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Sharma S, Gerber AN, Kraft M, Wenzel SE. Asthma Pathogenesis: Phenotypes, Therapies and Gaps. Summary of the Aspen Lung Conference 2023. Am J Respir Cell Mol Biol 2024. [PMID: 38635858 DOI: 10.1165/rcmb.2024-0082ws] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024] Open
Abstract
Although substantial progress has been made in our understanding of asthma pathogenesis and phenotypes over the 60-year history of Aspen Lung Conferences on asthma, many ongoing challenges exist in our understanding of the clinical and molecular heterogeneity of the disease and an individual patient's response to therapy. This report summarizes the proceedings of the 2023 Aspen Lung Conference, which was organized to review the clinical and molecular heterogeneity of asthma and to better understand the impact of genetic, environmental, cellular, and molecular influences on disease susceptibility, heterogeneity, and severity. The goals of the conference were to review new information about asthma phenotypes, cellular processes, and cellular signatures underlying disease heterogeneity and treatment response. The report concludes with ongoing gaps in our understanding of asthma pathobiology and provides some recommendations for future research to better understand the clinical and basic mechanisms underlying disease heterogeneity in asthma and to advance the development of new treatments for this growing public health problem.
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Affiliation(s)
- Sunita Sharma
- University of Colorado, 1878, Division of Pulmonary Sciences and Critical Care Medicine, Aurora, Colorado, United States
| | - Anthony N Gerber
- National Jewish Health, Medicine, Denver, Colorado, United States
| | - Monica Kraft
- Icahn School of Medicine at Mount Sinai, Medicine, New York, New York, United States
| | - Sally E Wenzel
- University of Pittsburgh School of Public Health, Dept of EOH, Pittsburgh, Pennsylvania, United States;
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2
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El Kharbili M, Sasse SK, Sanford L, Jacobson S, Aviszus K, Gupta A, Guo C, Majka SM, Dowell RD, Gerber AN, Bowler RP, Gally F. Noncoding SNPs decrease expression of FABP5 during COPD exacerbations. J Clin Invest 2023; 134:e175626. [PMID: 38113113 PMCID: PMC10849757 DOI: 10.1172/jci175626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Affiliation(s)
| | - Sarah K. Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | | | - Sean Jacobson
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | | | - Arnav Gupta
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
- Department of Medicine
| | - Claire Guo
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Susan M. Majka
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Robin D. Dowell
- BioFrontiers Institute
- Molecular, Cellular and Developmental Biology, and
- Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Anthony N. Gerber
- Department of Immunology and Genomic Medicine and
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
- Department of Medicine
| | - Russell P. Bowler
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Fabienne Gally
- Department of Immunology and Genomic Medicine and
- Department of Medicine
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3
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Liu H, Aviszus K, Zelarney P, Liao SY, Gerber AN, Make B, Wechsler ME, Marrack P, Reinhardt RL. Vaccine-elicited B- and T-cell immunity to SARS-CoV-2 is impaired in chronic lung disease patients. ERJ Open Res 2023; 9:00400-2023. [PMID: 37583809 PMCID: PMC10423317 DOI: 10.1183/23120541.00400-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023] Open
Abstract
Background While vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) provides significant protection from coronavirus disease 2019, the protection afforded to individuals with chronic lung disease is less well established. This study seeks to understand how chronic lung disease impacts SARS-CoV-2 vaccine-elicited immunity. Methods Deep immune phenotyping of humoral and cell-mediated responses to the SARS-CoV-2 vaccine was performed in patients with asthma, COPD and interstitial lung disease (ILD) compared to healthy controls. Results 48% of vaccinated patients with chronic lung diseases had reduced antibody titres to the SARS-CoV-2 vaccine antigen relative to healthy controls. Vaccine antibody titres were significantly reduced among asthma (p<0.035), COPD (p<0.022) and a subset of ILD patients as early as 3-4 months after vaccination, correlating with decreased vaccine-specific memory B-cells in circulation. Vaccine-specific memory T-cells were significantly reduced in patients with asthma (CD8+ p<0.004; CD4+ p<0.023) and COPD (CD8+ p<0.008) compared to healthy controls. Impaired T-cell responsiveness was also observed in a subset of ILD patients (CD8+ 21.4%; CD4+ 42.9%). Additional heterogeneity between healthy and disease cohorts was observed among bulk and vaccine-specific follicular T-helper cells. Conclusions Deep immune phenotyping of the SARS-CoV-2 vaccine response revealed the complex nature of vaccine-elicited immunity and highlights the need for more personalised vaccination schemes in patients with underlying lung conditions.
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Affiliation(s)
- Haolin Liu
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | - Katja Aviszus
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | | | - Shu-Yi Liao
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, CO, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Anthony N. Gerber
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - Barry Make
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - Michael E. Wechsler
- Department of Medicine, National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - Philippa Marrack
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - R. Lee Reinhardt
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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4
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Campeau S, McNulty C, Stanley JT, Gerber AN, Sasse SK, Dowell RD. Determination of steady-state transcriptome modifications associated with repeated homotypic stress in the rat rostral posterior hypothalamic region. Front Neurosci 2023; 17:1173699. [PMID: 37360161 PMCID: PMC10288150 DOI: 10.3389/fnins.2023.1173699] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/18/2023] [Indexed: 06/28/2023] Open
Abstract
Chronic stress is epidemiologically correlated with physical and psychiatric disorders. Whereas many animal models of chronic stress induce symptoms of psychopathology, repeated homotypic stressors to moderate intensity stimuli typically reduce stress-related responses with fewer, if any, pathological symptoms. Recent results indicate that the rostral posterior hypothalamic (rPH) region is a significant component of the brain circuitry underlying response reductions (habituation) associated with repeated homotypic stress. To test whether posterior hypothalamic transcriptional regulation associates with the neuroendocrine modifications induced by repeated homotypic stress, RNA-seq was performed in the rPH dissected from adult male rats that experienced either no stress, 1, 3, or 7 stressful loud noise exposures. Plasma samples displayed reliable increases of corticosterone in all stressed groups, with the smallest increase in the group exposed to 7 loud noises, indicating significant habituation compared to the other stressed groups. While few or no differentially expressed genes were detected 24-h after one or three loud noise exposures, relatively large numbers of transcripts were differentially expressed between the group exposed to 7 loud noises when compared to the control or 3-stress groups, respectively, which correlated with the corticosterone response habituation observed. Gene ontology analyses indicated multiple significant functional terms related to neuron differentiation, neural membrane potential, pre- and post-synaptic elements, chemical synaptic transmission, vesicles, axon guidance and projection, glutamatergic and GABAergic neurotransmission. Some of the differentially expressed genes (Myt1l, Zmat4, Dlx6, Csrnp3) encode transcription factors that were independently predicted by transcription factor enrichment analysis to target other differentially regulated genes in this study. A similar experiment employing in situ hybridization histochemical analysis in additional animals validated the direction of change of the 5 transcripts investigated (Camk4, Gabrb2, Gad1, Grin2a and Slc32a) with a high level of temporal and regional specificity for the rPH. In aggregate, the results suggest that distinct patterns of gene regulation are obtained in response to a repeated homotypic stress regimen; they also point to a significant reorganization of the rPH region that may critically contribute to the phenotypic modifications associated with repeated homotypic stress habituation.
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Affiliation(s)
- Serge Campeau
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, United States
| | - Connor McNulty
- Department of Psychology and Neuroscience, University of Colorado, Boulder, CO, United States
| | - Jacob T. Stanley
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, United States
- BioFrontiers Institute, University of Colorado, Boulder, CO, United States
| | - Anthony N. Gerber
- Department of Medicine, National Jewish Health, Denver, CO, United States
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Sarah K. Sasse
- Department of Medicine, National Jewish Health, Denver, CO, United States
| | - Robin D. Dowell
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, United States
- BioFrontiers Institute, University of Colorado, Boulder, CO, United States
- Department of Computer Science, University of Colorado, Boulder, CO, United States
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5
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Liu H, Aviszus K, Zelarney P, Liao SY, Gerber AN, Make B, Wechsler ME, Marrack P, Reinhardt RL. Vaccine-elicited B and T cell immunity to SARS-CoV-2 is impaired in chronic lung disease patients. medRxiv 2023:2023.01.25.23284971. [PMID: 36747750 PMCID: PMC9901055 DOI: 10.1101/2023.01.25.23284971] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The protection afforded by vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to individuals with chronic lung disease is not well established. To understand how chronic lung disease impacts SARS-CoV-2 vaccine-elicited immunity we performed deep immunophenotyping of the humoral and cell mediated SARS-CoV-2 vaccine response in an investigative cohort of vaccinated patients with diverse pulmonary conditions including asthma, chronic obstructive pulmonary disease (COPD), and interstitial lung disease (ILD). Compared to healthy controls, 48% of vaccinated patients with chronic lung diseases had reduced antibody titers to the SARS-CoV-2 vaccine antigen as early as 3-4 months after vaccination, correlating with decreased vaccine-specific memory B cells. Vaccine-specific CD4 and CD8 T cells were also significantly reduced in patients with asthma, COPD, and a subset of ILD patients compared to healthy controls. These findings reveal the complex nature of vaccine-elicited immunity in high-risk patients with chronic lung disease.
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Affiliation(s)
- Haolin Liu
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Katja Aviszus
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Pearlanne Zelarney
- Research Informatics Services, National Jewish Health, Denver, CO, 80206, USA
| | - Shu-Yi Liao
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver CO, 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Anthony N Gerber
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver CO, 80206, USA
| | - Barry Make
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver CO, 80206, USA
| | - Michael E Wechsler
- Department of Medicine, National Jewish Health, Denver, CO, 80206, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver CO, 80206, USA
| | - Philippa Marrack
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - R Lee Reinhardt
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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6
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Borie R, Cardwell J, Konigsberg IR, Moore CM, Zhang W, Sasse SK, Gally F, Dobrinskikh E, Walts A, Powers J, Brancato J, Rojas M, Wolters PJ, Brown KK, Blackwell TS, Nakanishi T, Richards JB, Gerber AN, Fingerlin TE, Sachs N, Pulit SL, Zappala Z, Schwartz DA, Yang IV. Colocalization of Gene Expression and DNA Methylation with Genetic Risk Variants Supports Functional Roles of MUC5B and DSP in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2022; 206:1259-1270. [PMID: 35816432 PMCID: PMC9746850 DOI: 10.1164/rccm.202110-2308oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: Common genetic variants have been associated with idiopathic pulmonary fibrosis (IPF). Objectives: To determine functional relevance of the 10 IPF-associated common genetic variants we previously identified. Methods: We performed expression quantitative trait loci (eQTL) and methylation quantitative trait loci (mQTL) mapping, followed by co-localization of eQTL and mQTL with genetic association signals and functional validation by luciferase reporter assays. Illumina multi-ethnic genotyping arrays, mRNA sequencing, and Illumina 850k methylation arrays were performed on lung tissue of participants with IPF (234 RNA and 345 DNA samples) and non-diseased controls (188 RNA and 202 DNA samples). Measurements and Main Results: Focusing on genetic variants within 10 IPF-associated genetic loci, we identified 27 eQTLs in controls and 24 eQTLs in cases (false-discovery-rate-adjusted P < 0.05). Among these signals, we identified associations of lead variants rs35705950 with expression of MUC5B and rs2076295 with expression of DSP in both cases and controls. mQTL analysis identified CpGs in gene bodies of MUC5B (cg17589883) and DSP (cg08964675) associated with the lead variants in these two loci. We also demonstrated strong co-localization of eQTL/mQTL and genetic signal in MUC5B (rs35705950) and DSP (rs2076295). Functional validation of the mQTL in MUC5B using luciferase reporter assays demonstrates that the CpG resides within a putative internal repressor element. Conclusions: We have established a relationship of the common IPF genetic risk variants rs35705950 and rs2076295 with respective changes in MUC5B and DSP expression and methylation. These results provide additional evidence that both MUC5B and DSP are involved in the etiology of IPF.
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Affiliation(s)
| | | | | | - Camille M. Moore
- Department of Biostatistics and Bioinformatics and
- Center for Genes, Environment, and Health
| | | | | | - Fabienne Gally
- Department of Medicine
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | | | | | | | | | - Mauricio Rojas
- Department of Internal Medicine, Ohio State College of Medicine, The Ohio State University, Columbus, Ohio
| | - Paul J. Wolters
- Department of Medicine, University of California, San Francisco, California
| | | | - Timothy S. Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tomoko Nakanishi
- Department of Human Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Canada
| | - J. Brent Richards
- Department of Human Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Canada
| | - Anthony N. Gerber
- Department of Medicine
- Department of Medicine, and
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | - Tasha E. Fingerlin
- Department of Biostatistics and Bioinformatics and
- Center for Genes, Environment, and Health
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | - Norman Sachs
- Cell Biology, Vertex Pharmaceuticals, San Diego, California; and
| | - Sara L. Pulit
- Computational Genomics, Vertex Pharmaceuticals, Boston, Massachusetts
| | - Zachary Zappala
- Computational Genomics, Vertex Pharmaceuticals, Boston, Massachusetts
| | - David A. Schwartz
- Department of Medicine
- Department of Microbiology and Immunology, University of Colorado Anschutz Medical Campus; Aurora, Colorado
| | - Ivana V. Yang
- Department of Medicine
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado
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7
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Bai X, Bai A, Tomasicchio M, Hagman JR, Buckle AM, Gupta A, Kadiyala V, Bevers S, Serban KA, Kim K, Feng Z, Spendier K, Hagen G, Fornis L, Griffith DE, Dzieciatkowska M, Sandhaus RA, Gerber AN, Chan ED. α1-Antitrypsin Binds to the Glucocorticoid Receptor with Anti-Inflammatory and Antimycobacterial Significance in Macrophages. J Immunol 2022; 209:1746-1759. [PMID: 36162872 PMCID: PMC10829398 DOI: 10.4049/jimmunol.2200227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/23/2022] [Indexed: 01/13/2024]
Abstract
α1-Antitrypsin (AAT), a serine protease inhibitor, is the third most abundant protein in plasma. Although the best-known function of AAT is irreversible inhibition of elastase, AAT is an acute-phase reactant and is increasingly recognized to have a panoply of other functions, including as an anti-inflammatory mediator and a host-protective molecule against various pathogens. Although a canonical receptor for AAT has not been identified, AAT can be internalized into the cytoplasm and is known to affect gene regulation. Because AAT has anti-inflammatory properties, we examined whether AAT binds the cytoplasmic glucocorticoid receptor (GR) in human macrophages. We report the finding that AAT binds to GR using several approaches, including coimmunoprecipitation, mass spectrometry, and microscale thermophoresis. We also performed in silico molecular modeling and found that binding between AAT and GR has a plausible stereochemical basis. The significance of this interaction in macrophages is evinced by AAT inhibition of LPS-induced NF-κB activation and IL-8 production as well as AAT induction of angiopoietin-like 4 protein, which are, in part, dependent on GR. Furthermore, this AAT-GR interaction contributes to a host-protective role against mycobacteria in macrophages. In summary, this study identifies a new mechanism for the gene regulation, anti-inflammatory, and host-defense properties of AAT.
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Affiliation(s)
- Xiyuan Bai
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Denver, CO;
- Department of Academic Affairs, National Jewish Health, Denver, CO
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO
| | - An Bai
- Department of Academic Affairs, National Jewish Health, Denver, CO
| | - Michele Tomasicchio
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, UCT Lung Institute and the MRC Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - James R Hagman
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- PTNG Bio, Melbourne, Victoria, Australia
| | - Arnav Gupta
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO
- Department of Medicine, National Jewish Health, Denver, CO
| | | | - Shaun Bevers
- Biophysics Core Facility, University of Colorado School of Medicine, Aurora, CO
| | | | - Kevin Kim
- Department of Academic Affairs, National Jewish Health, Denver, CO
| | - Zhihong Feng
- Department of Respiratory Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Kathrin Spendier
- Department of Physics & Energy Science, University of Colorado, Colorado Springs, CO
- BioFrontiers Center, University of Colorado, Colorado Springs, CO; and
| | - Guy Hagen
- Department of Physics & Energy Science, University of Colorado, Colorado Springs, CO
- BioFrontiers Center, University of Colorado, Colorado Springs, CO; and
| | | | | | - Monika Dzieciatkowska
- Proteomic Mass Spectrometry Facility, University of Colorado School of Medicine, Aurora, CO
| | | | - Anthony N Gerber
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO
- Department of Medicine, National Jewish Health, Denver, CO
| | - Edward D Chan
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Denver, CO;
- Department of Academic Affairs, National Jewish Health, Denver, CO
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO
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8
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Gupta A, Sasse SK, Berman R, Gruca MA, Dowell RD, Chu HW, Downey GP, Gerber AN. Integrated genomics approaches identify transcriptional mediators and epigenetic responses to Afghan desert particulate matter in small airway epithelial cells. Physiol Genomics 2022; 54:389-401. [PMID: 36062885 PMCID: PMC9550581 DOI: 10.1152/physiolgenomics.00063.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/15/2022] [Accepted: 08/29/2022] [Indexed: 01/14/2023] Open
Abstract
Military Deployment to Southwest Asia and Afghanistan and exposure to toxic airborne particulates have been associated with an increased risk of developing respiratory disease, collectively termed deployment-related respiratory diseases (DRRDs). Our knowledge about how particulates mediate respiratory disease is limited, precluding the appropriate recognition or management. Central to this limitation is the lack of understanding of how exposures translate into dysregulated cell identity with dysregulated transcriptional programs. The small airway epithelium is involved in both the pathobiology of DRRD and fine particulate matter deposition. To characterize small airway epithelial cell epigenetic and transcriptional responses to Afghan desert particulate matter (APM) and investigate the functional interactions of transcription factors that mediate these responses, we applied two genomics assays, the assay for transposase accessible chromatin with sequencing (ATAC-seq) and Precision Run-on sequencing (PRO-seq). We identified activity changes in a series of transcriptional pathways as candidate regulators of susceptibility to subsequent insults, including signal-dependent pathways, such as loss of cytochrome P450 or P53/P63, and lineage-determining transcription factors, such as GRHL2 loss or TEAD3 activation. We further demonstrated that TEAD3 activation was unique to APM exposure despite similar inflammatory responses when compared with wood smoke particle exposure and that P53/P63 program loss was uniquely positioned at the intersection of signal-dependent and lineage-determining transcriptional programs. Our results establish the utility of an integrated genomics approach in characterizing responses to exposures and identifying genomic targets for the advanced investigation of the pathogenesis of DRRD.
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Affiliation(s)
- Arnav Gupta
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Reena Berman
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Margaret A Gruca
- Biofrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Robin D Dowell
- Biofrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Hong Wei Chu
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Gregory P Downey
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado
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9
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Liao SY, Gerber AN, Zelarney P, Make B, Wechsler ME. SARS-CoV-2 mRNA Vaccine Antibody Response in Patients with Asthma Receiving Biologic Therapy: A Real-World Analysis. Am J Respir Crit Care Med 2022; 206:644-648. [PMID: 35549647 PMCID: PMC9716899 DOI: 10.1164/rccm.202203-0599le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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10
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Liao SY, Gerber AN, Zelarney P, Make B, Wechsler ME. Impaired SARS-CoV-2 mRNA Vaccine Antibody Response in Chronic Medical Conditions: A Real-World Analysis. Chest 2022; 161:1490-1493. [PMID: 35016912 PMCID: PMC8743857 DOI: 10.1016/j.chest.2021.12.654] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/13/2021] [Accepted: 12/27/2021] [Indexed: 01/03/2023] Open
Affiliation(s)
- Shu-Yi Liao
- Department of Medicine, National Jewish Health, Denver, CO.
| | | | | | - Barry Make
- Department of Medicine, National Jewish Health, Denver, CO
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11
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El Kharbili M, Aviszus K, Sasse SK, Zhao X, Serban KA, Majka SM, Gerber AN, Gally F. Macrophage programming is regulated by a cooperative interaction between fatty acid binding protein 5 and peroxisome proliferator-activated receptor γ. FASEB J 2022; 36:e22300. [PMID: 35436029 PMCID: PMC9320869 DOI: 10.1096/fj.202200128r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/07/2022] [Accepted: 03/24/2022] [Indexed: 11/11/2022]
Abstract
Resolution of inflammation is an active process that is tightly regulated to achieve repair and tissue homeostasis. In the absence of resolution, persistent inflammation underlies the pathogenesis of chronic lung disease such as chronic obstructive pulmonary disease (COPD) with recurrent exacerbations. Over the course of inflammation, macrophage programming transitions from pro-inflammatory to pro-resolving, which is in part regulated by the nuclear receptor Peroxisome Proliferator-Activated Receptor γ (PPARγ). Our previous work demonstrated an association between Fatty Acid Binding Protein 5 (FABP5) expression and PPARγ activity in peripheral blood mononuclear cells of healthy and COPD patients. However, a role for FABP5 in macrophage programming has not been examined. Here, using a combination of in vitro and in vivo approaches, we demonstrate that FABP5 is necessary for PPARγ activation. In turn, PPARγ acts directly to increase FABP5 expression in primary human alveolar macrophages. We further illustrate that lack of FABP5 expression promotes a pro-inflammatory macrophage programming with increased secretion of pro-inflammatory cytokines and increased chromatin accessibility for pro-inflammatory transcription factors (e.g., NF-κB and MAPK). And finally, real-time cell metabolic analysis using the Seahorse technology shows an inhibition of oxidative phosphorylation in FABP5-deficient macrophages. Taken together, our data indicate that FABP5 and PPARγ reciprocally regulate each other's expression and function, consistent with a novel positive feedback loop between the two factors that mediates macrophage pro-resolving programming. Our studies highlight the importance of defining targets and regulatory mechanisms that control the resolution of inflammation and may serve to inform novel interventional strategies directed towards COPD.
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Affiliation(s)
- Manale El Kharbili
- Department of Immunology and Genomic MedicineNational Jewish HealthDenverColoradoUSA
| | - Katja Aviszus
- Department of Immunology and Genomic MedicineNational Jewish HealthDenverColoradoUSA
| | - Sarah K. Sasse
- Department of MedicineNational Jewish HealthDenverColoradoUSA
| | - Xiaoyun Zhao
- Department of Immunology and Genomic MedicineNational Jewish HealthDenverColoradoUSA
| | - Karina A. Serban
- Department of MedicineNational Jewish HealthDenverColoradoUSA
- Department of MedicineUniversity of ColoradoAuroraColoradoUSA
| | - Susan M. Majka
- Department of Immunology and Genomic MedicineNational Jewish HealthDenverColoradoUSA
- Department of MedicineNational Jewish HealthDenverColoradoUSA
- Department of MedicineUniversity of ColoradoAuroraColoradoUSA
| | - Anthony N. Gerber
- Department of Immunology and Genomic MedicineNational Jewish HealthDenverColoradoUSA
- Department of MedicineNational Jewish HealthDenverColoradoUSA
- Department of MedicineUniversity of ColoradoAuroraColoradoUSA
| | - Fabienne Gally
- Department of Immunology and Genomic MedicineNational Jewish HealthDenverColoradoUSA
- Department of MedicineUniversity of ColoradoAuroraColoradoUSA
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12
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Bansal A, Mostafa MM, Kooi C, Sasse SK, Michi AN, Shah SV, Leigh R, Gerber AN, Newton R. Interplay between nuclear factor-κB, p38 MAPK and glucocorticoid receptor signaling synergistically induces functional TLR2 in lung epithelial cells. J Biol Chem 2022; 298:101747. [PMID: 35189144 PMCID: PMC8942839 DOI: 10.1016/j.jbc.2022.101747] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 09/09/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 12/05/2022] Open
Abstract
While glucocorticoids act via the glucocorticoid receptor (GR; NR3C1) to reduce the expression of many inflammatory genes, repression is not an invariable outcome. Here, we explore synergy occurring between synthetic glucocorticoids (dexamethasone and budesonide) and proinflammatory cytokines (IL1B and TNF) on the expression of the toll-like receptor 2 (TLR2). This effect is observed in epithelial cell lines and both undifferentiated and differentiated primary human bronchial epithelial cells (pHBECs). In A549 cells, IL1B-plus-glucocorticoid–induced TLR2 expression required nuclear factor (NF)-κB and GR. Likewise, in A549 cells, BEAS-2B cells, and pHBECs, chromatin immunoprecipitation identified GR- and NF-κB/p65-binding regions ∼32 kb (R1) and ∼7.3 kb (R2) upstream of the TLR2 gene. Treatment of BEAS-2B cells with TNF or/and dexamethasone followed by global run-on sequencing confirmed transcriptional activity at these regions. Furthermore, cloning R1 or R2 into luciferase reporters revealed transcriptional activation by budesonide or IL1B, respectively, while R1+R2 juxtaposition enabled synergistic activation by IL1B and budesonide. In addition, small-molecule inhibitors and siRNA knockdown showed p38α MAPK to negatively regulate both IL1B-induced TLR2 expression and R1+R2 reporter activity. Finally, agonism of IL1B-plus-dexamethasone–induced TLR2 in A549 cells and pHBECs stimulated NF-κB- and interferon regulatory factor-dependent reporter activity and chemokine release. We conclude that glucocorticoid-plus-cytokine-driven synergy at TLR2 involves GR and NF-κB acting via specific enhancer regions, which combined with the inhibition of p38α MAPK promotes TLR2 expression. Subsequent inflammatory effects that occur following TLR2 agonism may be pertinent in severe neutrophilic asthma or chronic obstructive pulmonary disease, where glucocorticoid-based therapies are less efficacious.
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Affiliation(s)
- Akanksha Bansal
- Department of Physiology & Pharmacology and Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mahmoud M Mostafa
- Department of Physiology & Pharmacology and Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Cora Kooi
- Department of Medicine and Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Aubrey N Michi
- Department of Physiology & Pharmacology and Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Suharsh V Shah
- Department of Physiology & Pharmacology and Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Richard Leigh
- Department of Physiology & Pharmacology and Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Department of Medicine and Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado, USA; Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Robert Newton
- Department of Physiology & Pharmacology and Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
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13
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Gupta A, Sasse SK, Gruca MA, Sanford L, Dowell RD, Gerber AN. Deconvolution of multiplexed transcriptional responses to wood smoke particles defines rapid aryl hydrocarbon receptor signaling dynamics. J Biol Chem 2021; 297:101147. [PMID: 34520756 PMCID: PMC8517214 DOI: 10.1016/j.jbc.2021.101147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 07/19/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
The heterogeneity of respirable particulates and compounds complicates our understanding of transcriptional responses to air pollution. Here, we address this by applying precision nuclear run-on sequencing and the assay for transposase-accessible chromatin sequencing to measure nascent transcription and chromatin accessibility in airway epithelial cells after wood smoke particle (WSP) exposure. We used transcription factor enrichment analysis to identify temporally distinct roles for ternary response factor-serum response factor complexes, the aryl hydrocarbon receptor (AHR), and NFκB in regulating transcriptional changes induced by WSP. Transcription of canonical targets of the AHR, such as CYP1A1 and AHRR, was robustly increased after just 30 min of WSP exposure, and we discovered novel AHR-regulated pathways and targets including the DNA methyltransferase, DNMT3L. Transcription of these genes and associated enhancers rapidly returned to near baseline by 120 min after exposure. The kinetics of AHR- and NFκB-regulated responses to WSP were distinguishable based on the timing of both transcriptional responses and chromatin remodeling, with induction of several cytokines implicated in maintaining NFκB-mediated responses through 120 min of exposure. In aggregate, our data establish a direct and primary role for AHR in mediating airway epithelial responses to WSP and identify crosstalk between AHR and NFκB signaling in controlling proinflammatory gene expression. This work also defines an integrated genomics-based strategy for deconvoluting multiplexed transcriptional responses to heterogeneous environmental exposures.
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Affiliation(s)
- Arnav Gupta
- Department of Medicine, National Jewish Health, Denver, Colorado, USA; Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Margaret A Gruca
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Lynn Sanford
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA; Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado, USA; Department of Medicine, University of Colorado, Aurora, Colorado, USA; Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.
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14
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Gally F, Sasse SK, Kurche JS, Gruca MA, Cardwell JH, Okamoto T, Chu HW, Hou X, Poirion OB, Buchanan J, Preissl S, Ren B, Colgan SP, Dowell RD, Yang IV, Schwartz DA, Gerber AN. The MUC5B-associated variant rs35705950 resides within an enhancer subject to lineage- and disease-dependent epigenetic remodeling. JCI Insight 2021; 6:144294. [PMID: 33320836 PMCID: PMC7934873 DOI: 10.1172/jci.insight.144294] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
The G/T transversion rs35705950, located approximately 3 kb upstream of the MUC5B start site, is the cardinal risk factor for idiopathic pulmonary fibrosis (IPF). Here, we investigate the function and chromatin structure of this –3 kb region and provide evidence that it functions as a classically defined enhancer subject to epigenetic programming. We use nascent transcript analysis to show that RNA polymerase II loads within 10 bp of the G/T transversion site, definitively establishing enhancer function for the region. By integrating Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analysis of fresh and cultured human airway epithelial cells with nuclease sensitivity data, we demonstrate that this region is in accessible chromatin that affects the expression of MUC5B. Through applying paired single-nucleus RNA- and ATAC-seq to frozen tissue from IPF lungs, we extend these findings directly to disease, with results indicating that epigenetic programming of the –3 kb enhancer in IPF occurs in both MUC5B-expressing and nonexpressing lineages. In aggregate, our results indicate that the MUC5B-associated variant rs35705950 resides within an enhancer that is subject to epigenetic remodeling and contributes to pathologic misexpression in IPF.
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Affiliation(s)
- Fabienne Gally
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Jonathan S Kurche
- Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Margaret A Gruca
- BioFrontiers Institute, University of Colorado-Boulder (CU Boulder), Boulder, Colorado, USA
| | | | - Tsukasa Okamoto
- Department of Medicine, University of Colorado, Aurora, Colorado, USA.,Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hong W Chu
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Xiaomeng Hou
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Olivier B Poirion
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Justin Buchanan
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA.,Ludwig Institute for Cancer Research, La Jolla, California, USA
| | - Sean P Colgan
- Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado-Boulder (CU Boulder), Boulder, Colorado, USA.,Molecular, Cellular and Developmental Biology, and.,Computer Science, CU Boulder, Boulder, Colorado, USA
| | - Ivana V Yang
- Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Anthony N Gerber
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Medicine, University of Colorado, Aurora, Colorado, USA.,Department of Medicine, National Jewish Health, Denver, Colorado, USA
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15
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Mostafa MM, Bansal A, Michi AN, Sasse SK, Proud D, Gerber AN, Newton R. Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells. J Biol Chem 2021; 296:100065. [PMID: 33184061 PMCID: PMC7949084 DOI: 10.1074/jbc.ra120.015755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/24/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
Ligand-activated glucocorticoid receptor (GR) elicits variable glucocorticoid-modulated transcriptomes in different cell types. However, some genes, including Krüppel-like factor 9 (KLF9), a putative transcriptional repressor, demonstrate conserved responses. We show that glucocorticoids induce KLF9 expression in the human airways in vivo and in differentiated human bronchial epithelial (HBE) cells grown at air-liquid interface (ALI). In A549 and BEAS-2B pulmonary epithelial cells, glucocorticoids induce KLF9 expression with similar kinetics to primary HBE cells in submersion culture. A549 and BEAS-2B ChIP-seq data reveal four common glucocorticoid-induced GR binding sites (GBSs). Two GBSs mapped to the 5'-proximal region relative to KLF9 transcription start site (TSS) and two occurred at distal sites. These were all confirmed in primary HBE cells. Global run-on (GRO) sequencing indicated robust enhancer RNA (eRNA) production from three of these GBSs in BEAS-2B cells. This was confirmed in A549 cells, plus submersion, and ALI culture of HBE cells. Cloning each GBS into luciferase reporters revealed glucocorticoid-induced activity requiring a glucocorticoid response element (GRE) within each distal GBS. While the proximal GBSs drove modest reporter induction by glucocorticoids, this region exhibited basal eRNA production, RNA polymerase II enrichment, and looping to the TSS, plausibly underlying constitutive KLF9 expression. Post glucocorticoid treatment, interactions between distal and proximal GBSs and the TSS correlated with KLF9 induction. CBP/P300 silencing reduced proximal GBS activity, but negligibly affected KLF9 expression. Overall, a model for glucocorticoid-mediated regulation of KLF9 involving multiple GBSs is depicted. This work unequivocally demonstrates that mechanistic insights gained from cell lines can translate to physiologically relevant systems.
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Affiliation(s)
- Mahmoud M Mostafa
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Akanksha Bansal
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Aubrey N Michi
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - David Proud
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado, USA; Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Robert Newton
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada.
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16
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Bansal A, Mostafa MM, Kooi C, Shah SV, Leigh R, Gerber AN, Newton R. Interplay between the Glucocorticoid Receptor and Inflammatory Signaling leads to Enhanced TLR2 Expression in Pulmonary Epithelial Cells. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Altonsy MO, Kurwa HA, Lauzon GJ, Amrein M, Gerber AN, Almishri W, Mydlarski PR. Corynebacterium tuberculostearicum, a human skin colonizer, induces the canonical nuclear factor-κB inflammatory signaling pathway in human skin cells. Immun Inflamm Dis 2020; 8:62-79. [PMID: 31912662 PMCID: PMC7016847 DOI: 10.1002/iid3.284] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Corynebacterium tuberculostearicum (C. t.) is a ubiquitous bacterium that colonizes human skin. In contrast to other members of the genus Corynebacterium, such as toxigenic Corynebacterium diphtheriae or the opportunistic pathogen Corynebacterium jeikeium, several studies suggest that C. t. may play a role in skin health and disease. However, the mechanisms underlying these effects remain poorly understood. METHODS To investigate whether C. t. induces inflammatory pathways in primary human epidermal keratinocytes (HEKs) and human cutaneous squamous carcinoma cells (SCCs), cell culture, reverse transcription-polymerase chain reaction (PCR), enzyme-linked immunosorbent assay, immunofluorescence microscopy, Western blot, chromatin immunoprecipitation-PCR, small interfering RNA knockdown and luciferase reporter expression system were used. RESULTS Herein, we demonstrate that C. t. upregulates the messenger RNA (mRNA) and protein levels of inflammatory mediators in two human skin cell lines, HEKs and SCCs. We further show activation of the canonical nuclear factor-κB (NF-κB) pathway in response to C. t. infection, including phosphorylation of the inhibitor of κB (IκB), the nuclear translocation of NF-κB subunit (NF-κB-P65 ) and the recruitment of NF-κB-P65 and RNA polymerase to the NF-κB response elements at the promoter region of the inflammatory genes. Lastly, the data confirm that C. t.-induced tumor necrosis factor mRNA expression in HEKs is toll-like receptor 2 (TLR2 ) dependent. CONCLUSION Our results offer a mechanistic model for C. t.-induced inflammation in human keratinocytes via TLR2 and activation of IκB kinase and downstream signaling through the canonical NF-κB pathway. Relevance to chronic inflammatory diseases of the skin and cutaneous oncology is discussed.
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Affiliation(s)
- Mohammed O Altonsy
- Division of Dermatology, Department of Medicine, University of Calgary, Calgary, Canada.,Department of Zoology, Faculty of Science, Sohag University, Sohag, Egypt
| | - Habib A Kurwa
- Division of Dermatology, Department of Medicine, University of Calgary, Calgary, Canada
| | - Gilles J Lauzon
- Division of Dermatology, Department of Medicine, University of Calgary, Calgary, Canada
| | - Matthias Amrein
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, Canada
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado.,Department of Medicine, University of Colorado, Denver, Colorado
| | - Wagdi Almishri
- Division of Gastroenterology, Department of Medicine, University of Calgary, Calgary, Canada
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18
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Sasse SK, Gruca M, Allen MA, Kadiyala V, Song T, Gally F, Gupta A, Pufall MA, Dowell RD, Gerber AN. Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression. Genome Res 2019; 29:1753-1765. [PMID: 31519741 PMCID: PMC6836729 DOI: 10.1101/gr.248187.119] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 01/18/2019] [Accepted: 09/06/2019] [Indexed: 12/16/2022]
Abstract
The glucocorticoid receptor (NR3C1, also known as GR) binds to specific DNA sequences and directly induces transcription of anti-inflammatory genes that contribute to cytokine repression, frequently in cooperation with NF-kB. Whether inflammatory repression also occurs through local interactions between GR and inflammatory gene regulatory elements has been controversial. Here, using global run-on sequencing (GRO-seq) in human airway epithelial cells, we show that glucocorticoid signaling represses transcription within 10 min. Many repressed regulatory regions reside within “hyper-ChIPable” genomic regions that are subject to dynamic, yet nonspecific, interactions with some antibodies. When this artifact was accounted for, we determined that transcriptional repression does not require local GR occupancy. Instead, widespread transcriptional induction through canonical GR binding sites is associated with reciprocal repression of distal TNF-regulated enhancers through a chromatin-dependent process, as evidenced by chromatin accessibility and motif displacement analysis. Simultaneously, transcriptional induction of key anti-inflammatory effectors is decoupled from primary repression through cooperation between GR and NF-kB at a subset of regulatory regions. Thus, glucocorticoids exert bimodal restraints on inflammation characterized by rapid primary transcriptional repression without local GR occupancy and secondary anti-inflammatory effects resulting from transcriptional cooperation between GR and NF-kB.
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Affiliation(s)
- Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
| | - Margaret Gruca
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Vineela Kadiyala
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
| | - Tengyao Song
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
| | - Fabienne Gally
- Department of Biomedical Research, National Jewish Health, Denver, Colorado 80206, USA
| | - Arnav Gupta
- Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA.,Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA.,Computer Science, University of Colorado, Boulder, Colorado 80309, USA
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA.,Department of Biomedical Research, National Jewish Health, Denver, Colorado 80206, USA.,Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA
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19
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Affiliation(s)
- Sarah K Sasse
- 1 Department of Medicine National Jewish Health Denver, Colorado and
| | - Anthony N Gerber
- 1 Department of Medicine National Jewish Health Denver, Colorado and.,2 Department of Medicine University of Colorado Denver, Colorado
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20
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Affiliation(s)
- Christopher M Evans
- 1 Division of Pulmonary Sciences and Critical Care Medicine University of Colorado Denver School of Medicine Aurora, Colorado
| | - Max A Seibold
- 2 Department of Pediatrics.,3 Center for Genes, Environment, and Health National Jewish Health Denver, Colorado and
| | - Anthony N Gerber
- 1 Division of Pulmonary Sciences and Critical Care Medicine University of Colorado Denver School of Medicine Aurora, Colorado.,4 Department of Medicine National Jewish Health Denver, Colorado
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21
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Bansal A, Mostafa MM, Shah SV, Gerber AN, Newton R. Glucocorticoids and Inflammatory Cytokines Synergize to Maintain TLR2 Expression in Airway Epithelial Cells. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.lb254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Akanksha Bansal
- Airway Inflammation Research GroupSnyder Institute of Chronic Diseases, University of CalgaryCalgaryABCanada
| | - Mahmoud M. Mostafa
- Airway Inflammation Research GroupSnyder Institute of Chronic Diseases, University of CalgaryCalgaryABCanada
| | - Suharsh V. Shah
- Airway Inflammation Research GroupSnyder Institute of Chronic Diseases, University of CalgaryCalgaryABCanada
| | - Anthony N. Gerber
- Department of Medicine, National Jewish HealthUniversity of ColoradoDenverCO
| | - Robert Newton
- Airway Inflammation Research GroupSnyder Institute of Chronic Diseases, University of CalgaryCalgaryABCanada
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22
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Riemondy KA, Jansing NL, Jiang P, Redente EF, Gillen AE, Fu R, Miller AJ, Spence JR, Gerber AN, Hesselberth JR, Zemans RL. Single cell RNA sequencing identifies TGFβ as a key regenerative cue following LPS-induced lung injury. JCI Insight 2019; 5:123637. [PMID: 30913038 PMCID: PMC6538357 DOI: 10.1172/jci.insight.123637] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [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: 07/18/2018] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
Many lung diseases result from a failure of efficient regeneration of damaged alveolar epithelial cells (AECs) after lung injury. During regeneration, AEC2s proliferate to replace lost cells, after which proliferation halts and some AEC2s transdifferentiate into AEC1s to restore normal alveolar structure and function. Although the mechanisms underlying AEC2 proliferation have been studied, the mechanisms responsible for halting proliferation and inducing transdifferentiation are poorly understood. To identify candidate signaling pathways responsible for halting proliferation and inducing transdifferentiation, we performed single cell RNA sequencing on AEC2s during regeneration in a murine model of lung injury induced by intratracheal LPS. Unsupervised clustering revealed distinct subpopulations of regenerating AEC2s: proliferating, cell cycle arrest, and transdifferentiating. Gene expression analysis of these transitional subpopulations revealed that TGFβ signaling was highly upregulated in the cell cycle arrest subpopulation and relatively downregulated in transdifferentiating cells. In cultured AEC2s, TGFβ was necessary for cell cycle arrest but impeded transdifferentiation. We conclude that during regeneration after LPS-induced lung injury, TGFβ is a critical signal halting AEC2 proliferation but must be inactivated to allow transdifferentiation. This study provides insight into the molecular mechanisms regulating alveolar regeneration and the pathogenesis of diseases resulting from a failure of regeneration.
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Affiliation(s)
- Kent A. Riemondy
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Nicole L. Jansing
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Peng Jiang
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeth F. Redente
- Program in Cell Biology, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Austin E. Gillen
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rui Fu
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Alyssa J. Miller
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jason R. Spence
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anthony N. Gerber
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Jay R. Hesselberth
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rachel L. Zemans
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado, USA
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Denver, Aurora, Colorado, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
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23
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Britt RD, Thompson MA, Sasse S, Pabelick CM, Gerber AN, Prakash YS. Th1 cytokines TNF-α and IFN-γ promote corticosteroid resistance in developing human airway smooth muscle. Am J Physiol Lung Cell Mol Physiol 2018; 316:L71-L81. [PMID: 30335498 DOI: 10.1152/ajplung.00547.2017] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Corticosteroids (CSs) are commonly used to manage wheezing and asthma in pediatric populations. Although corticosteroids are effective in alleviating airway diseases, some children with more moderate-severe asthma phenotypes show CS resistance and exhibit significant airflow obstruction, persistent inflammation, and more frequent exacerbations. Previous studies have demonstrated that Th1 cytokines, such as TNF-α and IFN-γ, promote CS resistance in adult human airway smooth muscle (ASM). In the present study, using a human fetal ASM cell model, we tested the hypothesis that TNF-α/IFN-γ induces CS resistance. In contrast to TNF-α or IFN-γ alone, the combination of TNF-α/IFN-γ blunted the ability of fluticasone propionate (FP) to reduce expression of the chemokines CCL5 and CXCL10 despite expression of key anti-inflammatory glucocorticoid receptor target genes being largely unaffected by TNF-α/IFN-γ. Expression of the NF-κB subunit p65 and phosphorylation of Stat1 were elevated in cells treated with TNF-α/IFN-γ, an effect that remained in the presence of FP. siRNA knockdown studies demonstrated the effects of TNF-α/IFN-γ on increased p65 are mediated by Stat1, a transcription factor activated by IFN-γ. Expression of TNFAIP3, a negative regulator of NF-κB activity, was not altered by TNF-α/IFN-γ. However, the effects of TNF-α/IFN-γ were partially reduced by overexpression of TNFAIP3 but did not influence p65 expression. Together, these data suggest that IFN-γ augments the effects of TNF-α on chemokines by enhancing expression of key inflammatory pathways in the presence of CS. Interactions between TNF-α- and IFN-γ-mediated pathways may promote inflammation in asthmatic children resistant to CSs.
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Affiliation(s)
- Rodney D Britt
- Department of Physiology and Biomedical Engineering, Mayo Clinic , Rochester, Minnesota.,Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital , Columbus, Ohio.,Department of Pediatrics, The Ohio State University , Columbus, Ohio
| | - Michael A Thompson
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic , Rochester, Minnesota
| | - Sarah Sasse
- Department of Medicine, National Jewish Health , Denver, Colorado
| | - Christina M Pabelick
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic , Rochester, Minnesota.,Department of Physiology and Biomedical Engineering, Mayo Clinic , Rochester, Minnesota
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health , Denver, Colorado
| | - Y S Prakash
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic , Rochester, Minnesota.,Department of Physiology and Biomedical Engineering, Mayo Clinic , Rochester, Minnesota
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24
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Rider CF, Altonsy MO, Mostafa MM, Shah SV, Sasse S, Manson ML, Yan D, Kärrman-Mårdh C, Miller-Larsson A, Gerber AN, Giembycz MA, Newton R. Long-Acting β2-Adrenoceptor Agonists Enhance Glucocorticoid Receptor (GR)-Mediated Transcription by Gene-Specific Mechanisms Rather Than Generic Effects via GR. Mol Pharmacol 2018; 94:1031-1046. [PMID: 29959223 DOI: 10.1124/mol.118.112755] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/25/2018] [Indexed: 12/16/2022] Open
Abstract
In asthma, the clinical efficacy of inhaled corticosteroids (ICSs) is enhanced by long-acting β2-adrenoceptor agonists (LABAs). ICSs, or more accurately, glucocorticoids, promote therapeutically relevant changes in gene expression, and, in primary human bronchial epithelial cells (pHBECs) and airway smooth muscle cells, this genomic effect can be enhanced by a LABA. Modeling this interaction in human bronchial airway epithelial BEAS-2B cells transfected with a 2× glucocorticoid response element (2×GRE)-driven luciferase reporter showed glucocorticoid-induced transcription to be enhanced 2- to 3-fold by LABA. This glucocorticoid receptor (GR; NR3C1)-dependent effect occurred rapidly, was insensitive to protein synthesis inhibition, and was maximal when glucocorticoid and LABA were added concurrently. The ability of LABA to enhance GR-mediated transcription was not associated with changes in GR expression, serine (Ser203, Ser211, Ser226) phosphorylation, ligand affinity, or nuclear translocation. Chromatin immunoprecipitation demonstrated that glucocorticoid-induced recruitment of GR to the integrated 2×GRE reporter and multiple gene loci, whose mRNAs were unaffected or enhanced by LABA, was also unchanged by LABA. Transcriptomic analysis revealed glucocorticoid-induced mRNAs were variably enhanced, unaffected, or repressed by LABA. Thus, events leading to GR binding at target genes are not the primary explanation for how LABAs modulate GR-mediated transcription. As many glucocorticoid-induced genes are independently induced by LABA, gene-specific control by GR- and LABA-activated transcription factors may explain these observations. Because LABAs promote similar effects in pHBECs, therapeutic relevance is likely. These data illustrate the need to understand gene function(s), and the mechanisms leading to gene-specific induction, if existing ICS/LABA combination therapies are to be improved.
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Affiliation(s)
- Christopher F Rider
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Mohammed O Altonsy
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Mahmoud M Mostafa
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Suharsh V Shah
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Sarah Sasse
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Martijn L Manson
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Dong Yan
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Carina Kärrman-Mårdh
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Anna Miller-Larsson
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Anthony N Gerber
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Mark A Giembycz
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
| | - Robert Newton
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada (C.F.R., M.O.A., M.M.M., S.V.S., D.Y., M.A.G., R.N.); Department of Zoology, Sohag University, Sohag, Egypt (M.O.A.); Department of Medicine, National Jewish Health, Denver, Colorado (S.S., A.N.G.); and Bioscience, Respiratory, Inflammation, and Autoimmunity, IMED Biotech Unit (M.L.M., C.K.-M.), and Respiratory GMed (A.M.-L.), AstraZeneca, Gothenburg, Molndal, Sweden
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25
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Li Y, Liu B, Harmacek L, Long Z, Liang J, Lukin K, Leach SM, O'Connor B, Gerber AN, Hagman J, Roers A, Finkelman FD, Huang H. The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis. J Allergy Clin Immunol 2017; 142:1173-1184. [PMID: 29277702 DOI: 10.1016/j.jaci.2017.10.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 10/12/2017] [Accepted: 10/25/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Histamine is a critical mediator of IgE/mast cell-mediated anaphylaxis. Histamine is synthesized by decarboxylating the amino acid histidine, a reaction catalyzed by the histidine decarboxylase (Hdc) gene-encoded enzyme HDC. However, regulation of the Hdc gene in mast cells is poorly understood. OBJECTIVE We sought to investigate the in vivo regulation of IgE/mast cell-mediated anaphylaxis by the transcription factors GATA2 and microphthalmia-associated transcription factor (MITF) and the mechanisms by which GATA2 and MITF regulate Hdc gene expression in mouse and human mast cells. METHODS Mice deficient in the transcription factors Gata2, aryl hydrocarbon receptor (Ahr), aryl hydrocarbon receptor repressor (Ahrr), or basic helix-loop-helix family member E40 (Bhlhe40) were assessed for anaphylactic reactions. Chromatin immunoprecipitation sequencing analysis identified putative Hdc enhancers. Luciferase reporter transcription assay confirmed enhancer activities of putative enhancers in the Hdc gene. The short hairpin RNA knockdown approach was used to determine the role of MITF in regulating mouse and human HDC gene expression. RESULTS Connective tissue mast cell-specific Gata2-deficient mice did not have IgE/mast cell-mediated anaphylaxis. GATA2 induced the expression of Mitf, Ahr, Ahrr, and Bhlhe40 in mast cells. MITF, but not AHR, AHRR, or BHLHE40, was required for anaphylaxis. MITF bound to an enhancer located 8.8 kb upstream of the transcription start site of the Hdc gene and directed enhancer activity. MITF overexpression largely restored Hdc gene expression in the Gata2-deficient mast cells. In the human mast cell line LAD2, MITF was required for the HDC gene expression and histamine synthesis. CONCLUSION The transcription factors GATA2 and MITF regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis.
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Affiliation(s)
- Yapeng Li
- Department of Biomedical Research, National Jewish Health, Denver, Colo
| | - Bing Liu
- Department of Biomedical Research, National Jewish Health, Denver, Colo; Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Laura Harmacek
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colo
| | - Zijie Long
- Department of Biomedical Research, National Jewish Health, Denver, Colo; Department of Hematology, The Third Affiliated Hospital, Institute of Hematology, Sun Yat-sen University, Guangzhou, China
| | - Jinyi Liang
- Department of Biomedical Research, National Jewish Health, Denver, Colo; Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kara Lukin
- Department of Biomedical Research, National Jewish Health, Denver, Colo
| | - Sonia M Leach
- Department of Biomedical Research, National Jewish Health, Denver, Colo; Center for Genes, Environment and Health, National Jewish Health, Denver, Colo
| | - Brian O'Connor
- Department of Biomedical Research, National Jewish Health, Denver, Colo; Center for Genes, Environment and Health, National Jewish Health, Denver, Colo
| | - Anthony N Gerber
- Department of Biomedical Research, National Jewish Health, Denver, Colo; Department of Medicine, National Jewish Health, Denver, Colo
| | - James Hagman
- Department of Biomedical Research, National Jewish Health, Denver, Colo; Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Colo
| | - Axel Roers
- Institute for Immunology, Technische Universit ät Dresden, Dresden, Germany
| | - Fred D Finkelman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Division of Immunology, Allergy and Rheumatology, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Hua Huang
- Department of Biomedical Research, National Jewish Health, Denver, Colo; Department of Immunology and Microbiology, University of Colorado School of Medicine, Denver, Colo.
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26
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Swaminathan S, Qirko K, Smith T, Corcoran E, Wysham NG, Bazaz G, Kappel G, Gerber AN. A machine learning approach to triaging patients with chronic obstructive pulmonary disease. PLoS One 2017; 12:e0188532. [PMID: 29166411 PMCID: PMC5699810 DOI: 10.1371/journal.pone.0188532] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 11/08/2017] [Indexed: 02/07/2023] Open
Abstract
COPD patients are burdened with a daily risk of acute exacerbation and loss of control, which could be mitigated by effective, on-demand decision support tools. In this study, we present a machine learning-based strategy for early detection of exacerbations and subsequent triage. Our application uses physician opinion in a statistically and clinically comprehensive set of patient cases to train a supervised prediction algorithm. The accuracy of the model is assessed against a panel of physicians each triaging identical cases in a representative patient validation set. Our results show that algorithm accuracy and safety indicators surpass all individual pulmonologists in both identifying exacerbations and predicting the consensus triage in a 101 case validation set. The algorithm is also the top performer in sensitivity, specificity, and ppv when predicting a patient's need for emergency care.
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Affiliation(s)
- Sumanth Swaminathan
- Revon Systems Inc, Louisville, KY, United States of America, 40014
- Department of Mathematics, University of Delaware, Newark, DE, United States of America, 19716
| | - Klajdi Qirko
- Revon Systems Inc, Louisville, KY, United States of America, 40014
- Department of Mathematics, University of Delaware, Newark, DE, United States of America, 19716
| | - Ted Smith
- Revon Systems Inc, Louisville, KY, United States of America, 40014
| | - Ethan Corcoran
- Department of Pulmonology, Kaiser Permanente, Clackamas, OR, United States of America, 97015
| | - Nicholas G. Wysham
- Vancouver Clinic Division of Pulmonology & Critical Care, Vancouver, WA, United States of America, 98664
- Washington State University School of Medicine, Spokane, WA, United States of America, 99210
| | - Gaurav Bazaz
- Revon Systems Inc, Louisville, KY, United States of America, 40014
| | - George Kappel
- Revon Systems Inc, Louisville, KY, United States of America, 40014
| | - Anthony N. Gerber
- Department of Medicine, National Jewish Health, Denver, CO, United States of America, 80206
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27
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Sasse SK, Kadiyala V, Danhorn T, Panettieri RA, Phang TL, Gerber AN. Glucocorticoid Receptor ChIP-Seq Identifies PLCD1 as a KLF15 Target that Represses Airway Smooth Muscle Hypertrophy. Am J Respir Cell Mol Biol 2017; 57:226-237. [PMID: 28375666 DOI: 10.1165/rcmb.2016-0357oc] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glucocorticoids exert important therapeutic effects on airway smooth muscle (ASM), yet few direct targets of glucocorticoid signaling in ASM have been definitively identified. Here, we show that the transcription factor, Krüppel-like factor 15 (KLF15), is directly induced by glucocorticoids in primary human ASM, and that KLF15 represses ASM hypertrophy. We integrated transcriptome data from KLF15 overexpression with genome-wide analysis of RNA polymerase (RNAP) II and glucocorticoid receptor (GR) occupancy to identify phospholipase C delta 1 as both a KLF15-regulated gene and a novel repressor of ASM hypertrophy. Our chromatin immunoprecipitation sequencing data also allowed us to establish numerous direct transcriptional targets of GR in ASM. Genes with inducible GR occupancy and putative antiinflammatory properties included IRS2, APPL2, RAMP1, and MFGE8. Surprisingly, we also observed GR occupancy in the absence of supplemental ligand, including robust GR binding peaks within the IL11 and LIF loci. Detection of antibody-GR complexes at these areas was abrogated by dexamethasone treatment in association with reduced RNA polymerase II occupancy, suggesting that noncanonical pathways contribute to cytokine repression by glucocorticoids in ASM. Through defining GR interactions with chromatin on a genome-wide basis in ASM, our data also provide an important resource for future studies of GR in this therapeutically relevant cell type.
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Affiliation(s)
| | | | - Thomas Danhorn
- 2 Center for Genes, Health, and the Environment, National Jewish Health, Denver, Colorado
| | - Reynold A Panettieri
- 3 Rutgers Institute for Translational Medicine and Science, Rutgers University, New Brunswick, New Jersey; and
| | - Tzu L Phang
- 4 Department of Medicine, University of Colorado, Denver, Colorado
| | - Anthony N Gerber
- 1 Department of Medicine and.,4 Department of Medicine, University of Colorado, Denver, Colorado
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28
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Helling BA, Gerber AN, Kadiyala V, Sasse SK, Pedersen BS, Sparks L, Nakano Y, Okamoto T, Evans CM, Yang IV, Schwartz DA. Regulation of MUC5B Expression in Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2017; 57:91-99. [PMID: 28272906 DOI: 10.1165/rcmb.2017-0046oc] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The gain-of-function mucin 5B (MUC5B) promoter variant, rs35705950, confers the largest risk, genetic or otherwise, for the development of idiopathic pulmonary fibrosis; however, the mechanisms underlying the regulation of MUC5B expression have yet to be elucidated. Here, we identify a critical regulatory domain that contains the MUC5B promoter variant and has a highly conserved forkhead box protein A2 (FOXA2) binding motif. This region is differentially methylated in association with idiopathic pulmonary fibrosis, MUC5B expression, and rs35705950. In addition, we show that this locus binds FOXA2 dynamically, and that binding of FOXA2 is necessary for enhanced expression of MUC5B. In aggregate, our findings identify novel targets to regulate the expression of MUC5B.
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Affiliation(s)
- Britney A Helling
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Anthony N Gerber
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado.,2 Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Vineela Kadiyala
- 2 Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Sarah K Sasse
- 2 Department of Medicine, National Jewish Health, Denver, Colorado; and
| | - Brent S Pedersen
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Lenore Sparks
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Yasushi Nakano
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Tsukasa Okamoto
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Christopher M Evans
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado
| | - Ivana V Yang
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado.,3 University of Colorado-Denver, School of Public Health, Denver, Colorado
| | - David A Schwartz
- 1 Department of Medicine, School of Medicine, University of Colorado-Denver, Denver, Colorado.,2 Department of Medicine, National Jewish Health, Denver, Colorado; and
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29
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Katial RK, Bensch GW, Busse WW, Chipps BE, Denson JL, Gerber AN, Jacobs JS, Kraft M, Martin RJ, Nair P, Wechsler ME. Changing Paradigms in the Treatment of Severe Asthma: The Role of Biologic Therapies. J Allergy Clin Immunol Pract 2017; 5:S1-S14. [PMID: 28143691 DOI: 10.1016/j.jaip.2016.11.029] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 11/30/2022]
Abstract
Cytokine antagonists are monoclonal antibodies that offer new treatment options for refractory asthma but will also increase complexity because they are effective only for patients with certain asthma subtypes that remain to be more clearly defined. The clinical and inflammatory heterogeneity within refractory asthma makes it difficult to manage the disease and to determine which, if any, biologic therapy is suitable for a specific patient. The purpose of this article is to provide a data-driven discussion to clarify the use of biologic therapies in patients with refractory asthma. We first discuss the epidemiology and pathophysiology of refractory asthma. We then interpret current evidence for biomarkers of eosinophilic or type 2-high asthma so that clinicians can determine potential treatments for patients based on knowledge of their effectiveness in specific asthma phenotypes. We then assess clinical data on the efficacy, safety, and mechanisms of action of approved and pipeline biologic therapies. We conclude by discussing the potential of phenotyping or endotyping refractory asthma and how biologic therapies can play a role in treating patients with refractory asthma.
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Affiliation(s)
- Rohit K Katial
- Department of Medicine, Division of Allergy and Clinical Immunology, National Jewish Health, Denver, Colo.
| | - Greg W Bensch
- Allergy, Immunology and Asthma Medical Group, Stockton, Calif
| | - William W Busse
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Bradley E Chipps
- Capital Allergy and Respiratory Disease Center, Sacramento, Calif
| | - Joshua L Denson
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colo; Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado at Denver, Anschutz Medical Campus, Aurora, Colo
| | - Anthony N Gerber
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colo; Department of Biomedical Research, National Jewish Health, Denver, Colo
| | - Joshua S Jacobs
- Allergy and Asthma Clinical Research, Inc., Walnut Creek, Calif
| | - Monica Kraft
- Department of Medicine, Asthma and Airway Disease Research Center, University of Arizona Health Sciences, Tucson, Ariz
| | | | - Parameswaran Nair
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Michael E Wechsler
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colo
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30
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Altonsy MO, Mostafa MM, Gerber AN, Newton R. Long-acting β 2-agonists promote glucocorticoid-mediated repression of NF-κB by enhancing expression of the feedback regulator TNFAIP3. Am J Physiol Lung Cell Mol Physiol 2016; 312:L358-L370. [PMID: 28039105 DOI: 10.1152/ajplung.00426.2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 12/27/2022] Open
Abstract
Glucocorticoids, or corticosteroids, are effective treatments for many chronic inflammatory diseases, and in mild/moderate asthma, long-acting β2-adrenoceptor agonists (LABAs) enhance the efficacy of inhaled corticosteroids (ICSs) more than increasing the ICS dose. In human bronchial epithelial, BEAS-2B, cells, expression of TNFα-induced protein-3 (TNFAIP3), or A20, a dual-ubiquitin ligase that provides feedback inhibition of NF-κB, was induced by budesonide, an ICS, and formoterol, a LABA, and was further enhanced by budesonide-formoterol combination. The proinflammatory cytokine TNF induced TNFAIP3 and TNF expression. Whereas subsequent budesonide treatment enhanced TNF-induced TNFAIP3 and reduced TNF expression, formoterol amplified these differential effects. In primary human airway smooth muscle cells, TNFAIP3 expression was induced by TNF. This was largely unaffected by budesonide but was acutely enhanced by budesonide-formoterol combination. In BEAS-2B cells, TNF recruited RELA, the main NF-κB transactivating subunit, to a 3' region of the TNF gene. RELA binding was reduced by budesonide, was further reduced by formoterol cotreatment, and was associated with reduced RNA polymerase II recruitment to the TNF gene. This is consistent with reduced TNF expression. TNFAIP3 knockdown enhanced TNF expression in the presence of TNF, TNF plus budesonide, and TNF plus budesonide-formoterol combination and confirms feedback inhibition. A luciferase reporter containing the TNF 3' RELA binding region recapitulated TNF inducibility and was inhibited by an IκB kinase inhibitor and TNFAIP3 overexpression. Repression of reporter activity by budesonide was increased by formoterol and involved TNFAIP3. Thus LABAs may improve the anti-inflammatory properties of ICSs by augmenting TNFAIP3 expression to negatively regulate NF-κB.
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Affiliation(s)
- Mohammed O Altonsy
- Department of Cell Biology and Anatomy, Airway Inflammation Research Group, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Zoology, Sohag University, Sohag, Egypt
| | - Mahmoud M Mostafa
- Department of Cell Biology and Anatomy, Airway Inflammation Research Group, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado; and.,Department of Medicine, University of Colorado, Denver, Colorado
| | - Robert Newton
- Department of Cell Biology and Anatomy, Airway Inflammation Research Group, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada;
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Sasse SK, Altonsy MO, Kadiyala V, Cao G, Panettieri RA, Gerber AN. Glucocorticoid and TNF signaling converge at A20 (TNFAIP3) to repress airway smooth muscle cytokine expression. Am J Physiol Lung Cell Mol Physiol 2016; 311:L421-32. [PMID: 27371733 DOI: 10.1152/ajplung.00179.2016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/29/2016] [Indexed: 12/29/2022] Open
Abstract
Airway smooth muscle is a major target tissue for glucocorticoid (GC)-based asthma therapies, however, molecular mechanisms through which the GC receptor (GR) exerts therapeutic effects in this key airway cell type have not been fully elucidated. We previously identified the nuclear factor-κB (NF-κB) inhibitor, A20 (TNFAIP3), as a mediator of cytokine repression by glucocorticoids (GCs) in airway epithelial cells and defined cooperative regulation of anti-inflammatory genes by GR and NF-κB as a key mechanistic underpinning of airway epithelial GR function. Here, we expand on these findings to determine whether a similar mechanism is operational in human airway smooth muscle (HASM). Using HASM cells derived from normal and fatal asthma samples as an in vitro model, we demonstrate that GCs spare or augment TNF-mediated induction of A20 (TNFAIP3), TNIP1, and NFKBIA, all implicated in negative feedback control of NF-κB-driven inflammatory processes. We applied chromatin immunoprecipitation and reporter analysis to show that GR and NF-κB directly regulate A20 expression in HASM through cooperative induction of an intronic enhancer. Using overexpression, we show for the first time that A20 and its interacting partner, TNIP1, repress TNF signaling in HASM cells. Moreover, we applied small interfering RNA-based gene knockdown to demonstrate that A20 is required for maximal cytokine repression by GCs in HASM. Taken together, our data suggest that inductive regulation of A20 by GR and NF-κB contributes to cytokine repression in HASM.
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Affiliation(s)
- Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado
| | | | - Vineela Kadiyala
- Department of Medicine, National Jewish Health, Denver, Colorado
| | - Gaoyuan Cao
- Rutgers Institute for Translational Medicine & Science, Rutgers University, New Brunswick, New Jersey; and
| | - Reynold A Panettieri
- Rutgers Institute for Translational Medicine & Science, Rutgers University, New Brunswick, New Jersey; and
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado; Department of Medicine, University of Colorado, Denver, Colorado
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Kadiyala V, Sasse SK, Altonsy MO, Berman R, Chu HW, Phang TL, Gerber AN. Cistrome-based Cooperation between Airway Epithelial Glucocorticoid Receptor and NF-κB Orchestrates Anti-inflammatory Effects. J Biol Chem 2016; 291:12673-12687. [PMID: 27076634 DOI: 10.1074/jbc.m116.721217] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 12/11/2022] Open
Abstract
Antagonism of pro-inflammatory transcription factors by monomeric glucocorticoid receptor (GR) has long been viewed as central to glucocorticoid (GC) efficacy. However, the mechanisms and targets through which GCs exert therapeutic effects in diseases such as asthma remain incompletely understood. We previously defined a surprising cooperative interaction between GR and NF-κB that enhanced expression of A20 (TNFAIP3), a potent inhibitor of NF-κB. Here we extend this observation to establish that A20 is required for maximal cytokine repression by GCs. To ascertain the global extent of GR and NF-κB cooperation, we determined genome-wide occupancy of GR, the p65 subunit of NF-κB, and RNA polymerase II in airway epithelial cells treated with dexamethasone, TNF, or both using chromatin immunoprecipitation followed by deep sequencing. We found that GR recruits p65 to dimeric GR binding sites across the genome and discovered additional regulatory elements in which GR-p65 cooperation augments gene expression. GR targets regulated by this mechanism include key anti-inflammatory and injury response genes such as SERPINA1, which encodes α1 antitrypsin, and FOXP4, an inhibitor of mucus production. Although dexamethasone treatment reduced RNA polymerase II occupancy of TNF targets such as IL8 and TNFAIP2, we were unable to correlate specific binding sequences for GR or occupancy patterns with repressive effects on transcription. Our results suggest that cooperative anti-inflammatory gene regulation by GR and p65 contributes to GC efficacy, whereas tethering interactions between GR and p65 are not universally required for GC-based gene repression.
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Affiliation(s)
- Vineela Kadiyala
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Sarah K Sasse
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Mohammed O Altonsy
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206,; Department of Zoology, Sohag University, Sohag 825224, Egypt, and
| | - Reena Berman
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Hong W Chu
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Tzu L Phang
- Department of Medicine, University of Colorado, Denver, Colorado 80045
| | - Anthony N Gerber
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206,; Department of Medicine, University of Colorado, Denver, Colorado 80045.
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Morrison-Nozik A, Anand P, Zhu H, Duan Q, Sabeh M, Prosdocimo DA, Lemieux ME, Nordsborg N, Russell AP, MacRae CA, Gerber AN, Jain MK, Haldar SM. Glucocorticoids enhance muscle endurance and ameliorate Duchenne muscular dystrophy through a defined metabolic program. Proc Natl Acad Sci U S A 2015; 112:E6780-9. [PMID: 26598680 PMCID: PMC4679037 DOI: 10.1073/pnas.1512968112] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Classic physiology studies dating to the 1930s demonstrate that moderate or transient glucocorticoid (GC) exposure improves muscle performance. The ergogenic properties of GCs are further evidenced by their surreptitious use as doping agents by endurance athletes and poorly understood efficacy in Duchenne muscular dystrophy (DMD), a genetic muscle-wasting disease. A defined molecular basis underlying these performance-enhancing properties of GCs in skeletal muscle remains obscure. Here, we demonstrate that ergogenic effects of GCs are mediated by direct induction of the metabolic transcription factor KLF15, defining a downstream pathway distinct from that resulting in GC-related muscle atrophy. Furthermore, we establish that KLF15 deficiency exacerbates dystrophic severity and muscle GC-KLF15 signaling mediates salutary therapeutic effects in the mdx mouse model of DMD. Thus, although glucocorticoid receptor (GR)-mediated transactivation is often associated with muscle atrophy and other adverse effects of pharmacologic GC administration, our data define a distinct GR-induced gene regulatory pathway that contributes to therapeutic effects of GCs in DMD through proergogenic metabolic programming.
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Affiliation(s)
- Alexander Morrison-Nozik
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Priti Anand
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106; Gladstone Institutes, San Francisco, CA 94158
| | - Han Zhu
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Qiming Duan
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106; Gladstone Institutes, San Francisco, CA 94158
| | - Mohamad Sabeh
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106; Harrington Heart & Vascular Institute, University Hospitals Case Medical Center, Cleveland, OH 44106
| | - Domenick A Prosdocimo
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | | | - Nikolai Nordsborg
- Department of Nutrition, Exercise and Sports Sciences, University of Copenhagen, DK-200 Copenhagen, Denmark
| | - Aaron P Russell
- Centre for Physical Activity and Nutrition Research, School of Exercise and Nutrition Science, Deakin University, Burwood, VIC 3125, Australia
| | - Calum A MacRae
- Cardiovascular Division, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Anthony N Gerber
- Department of Pulmonary Medicine, National Jewish Health and University of Colorado Denver School of Medicine, Denver, CO 80206
| | - Mukesh K Jain
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106; Harrington Heart & Vascular Institute, University Hospitals Case Medical Center, Cleveland, OH 44106
| | - Saptarsi M Haldar
- Case Cardiovascular Research Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106; Gladstone Institutes, San Francisco, CA 94158; Harrington Heart & Vascular Institute, University Hospitals Case Medical Center, Cleveland, OH 44106; Department of Medicine and Cardiovascular Research Institute, University of California, San Francisco, CA 94158
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Abstract
The lung is a major clinical target of glucocorticoid-based therapeutics, and GR signaling has broad effects on respiratory physiology and inflammation. During lung development, expression of GR in the mesenchyme is required for normal terminal alveolar epithelial differentiation. Prenatal administration of exogenous glucocorticoids (GCs) to prevent neonatal respiratory distress syndrome, however, promotes alveolar maturation and accelerates surfactant expression in a manner consistent with direct effects on the developing alveolar epithelium. Likewise, cell autonomous effects of GCs in regulating gene expression and phenotype of the airway epithelium and airway smooth muscle have been demonstrated to control important therapeutic effects of GCs in treating asthma and chronic obstructive pulmonary disease. Here, mechanisms and consequences of GR signaling in the developing lung and in treating obstructive lung disease are reviewed, with a focus on direct effects of GR signaling on alveolar differentiation, surfactant expression, and airway epithelial and smooth muscle pathophysiology.
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Affiliation(s)
- Anthony N Gerber
- Department of Medicine, National Jewish Health, University of Colorado, Denver, 1400 Jackson Street, Room K621b, Denver, CO, 80206, USA,
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Sasse SK, Zuo Z, Kadiyala V, Zhang L, Pufall MA, Jain MK, Phang TL, Stormo GD, Gerber AN. Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops. J Biol Chem 2015; 290:19756-69. [PMID: 26088140 DOI: 10.1074/jbc.m115.668558] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Indexed: 01/02/2023] Open
Abstract
Combinatorial gene regulation through feed-forward loops (FFLs) can bestow specificity and temporal control to client gene expression; however, characteristics of binding sites that mediate these effects are not established. We previously showed that the glucocorticoid receptor (GR) and KLF15 form coherent FFLs that cooperatively induce targets such as the amino acid-metabolizing enzymes AASS and PRODH and incoherent FFLs exemplified by repression of MT2A by KLF15. Here, we demonstrate that GR and KLF15 physically interact and identify low affinity GR binding sites within glucocorticoid response elements (GREs) for PRODH and AASS that contribute to combinatorial regulation with KLF15. We used deep sequencing and electrophoretic mobility shift assays to derive in vitro GR binding affinities across sequence space. We applied these data to show that AASS GRE activity correlated (r(2) = 0.73) with predicted GR binding affinities across a 50-fold affinity range in transfection assays; however, the slope of the linear relationship more than doubled when KLF15 was expressed. Whereas activity of the MT2A GRE was even more strongly (r(2) = 0.89) correlated with GR binding site affinity, the slope of the linear relationship was sharply reduced by KLF15, consistent with incoherent FFL logic. Thus, GRE architecture and co-regulator expression together determine the functional parameters that relate GR binding site affinity to hormone-induced transcriptional responses. Utilization of specific affinity response functions and GR binding sites by FFLs may contribute to the diversity of gene expression patterns within GR-regulated transcriptomes.
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Affiliation(s)
- Sarah K Sasse
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Zheng Zuo
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108-8510
| | - Vineela Kadiyala
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
| | - Liyang Zhang
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242
| | - Miles A Pufall
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242
| | - Mukesh K Jain
- Case Cardiovascular Research Institute and Harrington Heart and Vascular Institute, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-7290, and
| | - Tzu L Phang
- Department of Medicine, University of Colorado, Denver, Colorado 80045
| | - Gary D Stormo
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108-8510
| | - Anthony N Gerber
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206, Department of Medicine, University of Colorado, Denver, Colorado 80045
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36
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Altonsy MO, Sasse SK, Phang TL, Gerber AN. Context-dependent cooperation between nuclear factor κB (NF-κB) and the glucocorticoid receptor at a TNFAIP3 intronic enhancer: a mechanism to maintain negative feedback control of inflammation. J Biol Chem 2014; 289:8231-9. [PMID: 24500711 DOI: 10.1074/jbc.m113.545178] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
TNF expression is elevated in asthma and other inflammatory airway diseases that are commonly treated with glucocorticoid-based therapies, but the impact of glucocorticoids on negative feedback control of TNF is not well understood. We analyzed the effect of dexamethasone, a potent synthetic glucocorticoid, on TNF-regulated gene expression in cultured airway epithelial cells. Although dexamethasone-mediated activation of the glucocorticoid receptor (GR) potently repressed expression of IL1β, IL8, and several other pro-inflammatory TNF targets, the expression of anti-inflammatory TNF targets such as TNFAIP3 (A20) and NFKBIA was selectively spared or augmented by dexamethasone treatment. Despite divergent effects on gene expression, GR and NF-κB occupancy at the TNFAIP3 locus and GR-repressed targets was similar. A co-occupied intronic TNFAIP3 regulatory element mediated cooperative enhancement of transcription by GR and NF-κB that required the presence of a functional GR binding site (GBS). GBS exchanges between reporters for TNFAIP3 and FKBP5, a canonical GR-induced target, revealed substantial latitude in the GBS sequence requirements for GR/NF-κB cooperation, suggesting that the TNFAIP3 GBS acts primarily as a docking site in this context. Supporting this notion, a selective GR ligand with only weak agonist activity for induction of FKBP5 enabled robust GR/NF-κB cooperative induction of a mutant TNFAIP3 reporter harboring the FKBP5 GBS. Taken together, our data support a model in which the expression of anti-inflammatory targets of TNF is maintained during treatment with glucocorticoids through context-dependent cooperation between GR and NF-κB.
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Affiliation(s)
- Mohammed O Altonsy
- From the Department of Medicine, National Jewish Health, Denver, Colorado 80206
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Haldar SM, Jeyaraj D, Anand P, Zhu H, Lu Y, Prosdocimo DA, Eapen B, Kawanami D, Okutsu M, Brotto L, Fujioka H, Kerner J, Rosca MG, McGuinness OP, Snow RJ, Russell AP, Gerber AN, Bai X, Yan Z, Nosek TM, Brotto M, Hoppel CL, Jain MK. Kruppel-like factor 15 regulates skeletal muscle lipid flux and exercise adaptation. Proc Natl Acad Sci U S A 2012; 109:6739-44. [PMID: 22493257 PMCID: PMC3340075 DOI: 10.1073/pnas.1121060109] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of skeletal muscle to enhance lipid utilization during exercise is a form of metabolic plasticity essential for survival. Conversely, metabolic inflexibility in muscle can cause organ dysfunction and disease. Although the transcription factor Kruppel-like factor 15 (KLF15) is an important regulator of glucose and amino acid metabolism, its endogenous role in lipid homeostasis and muscle physiology is unknown. Here we demonstrate that KLF15 is essential for skeletal muscle lipid utilization and physiologic performance. KLF15 directly regulates a broad transcriptional program spanning all major segments of the lipid-flux pathway in muscle. Consequently, Klf15-deficient mice have abnormal lipid and energy flux, excessive reliance on carbohydrate fuels, exaggerated muscle fatigue, and impaired endurance exercise capacity. Elucidation of this heretofore unrecognized role for KLF15 now implicates this factor as a central component of the transcriptional circuitry that coordinates physiologic flux of all three basic cellular nutrients: glucose, amino acids, and lipids.
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Affiliation(s)
- Saptarsi M Haldar
- Harrington Heart and Vascular Institute and Department of Medicine, Case Western Reserve University School of Medicine and University Hospitals Case Medical Center, Cleveland, OH 44106, USA.
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Masuno K, Haldar SM, Jeyaraj D, Mailloux CM, Huang X, Panettieri RA, Jain MK, Gerber AN. Expression profiling identifies Klf15 as a glucocorticoid target that regulates airway hyperresponsiveness. Am J Respir Cell Mol Biol 2011; 45:642-9. [PMID: 21257922 DOI: 10.1165/rcmb.2010-0369oc] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Glucocorticoids (GCs), which activate GC receptor (GR) signaling and thus modulate gene expression, are widely used to treat asthma. GCs exert their therapeutic effects in part through modulating airway smooth muscle (ASM) structure and function. However, the effects of genes that are regulated by GCs on airway function are not fully understood. We therefore used transcription profiling to study the effects of a potent GC, dexamethasone, on human ASM (HASM) gene expression at 4 and 24 hours. After 24 hours of dexamethasone treatment, nearly 7,500 genes had statistically distinguishable changes in expression; quantitative PCR validation of a 40-gene subset of putative GR-regulated genes in 6 HASM cell lines suggested that the early transcriptional targets of GR signaling are similar in independent HASM lines. Gene ontology analysis implicated GR targets in controlling multiple aspects of ASM function. One GR-regulated gene, the transcription factor, Kruppel-like factor 15 (Klf15), was already known to modulate vascular smooth and cardiac muscle function, but had no known role in the lung. We therefore analyzed the pulmonary phenotype of Klf15(-/-) mice after ovalbumin sensitization and challenge. We found diminished airway responses to acetylcholine in ovalbumin-challenged Klf15(-/-) mice without a significant change in the induction of asthmatic inflammation. In cultured cells, overexpression of Klf15 reduced proliferation of HASM cells, whereas apoptosis in Klf15(-/-) murine ASM cells was increased. Together, these results further characterize the GR-regulated gene network in ASM and establish a novel role for the GR target, Klf15, in modulating airway function.
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Affiliation(s)
- Kiriko Masuno
- Department of Molecular and Cellular Pharmacology, University of California, San Francisco, California, USA
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Gerber AN, Wilson CW, Li YJ, Chuang PT. The hedgehog regulated oncogenes Gli1 and Gli2 block myoblast differentiation by inhibiting MyoD-mediated transcriptional activation. Oncogene 2006; 26:1122-36. [PMID: 16964293 PMCID: PMC3325095 DOI: 10.1038/sj.onc.1209891] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The mechanism by which activation of the Hedgehog (Hh) pathway modulates differentiation and promotes oncogenesis in specific tissues is poorly understood. We therefore, analysed rhabdomyosarcomas from mice that were haploinsufficient for the Hh-binding protein, Hip1, or for the Hh receptor, Patched 1 (Ptch1). Transfection of the Hh-regulated transcription factor Gli1, which is expressed in a subset of mouse and human rhabdomyosarcomas, suppressed differentiation of myogenic rhabdomyosarcoma lines generated from Hip1+/- and Ptch1+/- mice. The closely related factor, Gli2, had similar effects. Gli1 and Gli2 inhibited myogenesis by repressing the capacity of MyoD to activate transcription. Deletion analysis of Gli1 indicated that multiple domains of Gli1 are required for efficient inhibition of MyoD. Gli1 reduced the ability of MyoD to heterodimerize with E12 and bind DNA, providing one mechanism whereby the Gli proteins modulate the activity of MyoD. This novel activity of Gli proteins provides new insights into how Hh signaling modulates terminal differentiation through inhibition of tissue-specific factors such as MyoD. This mechanism may contribute to the broad role of Hh signaling and the Gli proteins in differentiation decisions and cancer formation.
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Affiliation(s)
- AN Gerber
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - CW Wilson
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Y-J Li
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - P-T Chuang
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
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Abstract
OBJECTIVE Many chronic diseases exhibit characteristic pulmonary distribution patterns, but the underlying biologic explanations remain elusive. On the basis of emerging evidence from systems biology, we propose that gradients of T helper immune function exist as an epiphenomenon of the hypoxic pulmonary vasoconstriction response. Regional variation of immune function may contribute to preferential distribution patterning of lung diseases. CONCLUSION The lungs represent but one example in which the distribution of immune function throughout the body may explain disease location. This hypothetic framework can apply to diseases outside the realm of pulmonary biology and illustrates the potential benefit of integrating advances in systems biology and medical imaging.
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Affiliation(s)
- Anthony J Yun
- Department of Radiology, Stanford University, 470 University Ave., Palo Alto, CA 94301, USA.
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Abstract
There is increasing recognition that stochastic processes regulate highly predictable patterns of gene expression in developing organisms, but the implications of stochastic gene expression for understanding haploinsufficiency remain largely unexplored. We have used simulations of stochastic gene expression to illustrate that gene copy number and expression deactivation rates are important variables in achieving predictable outcomes. In gene expression systems with non-zero expression deactivation rates, diploid systems had a higher probability of uninterrupted gene expression than haploid systems and were more successful at maintaining gene product above a very low threshold. Systems with relatively rapid expression deactivation rates (unstable gene expression) had more predictable responses to a gradient of inducer than systems with slow or zero expression deactivation rates (stable gene expression), and diploid systems were more predictable than haploid, with or without dosage compensation. We suggest that null mutations of a single allele in a diploid organism could decrease the probability of gene expression and present the hypothesis that some haploinsufficiency syndromes might result from an increased susceptibility to stochastic delays of gene initiation or interruptions of gene expression.
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Affiliation(s)
- D L Cook
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98105, USA
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Gredinger E, Gerber AN, Tamir Y, Tapscott SJ, Bengal E. Mitogen-activated protein kinase pathway is involved in the differentiation of muscle cells. J Biol Chem 1998; 273:10436-44. [PMID: 9553102 DOI: 10.1074/jbc.273.17.10436] [Citation(s) in RCA: 174] [Impact Index Per Article: 6.7] [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 differentiation of muscle cells is controlled by the MyoD family of transcription factors. This family is regulated by extracellular growth factors that transmit largely unknown signals into the cells. Here we show that the activity of extracellular signal-regulated protein kinase (ERK), a kinase that is part of the mitogen-activated protein kinase (MAPK) cascade, is low in myoblasts and is induced with the onset of terminal differentiation of C2 cells. ERK activity is also induced in fibroblasts that were modified to express MyoD, but not in the parental fibroblast cells. Thus, ERK induction is an intrinsic property of muscle cells. A specific MAPK kinase inhibitor (PD098059) that was added to C2 cells partially inhibited the fusion of myoblasts to multinucleated myotubes without affecting the expression of muscle-specific markers. This inhibitor blocked the induction of MyoD expression that normally takes place during terminal differentiation. Two lines of evidence suggest that the MAPK cascade induces the activity of MyoD: 1) the expression of constitutively activated forms of MEK1 or Raf1 enhanced the transcriptional activity of MyoD in 10T1/2 fibroblasts; and 2) the addition of PD098059 to fibroblast cells expressing a conditional MyoD-estrogen fusion protein significantly inhibited the expression of MyoD-responsive genes. Our results indicate that the MAPK pathway is activated in differentiating muscle cells and that it positively regulates the expression and activity of MyoD protein.
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Affiliation(s)
- E Gredinger
- Department of Biochemistry, Rappaport Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
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Otten AD, Firpo EJ, Gerber AN, Brody LL, Roberts JM, Tapscott SJ. Inactivation of MyoD-mediated expression of p21 in tumor cell lines. Cell Growth Differ 1997; 8:1151-60. [PMID: 9372238] [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] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The basic helix-loop-helix protein MyoD induces muscle structural gene expression and cell cycle withdrawal in many nontransformed cell lines. We show that MyoD activation of transcription of the cyclin-dependent kinase inhibitor p21 does not require synthesis of an intermediary protein. In most of the rhabdomyosarcoma and other solid tumor cell lines that we analyzed, p21 levels were abnormally low and correlated with the combined inactivity of MyoD and p53, two known transcriptional activators of p21. Loss of MyoD activation of p21 transcription correlated with the failure to arrest in G1, and expression of p21 caused accumulation of cells in G1, further supporting a role for p21 in MyoD-induced cell cycle arrest. Finally, different tumor types have inactivated distinct factors necessary for p21 expression, because p21 expression was reconstituted in hybrid cell lines. We propose that p21 integrates growth-inhibitory signals from independent p53 and basic helix-loop-helix pathways, and that in the majority of tumor cell lines, both pathways are abrogated.
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Affiliation(s)
- A D Otten
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Gerber AN, Klesert TR, Bergstrom DA, Tapscott SJ. Two domains of MyoD mediate transcriptional activation of genes in repressive chromatin: a mechanism for lineage determination in myogenesis. Genes Dev 1997; 11:436-50. [PMID: 9042858 DOI: 10.1101/gad.11.4.436] [Citation(s) in RCA: 230] [Impact Index Per Article: 8.5] [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: 02/03/2023]
Abstract
Genetic studies have demonstrated that MyoD and Myf5 establish the skeletal muscle lineage, whereas myogenin mediates terminal differentiation, yet the molecular basis for this distinction is not understood. We show that MyoD can remodel chromatin at binding sites in muscle gene enhancers and activate transcription at previously silent loci. TGF-beta, basic-FGF, and sodium butyrate blocked MyoD-mediated chromatin reorganization and the initiation of transcription. In contrast, TGF-beta and sodium butyrate did not block transcription when added after chromatin remodeling had occurred. MyoD and Myf-5 were 10-fold more efficient than myogenin at activating genes in regions of transcriptionally silent chromatin. Deletion mutagenesis of the MyoD protein demonstrated that the ability to activate endogenous genes depended on two regions: a region rich in cysteine and histidine residues between the acidic activation domain and the bHLH domain, and a second region in the carboxyl terminus of the protein. Neither region has been shown previously to regulate gene transcription and both have domains that are conserved in the Myf5 protein. Our results establish a mechanism for chromatin modeling in the skeletal muscle lineage and define domains of MyoD, independent of the activation domain, that participate in chromatin reorganization.
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Affiliation(s)
- A N Gerber
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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Gerber AN, Tapscott SJ. Tumor cell complementation groups based on myogenic potential: evidence for inactivation of loci required for basic helix-loop-helix protein activity. Mol Cell Biol 1996; 16:3901-8. [PMID: 8668208 PMCID: PMC231387 DOI: 10.1128/mcb.16.7.3901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [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: 02/01/2023] Open
Abstract
Basic helix-loop-helix (bHLH) proteins mediate terminal differentiation in many lineages. By using the bHLH protein MyoD, which can dominantly activate the myogenic differentiation program in numerous cell types, we demonstrated that recessive defects in bHLH protein function are present in human tumor lines. In contrast to prior work with primary cell cultures, MyoD did not activate the myogenic program in six of the eight tumor lines we tested. Cell fusions between the MyoD-defective lines and fibroblasts restored MyoD activity, indicating that the deficiency of a gene or factor prevents bHLH protein function in the tumor lines. Fusions between certain pairings of the MyoD-defective lines also restored MyoD activity, allowing the tumor lines to be assigned to complementation groups on the basis of their ability to execute the myogenic program and indicating that multiple mechanisms exist for abrogation of bHLH protein activity. These groups provide a basis for identifying genes critical for bHLH-mediated differentiation and tumor progression by using genetic complementation.
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Affiliation(s)
- A N Gerber
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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