogenicity of ABCs, resulting in severe pulmonary inflammation and early mortality. Thus, sexual dimorphism shapes the expansion, function and differentiation of ABCs that accompanies TLR7-driven immunopathogenesis.
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Affiliation(s)
- Edd Ricker
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Michela Manni
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
| | - Danny Flores-Castro
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
| | - Daniel Jenkins
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
| | - Sanjay Gupta
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
| | - Juan Rivera-Correa
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, USA
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, USA
| | - Tania Pannellini
- Research Division and Precision Medicine Laboratory, Hospital for Special Surgery, New York, NY, USA
| | - Mahesh Bachu
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
| | - Yurii Chinenov
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Peter K Sculco
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Technische Universitat, Dresden, Germany
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA, USA
| | - Alessandra B Pernis
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, NY, USA.
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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4
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Zahir H, Dehghani B, Yuan X, Chinenov Y, Kim C, Burge A, Bandhari R, Nemirov D, Fava P, Moley P, Potter H, Nguyen J, Halpern B, Donlin L, Ivashkiv L, Rodeo S, Otero M. In vitro responses to platelet-rich-plasma are associated with variable clinical outcomes in patients with knee osteoarthritis. Sci Rep 2021; 11:11493. [PMID: 34075069 PMCID: PMC8169703 DOI: 10.1038/s41598-021-90174-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/07/2021] [Indexed: 12/19/2022] Open
Abstract
Autologous blood-derived products such as platelet-rich plasma (PRP) are widely used to treat musculoskeletal conditions, including knee osteoarthritis (OA). However, the clinical outcomes after PRP administration are often variable, and there is limited information about the specific characteristics of PRP that impact bioactivity and clinical responses. In this study, we aimed to develop an integrative workflow to evaluate responses to PRP in vitro, and to assess if the in vitro responses to PRP are associated with the PRP composition and clinical outcomes in patients with knee OA. To do this, we used a coculture system of macrophages and fibroblasts paired with transcriptomic analyses to comprehensively characterize the modulation of inflammatory responses by PRP in vitro. Relying on patient-reported outcomes and achievement of minimal clinically important differences in OA patients receiving PRP injections, we identified responders and non-responders to the treatment. Comparisons of PRP from these patient groups allowed us to identify differences in the composition and in vitro activity of PRP. We believe that our integrative workflow may enable the development of targeted approaches that rely on PRP and other orthobiologics to treat musculoskeletal pathologies.
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Affiliation(s)
- Habib Zahir
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA.,New York Institute of Technology, Old Westbury, NY, USA
| | - Bijan Dehghani
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA
| | - Xiaoning Yuan
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA.,NewYork-Presbyterian Hospital, New York, NY, USA
| | - Yurii Chinenov
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA.,The David Z. Rosensweig Genomics Research Center, New York, NY, USA
| | - Christine Kim
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA.,Columbia University, New York, NY, USA
| | - Alissa Burge
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA
| | - Reyna Bandhari
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA
| | - Daniel Nemirov
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA
| | - Patrick Fava
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA
| | - Peter Moley
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA.,HSS Center for Regenerative Medicine, New York, NY, USA
| | - Hollis Potter
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA
| | - Joseph Nguyen
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA
| | - Brian Halpern
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA.,HSS Center for Regenerative Medicine, New York, NY, USA
| | - Laura Donlin
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA.,Derfner Foundation Precision Medicine Laboratory, New York, NY, USA
| | - Lionel Ivashkiv
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA.,The David Z. Rosensweig Genomics Research Center, New York, NY, USA
| | - Scott Rodeo
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA.,HSS Center for Regenerative Medicine, New York, NY, USA
| | - Miguel Otero
- Hospital for Special Surgery, 535 E 70th Street, New York, NY, 10021, USA. .,HSS Center for Regenerative Medicine, New York, NY, USA. .,Derfner Foundation Precision Medicine Laboratory, New York, NY, USA.
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5
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Mimouna S, Rollins DA, Shibu G, Tharmalingam B, Deochand DK, Chen X, Oliver D, Chinenov Y, Rogatsky I. Correction: Transcription cofactor GRIP1 differentially affects myeloid cell-driven neuroinflammation and response to IFN-β therapy. J Exp Med 2021; 218:211557. [PMID: 33226409 PMCID: PMC7953629 DOI: 10.1084/jem.2019238611162020c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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6
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Mimouna S, Rollins DA, Shibu G, Tharmalingam B, Deochand DK, Chen X, Oliver D, Chinenov Y, Rogatsky I. Transcription cofactor GRIP1 differentially affects myeloid cell-driven neuroinflammation and response to IFN-β therapy. J Exp Med 2021; 218:e20192386. [PMID: 33045064 PMCID: PMC7555412 DOI: 10.1084/jem.20192386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/29/2020] [Accepted: 09/04/2020] [Indexed: 11/18/2022] Open
Abstract
Macrophages (MФ) and microglia (MG) are critical in the pathogenesis of multiple sclerosis (MS) and its mouse model, experimental autoimmune encephalomyelitis (EAE). Glucocorticoids (GCs) and interferon β (IFN-β) are frontline treatments for MS, and disrupting each pathway in mice aggravates EAE. Glucocorticoid receptor-interacting protein 1 (GRIP1) facilitates both GR and type I IFN transcriptional actions; hence, we evaluated the role of GRIP1 in neuroinflammation. Surprisingly, myeloid cell-specific loss of GRIP1 dramatically reduced EAE severity, immune cell infiltration of the CNS, and MG activation and demyelination specifically during the neuroinflammatory phase of the disease, yet also blunted therapeutic properties of IFN-β. MФ/MG transcriptome analyses at the bulk and single-cell levels revealed that GRIP1 deletion attenuated nuclear receptor, inflammatory and, interestingly, type I IFN pathways and promoted the persistence of a homeostatic MG signature. Together, these results uncover the multifaceted function of type I IFN in MS/EAE pathogenesis and therapy, and an unexpectedly permissive role of myeloid cell GRIP1 in neuroinflammation.
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Affiliation(s)
- Sanda Mimouna
- The David Z. Rosensweig Genomics Center, Hospital for Special Surgery Research Institute, New York, NY
| | - David A. Rollins
- The David Z. Rosensweig Genomics Center, Hospital for Special Surgery Research Institute, New York, NY
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Gayathri Shibu
- The David Z. Rosensweig Genomics Center, Hospital for Special Surgery Research Institute, New York, NY
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Bowranigan Tharmalingam
- The David Z. Rosensweig Genomics Center, Hospital for Special Surgery Research Institute, New York, NY
| | - Dinesh K. Deochand
- The David Z. Rosensweig Genomics Center, Hospital for Special Surgery Research Institute, New York, NY
| | - Xi Chen
- The David Z. Rosensweig Genomics Center, Hospital for Special Surgery Research Institute, New York, NY
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - David Oliver
- The David Z. Rosensweig Genomics Center, Hospital for Special Surgery Research Institute, New York, NY
| | - Yurii Chinenov
- The David Z. Rosensweig Genomics Center, Hospital for Special Surgery Research Institute, New York, NY
| | - Inez Rogatsky
- The David Z. Rosensweig Genomics Center, Hospital for Special Surgery Research Institute, New York, NY
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY
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7
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Ricker E, Chinenov Y, Pannellini T, Flores-Castro D, Ye C, Gupta S, Manni M, Liao JK, Pernis AB. Serine-threonine kinase ROCK2 regulates germinal center B cell positioning and cholesterol biosynthesis. J Clin Invest 2020; 130:3654-3670. [PMID: 32229726 PMCID: PMC7324193 DOI: 10.1172/jci132414] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/24/2020] [Indexed: 12/16/2022] Open
Abstract
Germinal center (GC) responses require B cells to respond to a dynamic set of intercellular and microenvironmental signals that instruct B cell positioning, differentiation, and metabolic reprogramming. RHO-associated coiled-coil-containing protein kinase 2 (ROCK2), a serine-threonine kinase that can be therapeutically targeted by ROCK inhibitors or statins, is a key downstream effector of RHOA GTPases. Although RHOA-mediated pathways are emerging as critical regulators of GC responses, the role of ROCK2 in B cells is unknown. Here, we found that ROCK2 was activated in response to key T cell signals like CD40 and IL-21 and that it regulated GC formation and maintenance. RNA-Seq analyses revealed that ROCK2 controlled a unique transcriptional program in GC B cells that promoted optimal GC polarization and cholesterol biosynthesis. ROCK2 regulated this program by restraining AKT activation and subsequently enhancing FOXO1 activity. ATAC-Seq (assay for transposase-accessible chromatin with high-throughput sequencing) and biochemical analyses revealed that the effects of ROCK2 on cholesterol biosynthesis were instead mediated via a novel mechanism. ROCK2 directly phosphorylated interferon regulatory factor 8 (IRF8), a crucial mediator of GC responses, and promoted its interaction with sterol regulatory element-binding transcription factor 2 (SREBP2) at key regulatory regions controlling the expression of cholesterol biosynthetic enzymes, resulting in optimal recruitment of SREBP2 at these sites. These findings thus uncover ROCK2 as a multifaceted and therapeutically targetable regulator of GC responses.
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Affiliation(s)
- Edd Ricker
- Autoimmunity and Inflammation Program, Hospital for Special Surgery (HSS), New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | | | - Tania Pannellini
- Research Division and
- Precision Medicine Laboratory, HSS, New York, New York, USA
| | - Danny Flores-Castro
- Autoimmunity and Inflammation Program, Hospital for Special Surgery (HSS), New York, New York, USA
| | - Chao Ye
- Autoimmunity and Inflammation Program, Hospital for Special Surgery (HSS), New York, New York, USA
| | - Sanjay Gupta
- Autoimmunity and Inflammation Program, Hospital for Special Surgery (HSS), New York, New York, USA
| | - Michela Manni
- Autoimmunity and Inflammation Program, Hospital for Special Surgery (HSS), New York, New York, USA
| | - James K. Liao
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Alessandra B. Pernis
- Autoimmunity and Inflammation Program, Hospital for Special Surgery (HSS), New York, New York, USA
- David Z. Rosensweig Genomics Research Center
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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8
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Yu L, Zhang B, Deochand D, Sacta MA, Coppo M, Shang Y, Guo Z, Rollins DA, Tharmalingam B, Li R, Chinenov Y, Rogatsky I, Hu X. Negative elongation factor complex enables macrophage inflammatory responses by controlling anti-inflammatory gene expression. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.152.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Studies on macrophage gene expression have historically focused on events leading to RNA polymerase II recruitment and transcription initiation whereas the contribution of post-initiation steps to macrophage activation remains poorly understood. Here, we report widespread promoter-proximal RNA polymerase II pausing in resting macrophages, marked by broad co-localization of the negative elongation factor (NELF) complex and facilitated by PU.1. Upon inflammatory stimulation, over 60% of activated transcriptome is regulated by polymerase pause-release and a transient genome-wide NELF dissociation from chromatin, unexpectedly, independent of CDK9, a presumed NELF kinase. Genetic disruption of NELF in macrophages enhanced transcription of AP-1-encoding Fos and Jun and, consequently, AP-1 targets including Il10. Augmented expression of IL-10, a critical anti-inflammatory cytokine, in turn, attenuated production of pro-inflammatory mediators and, ultimately, macrophage-mediated inflammation in vivo. Together, these findings establish a previously unappreciated role of NELF in constraining transcription of inflammation inhibitors thereby enabling inflammatory macrophage activation.
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Affiliation(s)
- Li Yu
- 1Institute for Immunology and School of Medicine, Tsinghua University, China
| | - Bin Zhang
- 1Institute for Immunology and School of Medicine, Tsinghua University, China
| | | | | | | | - Yingli Shang
- 3College of Veterinary Medicine, Shandong Agricultural Uni., China, China
| | - Ziyi Guo
- 1Institute for Immunology and School of Medicine, Tsinghua University, China
| | | | | | - Rong Li
- 4The George Washington University
| | | | | | - Xiaoyu Hu
- 1Institute for Immunology and School of Medicine, Tsinghua University, China
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9
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Qing X, Chinenov Y, Redecha P, Madaio M, Roelofs JJ, Farber G, Issuree PD, Donlin L, Mcllwain DR, Mak TW, Blobel CP, Salmon JE. iRhom2 promotes lupus nephritis through TNF-α and EGFR signaling. J Clin Invest 2018; 128:1397-1412. [PMID: 29369823 DOI: 10.1172/jci97650] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/23/2018] [Indexed: 12/14/2022] Open
Abstract
Lupus nephritis (LN) often results in progressive renal dysfunction. The inactive rhomboid 2 (iRhom2) is a newly identified key regulator of A disintegrin and metalloprotease 17 (ADAM17), whose substrates, such as TNF-α and heparin-binding EGF (HB-EGF), have been implicated in the pathogenesis of chronic kidney diseases. Here, we demonstrate that deficiency of iRhom2 protects the lupus-prone Fcgr2b-/- mice from developing severe kidney damage without altering anti-double-stranded DNA (anti-dsDNA) Ab production by simultaneously blocking HB-EGF/EGFR and TNF-α signaling in the kidney tissues. Unbiased transcriptome profiling of kidneys and kidney macrophages revealed that TNF-α and HB-EGF/EGFR signaling pathways are highly upregulated in Fcgr2b-/- mice, alterations that were diminished in the absence of iRhom2. Pharmacological blockade of either TNF-α or EGFR signaling protected Fcgr2b-/- mice from severe renal damage. Finally, kidneys from LN patients showed increased iRhom2 and HB-EGF expression, with interstitial HB-EGF expression significantly associated with chronicity indices. Our data suggest that activation of iRhom2/ADAM17-dependent TNF-α and EGFR signaling plays a crucial role in mediating irreversible kidney damage in LN, thereby uncovering a target for selective and simultaneous dual inhibition of 2 major pathological pathways in the effector arm of the disease.
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Affiliation(s)
| | - Yurii Chinenov
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA
| | | | - Michael Madaio
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Joris Jth Roelofs
- Department of Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Gregory Farber
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York, USA
| | - Priya D Issuree
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA
| | - Laura Donlin
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA
| | - David R Mcllwain
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Tak W Mak
- Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Carl P Blobel
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA.,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York, USA.,Institute for Advanced Study, Technical University Munich, Munich, Germany.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jane E Salmon
- Program in Inflammation and Autoimmunity, and.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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10
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Sacta MA, Tharmalingam B, Coppo M, Rollins DA, Deochand DK, Benjamin B, Yu L, Zhang B, Hu X, Li R, Chinenov Y, Rogatsky I. Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages. eLife 2018; 7:34864. [PMID: 29424686 PMCID: PMC5821458 DOI: 10.7554/elife.34864] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 01/28/2018] [Indexed: 01/13/2023] Open
Abstract
The glucocorticoid receptor (GR) potently represses macrophage-elicited inflammation, however, the underlying mechanisms remain obscure. Our genome-wide analysis in mouse macrophages reveals that pro-inflammatory paused genes, activated via global negative elongation factor (NELF) dissociation and RNA Polymerase (Pol)2 release from early elongation arrest, and non-paused genes, induced by de novo Pol2 recruitment, are equally susceptible to acute glucocorticoid repression. Moreover, in both cases the dominant mechanism involves rapid GR tethering to p65 at NF-kB-binding sites. Yet, specifically at paused genes, GR activation triggers widespread promoter accumulation of NELF, with myeloid cell-specific NELF deletion conferring glucocorticoid resistance. Conversely, at non-paused genes, GR attenuates the recruitment of p300 and histone acetylation, leading to a failure to assemble BRD4 and Mediator at promoters and enhancers, ultimately blocking Pol2 initiation. Thus, GR displays no preference for a specific pro-inflammatory gene class; however, it effects repression by targeting distinct temporal events and components of transcriptional machinery.
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Affiliation(s)
- Maria A Sacta
- Weill Cornell/ Rockefeller/ Sloan Kettering Tri-Institutional MD-PhD Program, New York, United States.,Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States.,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Bowranigan Tharmalingam
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - Maddalena Coppo
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - David A Rollins
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States.,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Dinesh K Deochand
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - Bradley Benjamin
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - Li Yu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Bin Zhang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Xiaoyu Hu
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States.,Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Rong Li
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, United States
| | - Yurii Chinenov
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - Inez Rogatsky
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States.,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, United States
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11
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Chandrasekaran U, Yi W, Gupta S, Weng CH, Giannopoulou E, Chinenov Y, Jessberger R, Weaver CT, Bhagat G, Pernis AB. Regulation of Effector Treg Cells in Murine Lupus. Arthritis Rheumatol 2017; 68:1454-66. [PMID: 26816213 DOI: 10.1002/art.39599] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/14/2016] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Treg cells need to acquire an effector phenotype to function in settings of inflammation. Whether effector Treg cells can limit disease severity in lupus is unknown. Interferon regulatory factor 4 (IRF-4) is an essential controller of effector Treg cells and regulates their ability to express interleukin-10 (IL-10). In non-Treg cells, IRF-4 activity is modulated by interactions with DEF-6 and its homolog switch-associated protein 70 (SWAP-70). Although mice lacking both DEF-6 and SWAP-70 (double-knockout [DKO] mice) develop lupus, they display normal survival, suggesting that in DKO mice, Treg cells can moderate disease development. The purpose of this study was to investigate whether Treg cells from DKO mice have an increased capacity to become effector Treg cells due to the ability of DEF-6 and SWAP-70 to restrain IRF-4 activity. METHODS Treg cells were evaluated by fluorescence-activated cell sorting. The B lymphocyte-induced maturation protein 1 (BLIMP-1)/IL-10 axis was assessed by crossing DKO mice with BLIMP-1-YFP-10BiT dual-reporter mice. Deletion of IRF-4 in Treg cells from DKO mice was achieved by generating FoxP3(Cre) IRF-4(fl/fl) DKO mice. RESULTS The concomitant absence of DEF-6 and SWAP-70 led to increased numbers of Treg cells, which acquired an effector phenotype in a cell-intrinsic manner. In addition, Treg cells from DKO mice exhibited enhanced expression of the BLIMP-1/IL-10 axis. Notably, DKO effector Treg cells survived and expanded as disease progressed. The accumulation of Treg cells from DKO mice was associated with the up-regulation of genes controlling autophagy. IRF-4 was required for the expansion and function of effector Treg cells from DKO mice. CONCLUSION This study revealed the existence of mechanisms that, by acting on IRF-4, can fine-tune the function and survival of effector Treg cells in lupus. These findings suggest that the existence of a powerful effector Treg cell compartment that successfully survives in an unfavorable inflammatory environment could limit disease development.
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Affiliation(s)
| | - Woelsung Yi
- Hospital for Special Surgery, New York, New York
| | - Sanjay Gupta
- Hospital for Special Surgery, New York, New York
| | - Chien-Huan Weng
- Hospital for Special Surgery and Weill Cornell Graduate School of Medical Sciences, New York, New York
| | - Eugenia Giannopoulou
- Hospital for Special Surgery, New York, and New York City College of Technology, City University of New York, Brooklyn, New York
| | | | | | | | - Govind Bhagat
- Columbia University Medical Center and New York Presbyterian Hospital, New York, New York
| | - Alessandra B Pernis
- Hospital for Special Surgery, Weill Cornell Graduate School of Medical Sciences, and Weill Cornell Medicine, Cornell University, New York, New York
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12
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Abstract
Glucocorticoid hormones (GC) regulate essential physiological functions including energy homeostasis, embryonic and postembryonic development, and the stress response. From the biomedical perspective, GC have garnered a tremendous amount of attention as highly potent anti-inflammatory and immunosuppressive medications indispensable in the clinic. GC signal through the GC receptor (GR), a ligand-dependent transcription factor whose structure, DNA binding, and the molecular partners that it employs to regulate transcription have been under intense investigation for decades. In particular, next-generation sequencing-based approaches have revolutionized the field by introducing a unified platform for a simultaneous genome-wide analysis of cellular activities at the level of RNA production, binding of transcription factors to DNA and RNA, and chromatin landscape and topology. Here we describe fundamental concepts of GC/GR function as established through traditional molecular and in vivo approaches and focus on the novel insights of GC biology that have emerged over the last 10 years from the rapidly expanding arsenal of system-wide genomic methodologies.
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Affiliation(s)
- Maria A Sacta
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
| | - Yurii Chinenov
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021;
| | - Inez Rogatsky
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
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13
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Rozo C, Chinenov Y, Maharaj RK, Gupta S, Leuenberger L, Kirou KA, Bykerk VP, Goodman SM, Salmon JE, Pernis AB. Targeting the RhoA-ROCK pathway to reverse T-cell dysfunction in SLE. Ann Rheum Dis 2016; 76:740-747. [PMID: 28283529 DOI: 10.1136/annrheumdis-2016-209850] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/04/2016] [Accepted: 10/09/2016] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Deregulated production of interleukin (IL)-17 and IL-21 contributes to the pathogenesis of autoimmune disorders such as systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). Production of IL-17 and IL-21 can be regulated by ROCK2, one of the two Rho kinases. Increased ROCK activation was previously observed in an SLE cohort. Here, we evaluated ROCK activity in a new SLE cohort, and an RA cohort, and assessed the ability of distinct inhibitors of the ROCK pathway to suppress production of IL-17 and IL-21 by SLE T cells or human Th17 cells. METHODS ROCK activity in peripheral blood mononuclear cells (PBMCs) from 29 patients with SLE, 31 patients with RA and 28 healthy controls was determined by ELISA. SLE T cells or in vitro-differentiated Th17 cells were treated with Y27632 (a pan-ROCK inhibitor), KD025 (a selective ROCK2 inhibitor) or simvastatin (which inhibits RhoA, a major ROCK activator). ROCK activity and IL-17 and IL-21 production were assessed. The transcriptional profile altered by ROCK inhibitors was evaluated by NanoString technology. RESULTS ROCK activity levels were significantly higher in patients with SLE and RA than healthy controls. Th17 cells exhibited high ROCK activity that was inhibited by Y27632, KD025 or simvastatin; each also decreased IL-17 and IL-21 production by purified SLE T cells or Th17 cells. Immune profiling revealed both overlapping and distinct effects of the different ROCK inhibitors. CONCLUSIONS ROCK activity is elevated in PBMCs from patients with SLE and RA. Production of IL-17 and IL-21 by SLE T cells or Th17 cells can furthermore be inhibited by targeting the RhoA-ROCK pathway via both non-selective and selective approaches.
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Affiliation(s)
- Cristina Rozo
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA
| | - Yurii Chinenov
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA.,David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
| | - Reena Khianey Maharaj
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA
| | - Sanjay Gupta
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA
| | - Laura Leuenberger
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA
| | - Kyriakos A Kirou
- Department of Rheumatology, Hospital for Special Surgery, New York, New York, USA
| | - Vivian P Bykerk
- Department of Rheumatology, Hospital for Special Surgery, New York, New York, USA.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Susan M Goodman
- Department of Rheumatology, Hospital for Special Surgery, New York, New York, USA.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Jane E Salmon
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA.,Department of Rheumatology, Hospital for Special Surgery, New York, New York, USA.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Alessandra B Pernis
- Autoimmunity and Inflammation Program, Hospital for Special Surgery, New York, New York, USA.,David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York, USA
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14
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Coppo M, Chinenov Y, Sacta MA, Rogatsky I. The transcriptional coregulator GRIP1 controls macrophage polarization and metabolic homeostasis. Nat Commun 2016; 7:12254. [PMID: 27464507 PMCID: PMC4974480 DOI: 10.1038/ncomms12254] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 06/14/2016] [Indexed: 12/27/2022] Open
Abstract
Diet-induced obesity causes chronic macrophage-driven inflammation in white adipose tissue (WAT) leading to insulin resistance. WAT macrophages, however, differ in their origin, gene expression and activities: unlike infiltrating monocyte-derived inflammatory macrophages, WAT-resident macrophages counteract inflammation and insulin resistance, yet, the mechanisms underlying their transcriptional programming remain poorly understood. We recently reported that a nuclear receptor cofactor—glucocorticoid receptor (GR)-interacting protein (GRIP)1—cooperates with GR to repress inflammatory genes. Here, we show that GRIP1 facilitates macrophage programming in response to IL4 via a GR-independent pathway by serving as a coactivator for Kruppel-like factor (KLF)4—a driver of tissue-resident macrophage differentiation. Moreover, obese mice conditionally lacking GRIP1 in macrophages develop massive macrophage infiltration and inflammation in metabolic tissues, fatty livers, hyperglycaemia and insulin resistance recapitulating metabolic disease. Thus, GRIP1 is a critical regulator of immunometabolism, which engages distinct transcriptional mechanisms to coordinate the balance between macrophage populations and ultimately promote metabolic homeostasis. GRIP1 cooperates with the glucocorticoid receptor to repress inflammatory genes. Here the authors show that GRIP1 also controls macrophage polarization, by promoting KLF4-driven activation in response to IL-4, and that mice lacking GRIP1 in macrophages develop severe metabolic dysfunction on a high-fat diet.
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Affiliation(s)
- Maddalena Coppo
- The David Rosensweig Genomics Center, Hospital for Special Surgery, 535 East 70th Street, New York, New York 10021, USA
| | - Yurii Chinenov
- The David Rosensweig Genomics Center, Hospital for Special Surgery, 535 East 70th Street, New York, New York 10021, USA
| | - Maria A Sacta
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, 1300 York Avenue, New York, New York 10021, USA
| | - Inez Rogatsky
- The David Rosensweig Genomics Center, Hospital for Special Surgery, 535 East 70th Street, New York, New York 10021, USA.,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, New York 10021, USA.,Department of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10021, USA
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15
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Chinenov Y, Coppo M, Gupte R, Sacta MA, Rogatsky I. Glucocorticoid receptor coordinates transcription factor-dominated regulatory network in macrophages. BMC Genomics 2014; 15:656. [PMID: 25099603 PMCID: PMC4133603 DOI: 10.1186/1471-2164-15-656] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/25/2014] [Indexed: 12/11/2022] Open
Abstract
Background Inflammation triggered by infection or injury is tightly controlled by glucocorticoid hormones which signal via a dedicated transcription factor, the Glucocorticoid Receptor (GR), to regulate hundreds of genes. However, the hierarchy of transcriptional responses to GR activation and the molecular basis of their oftentimes non-linear dynamics are not understood. Results We investigated early glucocorticoid-driven transcriptional events in macrophages, a cell type highly responsive to both pro- and anti-inflammatory stimuli. Using whole transcriptome analyses in resting and acutely lipopolysaccharide (LPS)-stimulated macrophages, we show that early GR target genes form dense networks with the majority of control nodes represented by transcription factors. The expression dynamics of several glucocorticoid-responsive genes are consistent with feed forward loops (FFL) and coincide with rapid GR recruitment. Notably, GR binding sites in genes encoding members of the KLF transcription factor family colocalize with KLF binding sites. Moreover, our gene expression, transcription factor binding and computational data are consistent with the existence of the GR-KLF9-KLF2 incoherent FFL. Analysis of LPS-downregulated genes revealed striking enrichment in multimerized Zn-fingers- and KRAB domain-containing proteins known to bind nucleic acids and repress transcription by propagating heterochromatin. This raises an intriguing possibility that an increase in chromatin accessibility in inflammatory macrophages results from broad downregulation of negative chromatin remodelers. Conclusions Pro- and anti-inflammatory stimuli alter the expression of a vast array of transcription factors and chromatin remodelers. By regulating multiple transcription factors, which propagate the initial hormonal signal, GR acts as a coordinating hub in anti-inflammatory responses. As several KLFs promote the anti-inflammatory program in macrophages, we propose that GR and KLFs functionally cooperate to curb inflammation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-656) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yurii Chinenov
- Hospital for Special Surgery, The David Rosensweig Genomics Center, 535 East 70th Street, New York, NY 10021, USA.
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16
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Chinenov Y, Gupte R, Rogatsky I. Nuclear receptors in inflammation control: repression by GR and beyond. Mol Cell Endocrinol 2013; 380:55-64. [PMID: 23623868 PMCID: PMC3787948 DOI: 10.1016/j.mce.2013.04.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/14/2013] [Accepted: 04/15/2013] [Indexed: 01/05/2023]
Abstract
Inflammation is a protective response of organisms to pathogens, irritation or injury. Primary inflammatory sensors activate an array of signaling pathways that ultimately converge upon a few transcription factors such as AP1, NFκB and STATs that in turn stimulate expression of inflammatory genes to ultimately eradicate infection and repair the damage. A disturbed balance between activation and inhibition of inflammatory pathways can set the stage for chronic inflammation which is increasingly recognized as a key pathogenic component of autoimmune, metabolic, cardiovascular and neurodegenerative disorders. Nuclear receptors (NRs) are a large family of transcription factors many of which are known for their potent anti-inflammatory actions. Activated by small lipophilic ligands, NRs interact with a wide range of transcription factors, cofactors and chromatin-modifying enzymes, assembling numerous cell- and tissue-specific DNA-protein transcriptional regulatory complexes with diverse activities. Here we discuss established and emerging roles and mechanisms by which NRs and, in particular, the glucocorticoid receptor (GR) repress genes encoding cytokines, chemokines and other pro-inflammatory mediators.
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Affiliation(s)
- Yurii Chinenov
- Hospital for Special Surgery, 535 East 70th Street, New York, NY, 10021
| | - Rebecca Gupte
- Hospital for Special Surgery, 535 East 70th Street, New York, NY, 10021
- Graduate Program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
| | - Inez Rogatsky
- Hospital for Special Surgery, 535 East 70th Street, New York, NY, 10021
- Graduate Program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10021
- Corresponding author: , Tel: 1 212-606-1462, Fax: 1 212-774-2560
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Rogatsky I, Chinenov Y, Gupte R, Flammer JR, Dobrovolna J, Kennedy MA, Liu B. CS13-5. Anti-inflammatory actions of glucocorticoids: the role of transcriptional coregulator GRIP1 in shaping macrophage transcriptome and systemic inflammation. Cytokine 2011. [DOI: 10.1016/j.cyto.2011.07.387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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18
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Flammer JR, Kennedy MA, Reily M, Chinenov Y, Ivashkiv LB, Rogatsky I. PL2-6 A dual action of glucocorticoids on the type I interferon network. Cytokine 2010. [DOI: 10.1016/j.cyto.2010.07.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Flammer JR, Kennedy MA, Chinenov Y, Ivashkiv LB, Rogatsky I. Type I Interferon-dependent gene expression is a target for glucocorticoid inhibition. Cytokine 2009. [DOI: 10.1016/j.cyto.2009.07.309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Kennedy M, Nechaev S, Gilchrist DA, Muse GW, Chinenov Y, Adelman K, Rogatsky I. Immediate mediators of the inflammatory response are poised for rapid gene activation through RNA polymerase stalling. Cytokine 2009. [DOI: 10.1016/j.cyto.2009.07.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Flammer JR, Kennedy MA, Chinenov Y, Ivashkiv LB, Rogatsky I. 187 Glucocorticoid regulation of the type I interferon-JAK/STAT signaling pathway. Cytokine 2008. [DOI: 10.1016/j.cyto.2008.07.249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Kennedy MA, Nechaev S, Gilchrist DA, Muse GW, Chinenov Y, Adelman K, Rogatsky I. 172 Regulation of TNFα gene transcription at the post-initiation step. Cytokine 2008. [DOI: 10.1016/j.cyto.2008.07.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Chinenov Y, Rogatsky I. Glucocorticoids and the innate immune system: crosstalk with the toll-like receptor signaling network. Mol Cell Endocrinol 2007; 275:30-42. [PMID: 17576036 DOI: 10.1016/j.mce.2007.04.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 04/28/2007] [Indexed: 02/07/2023]
Abstract
Toll-like receptors (TLRs) are responsible for the recognition of a variety of microbial pathogens and the initial induction of immune and inflammatory responses. These responses are normally restricted by the adrenally produced glucocorticoid hormones which provide a feedback mechanism to curb unabated inflammation. Glucocorticoids act through a ligand-dependent transcription factor-the glucocorticoid receptor (GR), which engages in a complex network of protein:protein and protein:DNA interactions ultimately activating or repressing target gene transcription. Not surprisingly, multiple mechanisms account for the glucocorticoid interference with TLR signaling including enhanced expression of the natural inhibitors of TLR pathways, direct repression of TLR-activated transcriptional regulators and cross-utilization of cofactors essential for both GR and TLR signaling. Here we discuss recent and unexpected examples of crosstalk between the two transcriptional networks and the emerging role of GR in the regulation of innate immunity.
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Affiliation(s)
- Yurii Chinenov
- Hospital for Special Surgery, Department of Microbiology & Immunology, Weill Medical College of Cornell University, 535 E70th Street, Research Building Room 425, New York, NY 10021,USA
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Reily MM, Pantoja C, Hu X, Chinenov Y, Rogatsky I. The GRIP1:IRF3 interaction as a target for glucocorticoid receptor-mediated immunosuppression. EMBO J 2005; 25:108-17. [PMID: 16362036 PMCID: PMC1356362 DOI: 10.1038/sj.emboj.7600919] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Accepted: 11/24/2005] [Indexed: 01/11/2023] Open
Abstract
Glucocorticoids dramatically inhibit cytokine and chemokine production. They act through the glucocorticoid receptor (GR), a ligand-dependent transcription factor that binds to and represses activities of other DNA-bound regulators, activator protein 1 and nuclear factor kappaB, utilizing a p160 GRIP1 as a corepressor. A yeast two-hybrid screen with the GRIP1 corepression domain (RD) yielded interferon (IFN) regulatory factor (IRF)3-a downstream effector of Toll-like receptors (TLR) 3/4 and an essential activator of several IFN and chemokine genes. We defined the GRIP1:IRF3 interface and showed that endogenous GRIP1 and IRF3 interact in mammalian cells. Interestingly, GR and IRF3 competed for GRIP1 binding; GR activation or GRIP1 knockdown in macrophages blocked whereas GRIP1 overexpression rescued IRF3-dependent gene expression. GR interference persisted in MyD88- and IFNA receptor-deficient mice, suggesting a specific disruption of TLR3-IRF3 pathway, not of autocrine IFN signaling. Finally, IRF3-stimulated response elements were necessary and sufficient for TLR3-dependent induction and glucocorticoid inhibition. Thus, GRIP1 plays a cofactor role in innate immunity. Competition with GR for GRIP1 antagonizes IRF3-mediated transcription, identifying the GRIP1:IRF3 interaction as a novel target for glucocorticoid immunosuppression.
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Affiliation(s)
- Michael M Reily
- Hospital for Special Surgery, Department of Microbiology & Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Carlos Pantoja
- Department of Cellular & Molecular Pharmacology, UC San Francisco, San Francisco, CA, USA
| | - Xiaoyu Hu
- Hospital for Special Surgery, Department of Microbiology & Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Yurii Chinenov
- Hospital for Special Surgery, Department of Microbiology & Immunology, Weill Medical College of Cornell University, New York, NY, USA
| | - Inez Rogatsky
- Hospital for Special Surgery, Department of Microbiology & Immunology, Weill Medical College of Cornell University, New York, NY, USA
- Hospital for Special Surgery, Department of Microbiology & Immunology, Weill Medical College of Cornell University, 535 E70th Street, Research Building Room 425, New York, NY 10021, USA. Tel.: +1 212 606 1462; Fax: +1 212 774 2560; E-mail:
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25
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Kazmin DA, Chinenov Y, Larson E, Starkey JR. Comparative modeling of the N-terminal domain of the 67kDa laminin-binding protein: implications for putative ribosomal function. Biochem Biophys Res Commun 2003; 300:161-6. [PMID: 12480536 DOI: 10.1016/s0006-291x(02)02772-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Laminin-binding protein/p40 (LBP/p40) precursor appears to be involved in two seemingly unrelated activities-cell adhesion and ribosomal biogenesis. Analysis of primary structure revealed a two-domain organization of the LBP/p40. The N-terminal portion of LBP is similar to the S2 family of prokaryotic ribosomal proteins, while the C-terminus is unique for Metazoa and is involved in extraribosomal functions. To gain insight into putative ribosomal functions of LBP we performed comparative modeling of the N-terminal domain using crystal structures of S2p from Thermus thermophilus. The LBP model assumes an alpha-beta sandwich fold similar to that of S2. Modeling revealed the loss of a significant portion of ribosomal RNA (rRNA) interaction domain, lack of conservation of many residues involved in interactions with rRNA, and a major shift in surface charge distribution (compared to the S2 protein). The overall stability of the fold argues against a proposed transmembrane domain in the central part of the protein. Partial overlap in S2 and laminin-binding domains suggests that ribosomal and surface receptor functions would be mutually exclusive. The possible biological role of LBP/p40 bifunctionality is discussed.
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Affiliation(s)
- Dmitri A Kazmin
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
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26
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Affiliation(s)
- Alexei Tulin
- HHMI Laboratories, Carnegie Institution of Washington, Baltimore, Maryland 21210, USA
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27
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Abstract
Networks of protein interactions coordinate cellular functions. We describe a bimolecular fluorescence complementation (BiFC) assay for determination of the locations of protein interactions in living cells. This approach is based on complementation between two nonfluorescent fragments of the yellow fluorescent protein (YFP) when they are brought together by interactions between proteins fused to each fragment. BiFC analysis was used to investigate interactions among bZIP and Rel family transcription factors. Regions outside the bZIP domains determined the locations of bZIP protein interactions. The subcellular sites of protein interactions were regulated by signaling. Cross-family interactions between bZIP and Rel proteins affected their subcellular localization and modulated transcription activation. These results attest to the general applicability of the BiFC assay for studies of protein interactions.
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Affiliation(s)
- Chang-Deng Hu
- Howard Hughes Medical Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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28
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Abstract
A new subfamily of two-domain histone acetyltransferases (HATs) related to Elp3 has been identified. In addition to a HAT domain in the C terminus, these proteins have an N-terminal domain similar to the catalytic domain of S-adenosylmethionine radical enzymes. Two-domain organization is preserved in evolution, suggesting that both enzymatic activities are functionally or mechanistically coupled and directed towards highly conserved substrates. The functional implications of this similarity and a possible role for Elp3-related proteins as histone demethylases are discussed.
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Affiliation(s)
- Yurii Chinenov
- Howard Hughes Medical Institute, University of Michigan Medical Center, 1150 W. Medical Center Dr., Ann Arbor, MI 48109-0650, USA.
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29
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Abstract
Fos and Jun family proteins regulate the expression of a myriad of genes in a variety of tissues and cell types. This functional versatility emerges from their interactions with related bZIP proteins and with structurally unrelated transcription factors. These interactions at composite regulatory elements produce nucleoprotein complexes with high sequence-specificity and regulatory selectivity. Several general principles including binding cooperativity and conformational adaptability have emerged from studies of regulatory complexes containing Fos-Jun family proteins. The structural properties of Fos-Jun family proteins including opposite orientations of heterodimer binding and the ability to bend DNA can contribute to the assembly and functions of such complexes. The cooperative recruitment of transcription factors, coactivators and chromatin remodeling factors to promoter and enhancer regions generates multiprotein transcription regulatory complexes with cell- and stimulus-specific transcriptional activities. The gene-specific architecture of these complexes can mediate the selective control of transcriptional activity.
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Affiliation(s)
- Y Chinenov
- Howard Hughes Medical Institute, University of Michigan Medical School Ann Arbor, Michigan, MI 48109-0650, USA
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30
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Abstract
The GA-binding protein (GABP) is a ubiquitous heteromeric transcription factor implicated in the regulation of several genes involved in mitochondrial energy metabolism including subunits of cytochrome c oxidase, ATP synthase, and mitochondrial transcription factor 1 (mtTF1). GABPalpha subunit binds the PEA3/Ets binding sites (EBS), while GABPbeta contains a transcription activation domain and mediates alphabeta dimer and alpha(2)beta(2) tetramer formation essential for activation of transcription. Here we report the cloning of 2449 bp of the mouse (m) GABPalpha promoter region including 201 bp of the 5' end of the published mGABPalpha cDNA sequence. Surprisingly, sequences homologous to the 5'UTR of mouse, rat and human mitochondrial ATP synthase coupling factor 6 (ATPsynCF6) cDNAs were found165-240 bp upstream of the mGABPalpha cDNA. A search of the non-redundant nucleotide database revealed a human genomic sequence derived from chromosome 21 (21q22) bearing significant homology to the mGABPalpha/ATPsynCF6 promoter region and encompassed the entire hGABPalpha and hATPsynCF6 genes. Primer extension analysis revealed multiple transcription start sites for both mGABPalpha and mATPsynCF6 mRNAs that mapped near the published cDNA 5' ends. Sequence analysis identified several binding sites upstream of the GABPalpha cDNA sequence including sites for GABP (-86, -104, -169, -257, and -994), YY1 (-57), Sp1 (-242 and -226), and NRF1 (-5). No 'TATA' motif was identified near either the GABPalpha or ATPsynCF6 transcription start sites. The human and mouse promoters retain significant sequence identity including binding sites for several tissue-specific transcription factors. Transient transfection assays using Luciferase reporter constructs containing the intergenic region and flanking sequences confirmed that this region of DNA promotes transcription in both directions.
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Affiliation(s)
- Y Chinenov
- Department of Biochemistry, University of Missouri at Columbia, MO, Columbia 65212, USA
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31
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Chinenov Y, Henzl M, Martin ME. The alpha and beta subunits of the GA-binding protein form a stable heterodimer in solution. Revised model of heterotetrameric complex assembly. J Biol Chem 2000; 275:7749-56. [PMID: 10713087 DOI: 10.1074/jbc.275.11.7749] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We have studied the assembly of GA-binding protein (GABP) in solution and established the role of DNA in the assembly of the transcriptionally active GABPalpha(2)beta(2) heterotetrameric complex. GABP binds DNA containing a single PEA3/Ets-binding site (PEA3/EBS) exclusively as the alphabeta heterodimer complex, but readily binds as the GABPalpha(2)beta(2) heterotetramer complex on DNA containing two PEA3/EBSs. Positioning of the PEA3/EBSs on the same face of the DNA helix stabilizes heterotetramer complex binding. These observations suggest that GABPalphabeta heterodimers are the predominant molecular species in solution and that DNA containing two PEA3/EBSs promotes formation of the GABPalpha(2)beta(2) heterotetrameric complex. We analyzed the assembly of GABPalpha(2)beta(2) heteromeric complexes in solution by analytical ultracentrifugation. GABPalpha exists as a monomer in solution while GABPbeta exists in a monomer-dimer equilibrium (K(d) = 1.8 +/- 0.27 microM). In equimolar mixtures of the two subunits, GABPalpha and GABPbeta formed a stable heterodimer, with no heterotetramer complex detected. Thus, GABP exists in solution as the heterodimer previously shown to be a weak transcriptional activator. Assembly of the transcriptionally active GABPalpha(2)beta(2) heterotetramer complex requires the presence of specific DNA containing at least two PEA3/EBSs.
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Affiliation(s)
- Y Chinenov
- Department of Biochemistry, University of Missouri at Columbia, Columbia, Missouri 65212, USA
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32
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Chinenov Y, Schmidt T, Yang XY, Martin ME. Identification of redox-sensitive cysteines in GA-binding protein-alpha that regulate DNA binding and heterodimerization. J Biol Chem 1998; 273:6203-9. [PMID: 9497343 DOI: 10.1074/jbc.273.11.6203] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transcription factor GA-binding protein (GABP) is composed of two subunits, GABPalpha and GABPbeta. The DNA-binding subunit, GABPalpha, is a member of the Ets family of transcription factors, characterized by the conserved Ets-domain that mediates DNA binding and associates with GABPbeta, which lacks a discernible DNA binding domain, through ankyrin repeats in the NH2 terminus of GABPbeta. We previously demonstrated that GABP is subject to redox regulation in vitro and in vivo through four COOH-terminal cysteines in GABPalpha. To determine the roles of individual cysteines in GABP redox regulation, we generated a series of serine substitution mutants by site-directed mutagenesis and identified three redox-sensitive cysteine residues in GABPalpha (Cys388, Cys401, and Cys421). Sulfhydryl modification of Cys388 and Cys401 inhibits DNA binding by GABPalpha, whereas, modification of Cys421 has no effect on GABPalpha DNA binding but inhibits dimerization with GABPbeta. The positions of Cys388 and Cys401 within the known Ets-domain structure suggest two very different mechanisms for redox regulation of DNA binding. Sulfhydryl modification of Cys388 could directly interfere with DNA binding or might alter the positioning of the DNA-binding helix 3. Modification of Cys401 may inhibit DNA binding through stabilization of an inhibitory helix similar to that described in the Ets-1 protein. Thus, GABP is regulated through at least two redox-sensitive activities, DNA binding and heterodimerization.
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Affiliation(s)
- Y Chinenov
- Department of Biochemistry, University of Missouri at Columbia, Columbia, Missouri 65212, USA
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Yu M, Yang XY, Schmidt T, Chinenov Y, Wang R, Martin ME. GA-binding protein-dependent transcription initiator elements. Effect of helical spacing between polyomavirus enhancer a factor 3(PEA3)/Ets-binding sites on initiator activity. J Biol Chem 1997; 272:29060-7. [PMID: 9360980 DOI: 10.1074/jbc.272.46.29060] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Many eukaryotic RNA polymerase II promoters contain initiator elements which direct accurate transcription in a TATA-independent manner. The PEA3/Ets-binding site (PEA3/EBS) is a common enhancer element in eukaryotic genes and is also found near the transcriptional start sites of many TATA-less promoters. We demonstrate that two PEA3/EBSs driving expression of the luciferase reporter gene, function as a minimal transcriptional initiator element. Maximal levels of transcription was achieved when two PEA3/EBSs, in either orientation, were located on the same face of the DNA helix, and the sites could be separated by up to three helical turns. In vitro transcription start sites directed by PEA3/EBS elements were clustered on either side of the upstream PEA3/EBS and were abolished by immunodepletion of GA-binding protein (GABP) from FM3A cell nuclear extracts. In vivo, co-transfection of GABPalpha and GABPbeta expression vectors enhanced reporter gene expression driven from PEA3/EBS initiator elements. Like other initiator elements, the PEA3/EBS elements were activated synergistically by upstream Sp1-binding sites. Thus, our results establish GABP as both a transcriptional activator factor and as an initiator factor.
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Affiliation(s)
- M Yu
- Department of Biochemistry, University of Missouri at Columbia, Columbia, Missouri 65212, USA
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Abstract
We have investigated the reduction/oxidation (redox) regulation of the heteromeric transcription factor GA-binding protein (GABP). GABP, also known as nuclear respiratory factor 2, regulates the expression of nuclear encoded mitochondrial proteins involved in oxidative phosphorylation, including cytochrome c oxidase subunits IV and Vb, as well as the expression of mitochondrial transcription factor 1. GABP is composed of two subunits, the Ets-related GABP-alpha, which mediates specific DNA binding, and GABP-beta, which forms heterodimers and heterotetramers on DNA sequences containing the PEA3/Ets motif ((C/A)GGA(A/T)(G/A)). We demonstrate here that GABP DNA binding activity and GABP-dependent gene expression in 3T3 cells are inhibited by pro-oxidant conditions. DNA binding of recombinant GABP-alpha was activated by chemical reduction (dithiothreitol) and by thioredoxin; however, GSSG inhibited GABP DNA binding activity. Treatment of GABP-alpha, but not GABP-beta1, with sulfhydryl-alkylating agents also inhibited GABP DNA binding activity. Our results suggest that GABP DNA binding activity is redox-regulated in vivo, possibly by thioredoxin-mediated reduction and by GSSG-mediated oxidation of the GABP-alpha subunit. The regulation of GABP (nuclear respiratory factor 2) DNA binding activity by cellular redox changes provides an important link between mitochondrial and nuclear gene expression and the redox state of the cell.
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Affiliation(s)
- M E Martin
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65212, USA
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