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Liu T, Liu S, Rui X, Cao Y, Hecker J, Guo F, Zhang Y, Gong L, Zhou Y, Yu Y, Krishnamoorthyni N, Bates S, Chun S, Boyer N, Xu S, Park JA, Perrella MA, Levy BD, Weiss ST, Mou H, Raby BA, Zhou X. Gasdermin B, an asthma-susceptibility gene, promotes MAVS-TBK1 signalling and airway inflammation. Eur Respir J 2024; 63:2301232. [PMID: 38514093 PMCID: PMC11063620 DOI: 10.1183/13993003.01232-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 12/31/2023] [Indexed: 03/23/2024]
Abstract
RATIONALE Respiratory virus-induced inflammation is the leading cause of asthma exacerbation, frequently accompanied by induction of interferon-stimulated genes (ISGs). How asthma-susceptibility genes modulate cellular response upon viral infection by fine-tuning ISG induction and subsequent airway inflammation in genetically susceptible asthma patients remains largely unknown. OBJECTIVES To decipher the functions of gasdermin B (encoded by GSDMB) in respiratory virus-induced lung inflammation. METHODS In two independent cohorts, we analysed expression correlation between GSDMB and ISG s. In human bronchial epithelial cell line or primary bronchial epithelial cells, we generated GSDMB-overexpressing and GSDMB-deficient cells. A series of quantitative PCR, ELISA and co-immunoprecipitation assays were performed to determine the function and mechanism of GSDMB for ISG induction. We also generated a novel transgenic mouse line with inducible expression of human unique GSDMB gene in airway epithelial cells and infected the mice with respiratory syncytial virus to determine the role of GSDMB in respiratory syncytial virus-induced lung inflammation in vivo. RESULTS GSDMB is one of the most significant asthma-susceptibility genes at 17q21 and acts as a novel RNA sensor, promoting mitochondrial antiviral-signalling protein (MAVS)-TANK binding kinase 1 (TBK1) signalling and subsequent inflammation. In airway epithelium, GSDMB is induced by respiratory viral infections. Expression of GSDMB and ISGs significantly correlated in respiratory epithelium from two independent asthma cohorts. Notably, inducible expression of human GSDMB in mouse airway epithelium led to enhanced ISGs induction and increased airway inflammation with mucus hypersecretion upon respiratory syncytial virus infection. CONCLUSIONS GSDMB promotes ISGs expression and airway inflammation upon respiratory virus infection, thereby conferring asthma risk in risk allele carriers.
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Affiliation(s)
- Tao Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Siqi Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Xianliang Rui
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Ye Cao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Feng Guo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yihan Zhang
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lu Gong
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yihan Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yuzhen Yu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nandini Krishnamoorthyni
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel Bates
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sung Chun
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nathan Boyer
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shuang Xu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jin-Ah Park
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark A Perrella
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bruce D Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hongmei Mou
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- These authors jointly conceptualised and supervised this work
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- These authors jointly conceptualised and supervised this work
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2
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Kong Q, Zhang Z. Cancer-associated pyroptosis: A new license to kill tumor. Front Immunol 2023; 14:1082165. [PMID: 36742298 PMCID: PMC9889862 DOI: 10.3389/fimmu.2023.1082165] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Pyroptosis is a programmed necrotic cell death mediated by pore-forming Gasdermin (GSDM) proteins. After being unleashed from the C-terminal auto-inhibitory domains by proteolytic cleavage, the N-terminal domains of GSDMs oligomerize and perforate on the plasma membrane to induce cytolytic pyroptosis, releasing immune mediators and alarming the immune system. Upon infection or danger signal perception, GSDMD that functions downstream of the inflammasome, a supramolecular complex for inflammatory caspase activation, is cleaved and activated by inflammasome-activated caspase-1/4/5/11 in immune cells and epithelial cells to trigger pyroptosis and exert anti-infection protection. Unlike this inflammasome-activated pyroptosis (IAP), recent studies also suggest an emerging role of cancer-associated pyroptosis (CAP), mediated by other GSDMs in cancer cells, in provoking anti-tumor immunity. IAP and CAP share common features like cell membrane rupture but also differ in occurrence sites, activating mechanisms, secreting cytokines and biological outcomes. Here we review the most recent knowledge of cancer-associated pyroptosis and present a promising avenue for developing therapeutic interventions to enhance anti-tumor immunity for cancer treatment.
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Affiliation(s)
- Qing Kong
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Zhibin Zhang
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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3
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Guo F, Hao Y, Zhang L, Croteau-Chonka DC, Thibault D, Kothari P, Li L, Levy BD, Zhou X, Raby BA. Asthma Susceptibility Gene ORMDL3 Promotes Autophagy in Human Bronchial Epithelium. Am J Respir Cell Mol Biol 2022; 66:661-670. [PMID: 35353673 PMCID: PMC9163638 DOI: 10.1165/rcmb.2021-0305oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/03/2022] [Indexed: 02/05/2023] Open
Abstract
The genome-wide association study (GWAS)-identified asthma susceptibility risk alleles on chromosome 17q21 increase the expression of ORMDL3 (ORMDL sphingolipid biosynthesis regulator 3) in lung tissue. Given the importance of epithelial integrity in asthma, we hypothesized that ORMDL3 directly impacted bronchial epithelial function. To determine whether and how ORMDL3 expression impacts the bronchial epithelium, in studies using both primary human bronchial epithelial cells and human bronchial epithelial cell line, 16HBE (16HBE14o-), we assessed the impact of ORMDL3 on autophagy. Studies included: autophagosome detection by electron microscopy, RFP-GFP-LC3B to assess autophagic activity, and Western blot analysis of autophagy-related proteins. Mechanistic assessments included immunoprecipitation assays, intracellular calcium mobilization assessments, and cell viability assays. Coexpression of ORMDL3 and autophagy-related genes was measured in primary human bronchial epithelial cells derived from 44 subjects. Overexpressing ORMDL3 demonstrated increased numbers of autophagosomes and increased levels of autophagy-related proteins LC3B, ATG3, ATG7, and ATG16L1. ORMDL3 overexpression promotes autophagy and subsequent cell death by impairing intracellular calcium mobilization through interacting with SERCA2. Strong correlation was observed between expression of ORMDL3 and autophagy-related genes in patient-derived bronchial epithelial cells. Increased ORMDL3 expression induces autophagy, possibly through interacting with SERCA2, thereby inhibiting intracellular calcium influx, and induces cell death, impairing bronchial epithelial function in asthma.
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Affiliation(s)
- Feng Guo
- Channing Division of Network Medicine and
| | - Yuan Hao
- Channing Division of Network Medicine and
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts; and
| | - Li Zhang
- Channing Division of Network Medicine and
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, P.R. China
| | | | | | | | - Lijia Li
- Channing Division of Network Medicine and
| | - Bruce D. Levy
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Xiaobo Zhou
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Benjamin A. Raby
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts; and
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4
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Bourdonnay E, Henry T. Transcriptional and Epigenetic Regulation of Gasdermins. J Mol Biol 2021; 434:167253. [PMID: 34537234 DOI: 10.1016/j.jmb.2021.167253] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/26/2021] [Accepted: 09/09/2021] [Indexed: 12/29/2022]
Abstract
Gasdermins (GSDM) are a family of six homologous proteins (GSDMA to E and Pejvakin) in humans. GSDMA-E are pore-forming proteins targeting the plasma membrane to trigger a rapid cell death termed pyroptosis or bacterial membranes to promote antibacterial immune defenses. Activation of GSDM relies on a proteolytic cleavage but is highly dependent on GSDM expression levels. The different GSDM genes have tissue-specific expression pattern although metabolic, environmental signals, cell stress and numerous cytokines modulate their expression levels in tissues. Furthermore, expression of GSDM genes can be modulated by polymorphisms and have been associated with susceptibility to asthma, inflammatory bowel diseases and rhinovirus wheezing illness. Finally, the expression level of GSDMs controls the balance between apoptosis and pyroptosis affecting both the response and the toxicity to chemotactic drugs and antitumoral treatments. Numerous cancer demonstrate positive or negative modulation of GSDM expression levels correlating with distinct tumor-specific prognosis. In this review, we present the transcriptional and epigenetic mechanisms controlling GSDM levels and their functional consequences in asthma, infection, cancers and inflammatory bowel disease to highlight how this first layer of regulations has key consequences on disease susceptibility and response to treatment.
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Affiliation(s)
- Emilie Bourdonnay
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007 Lyon, France
| | - Thomas Henry
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, F-69007 Lyon, France.
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5
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James BN, Oyeniran C, Sturgill JL, Newton J, Martin RK, Bieberich E, Weigel C, Maczis MA, Palladino END, Lownik JC, Trudeau JB, Cook-Mills JM, Wenzel S, Milstien S, Spiegel S. Ceramide in apoptosis and oxidative stress in allergic inflammation and asthma. J Allergy Clin Immunol 2021; 147:1936-1948.e9. [PMID: 33130063 PMCID: PMC8081742 DOI: 10.1016/j.jaci.2020.10.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Nothing is known about the mechanisms by which increased ceramide levels in the lung contribute to allergic responses and asthma severity. OBJECTIVE We sought to investigate the functional role of ceramide in mouse models of allergic airway disease that recapitulate the cardinal clinical features of human allergic asthma. METHODS Allergic airway disease was induced in mice by repeated intranasal administration of house dust mite or the fungal allergen Alternaria alternata. Processes that can be regulated by ceramide and are important for severity of allergic asthma were correlated with ceramide levels measured by mass spectrometry. RESULTS Both allergens induced massive pulmonary apoptosis and also significantly increased reactive oxygen species in the lung. Prevention of increases in lung ceramide levels mitigated allergen-induced apoptosis, reactive oxygen species, and neutrophil infiltration. In contrast, dietary supplementation of the antioxidant α-tocopherol decreased reactive oxygen species but had no significant effects on elevation of ceramide level or apoptosis, indicating that the increases in lung ceramide levels in allergen-challenged mice are not mediated by oxidative stress. Moreover, specific ceramide species were altered in bronchoalveolar lavage fluid from patients with severe asthma compared with in bronchoalveolar lavage fluid from individuals without asthma. CONCLUSION Our data suggest that elevation of ceramide level after allergen challenge contributes to the apoptosis, reactive oxygen species generation, and neutrophilic infiltrate that characterize the severe asthmatic phenotype. Ceramide might be the trigger of formation of Creola bodies found in the sputum of patients with severe asthma and could be a biomarker to optimize diagnosis and to monitor and improve clinical outcomes in this disease.
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Affiliation(s)
- Briana N James
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Clement Oyeniran
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Jamie L Sturgill
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Kentucky College of Medicine, Lexington, Ky
| | - Jason Newton
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Rebecca K Martin
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Erhard Bieberich
- Department of Physiology, University of Kentucky College of Medicine, Lexington, Ky
| | - Cynthia Weigel
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Melissa A Maczis
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Elisa N D Palladino
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Joseph C Lownik
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - John B Trudeau
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pa
| | - Joan M Cook-Mills
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana School of Medicine, Indianapolis, Ind
| | - Sally Wenzel
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pa
| | - Sheldon Milstien
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University School of Medicine, Richmond, Va.
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6
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The intersect of genetics, environment, and microbiota in asthma-perspectives and challenges. J Allergy Clin Immunol 2021; 147:781-793. [PMID: 33678251 DOI: 10.1016/j.jaci.2020.08.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/07/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023]
Abstract
In asthma, a significant portion of the interaction between genetics and environment occurs through microbiota. The proposed mechanisms behind this interaction are complex and at times contradictory. This review covers recent developments in our understanding of this interaction: the "microbial hypothesis" and the "farm effect"; the role of endotoxin and genetic variation in pattern recognition systems; the interaction with allergen exposure; the additional involvement of host gut and airway microbiota; the role of viral respiratory infections in interaction with the 17q21 and CDHR3 genetic loci; and the importance of in utero and early-life timing of exposures. We propose a unified framework for understanding how all these phenomena interact to drive asthma pathogenesis. Finally, we point out some future challenges for continued research in this field, in particular the need for multiomic integration, as well as the potential utility of asthma endotyping.
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7
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Raby BA, Weiss ST. Diversity and the Splice of Life: Mapping the 17q12-21.1 Locus for Variants Associated with Early-Onset Asthma in African American Individuals. Am J Respir Crit Care Med 2021; 203:401-403. [PMID: 33108222 PMCID: PMC7885835 DOI: 10.1164/rccm.202010-3802ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Benjamin A Raby
- Department of Pediatrics Boston Children's Hospital and Harvard Medical School Boston, Massachusetts and
- Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts
| | - Scott T Weiss
- Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts
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8
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Youssef M, De Sanctis JB, Shah J, Dumut DC, Hajduch M, Naumova AK, Radzioch D. Treatment of Allergic Asthma with Fenretinide Formulation (LAU-7b) Downregulates ORMDL Sphingolipid Biosynthesis Regulator 3 ( Ormdl3) Expression and Normalizes Ceramide Imbalance. J Pharmacol Exp Ther 2020; 373:476-487. [PMID: 32273303 DOI: 10.1124/jpet.119.263715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
Zona pellucida binding protein 2 (Zpbp2) and ORMDL sphingolipid biosynthesis regulator 3 (Ormdl3), mapped downstream of Zpbp2, were identified as two genes associated with airway hyper-responsiveness (AHR). Ormdl3 gene product has been shown to regulate the biosynthesis of ceramides. Allergic asthma was shown to be associated with an imbalance between very-long-chain ceramides (VLCCs) and long-chain ceramides (LCCs). We hypothesized that Fenretinide can prevent the allergic asthma-induced augmentation of Ormdl3 gene expression, normalize aberrant levels of VLCCs and LCCs, and treat allergic asthma symptoms. We induced allergic asthma by house dust mite (HDM) in A/J WT mice and Zpbp2 KO mice expressing lower levels of Ormdl3 mRNA than WT. We investigated the effect of a novel formulation of Fenretinide, LAU-7b, on the AHR, inflammatory cell infiltration, mucus production, IgE levels, and ceramide levels. Although lower Ormdl3 expression, which was observed in Zpbp2 KO mice, was associated with lower AHR, allergic Zpbp2 KO mice were not protected from inflammatory cell infiltration, mucus accumulation, or aberrant levels of VLCCs and LCCs induced by HDM. LAU-7b treatment protects both the Zpbp2 KO and WT mice. The treatment significantly lowers the gene expression of Ormdl3, normalizes the VLCCs and LCCs, and corrects all the other phenotypes associated with allergic asthma after HDM challenge, except the elevated levels of IgE. LAU-7b treatment prevents the augmentation of Ormdl3 expression and ceramide imbalance induced by HDM challenge and protects both WT and Zpbp2 KO mice against allergic asthma symptoms. SIGNIFICANCE STATEMENT: Compared with A/J WT mice, KO mice with Zpbp2 gene deletion have lower AHR and lower levels of Ormdl3 expression. The novel oral clinical formulation of Fenretinide (LAU-7b) effectively lowers the AHR and protects against inflammatory cell infiltration and mucus accumulation induced by house dust mite in both Zpbp2 KO and WT A/J mice. LAU-7b prevents Ormdl3 overexpression in WT allergic mice and corrects the aberrant levels of very-long-chain and long-chain ceramides in both WT and Zpbp2 KO allergic mice.
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Affiliation(s)
- Mina Youssef
- Department of Human Genetics (M.Y., A.K.N., D.R.), Department of Pharmacology and Therapeutics (J.S.), Division of Experimental Medicine, Department of Medicine (D.C.D., D.R.), and Department of Obstetrics and Gynecology (A.K.N.), McGill University, Montreal, Quebec, Canada; Program in Infectious Diseases and Immunity in Global Health, McGill University Health Center, Montreal, Quebec, Canada (M.Y., J.S., D.C.D., D.R.); and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic (J.B.D.S., M.H., D.R.)
| | - Juan B De Sanctis
- Department of Human Genetics (M.Y., A.K.N., D.R.), Department of Pharmacology and Therapeutics (J.S.), Division of Experimental Medicine, Department of Medicine (D.C.D., D.R.), and Department of Obstetrics and Gynecology (A.K.N.), McGill University, Montreal, Quebec, Canada; Program in Infectious Diseases and Immunity in Global Health, McGill University Health Center, Montreal, Quebec, Canada (M.Y., J.S., D.C.D., D.R.); and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic (J.B.D.S., M.H., D.R.)
| | - Juhi Shah
- Department of Human Genetics (M.Y., A.K.N., D.R.), Department of Pharmacology and Therapeutics (J.S.), Division of Experimental Medicine, Department of Medicine (D.C.D., D.R.), and Department of Obstetrics and Gynecology (A.K.N.), McGill University, Montreal, Quebec, Canada; Program in Infectious Diseases and Immunity in Global Health, McGill University Health Center, Montreal, Quebec, Canada (M.Y., J.S., D.C.D., D.R.); and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic (J.B.D.S., M.H., D.R.)
| | - Daciana Catalina Dumut
- Department of Human Genetics (M.Y., A.K.N., D.R.), Department of Pharmacology and Therapeutics (J.S.), Division of Experimental Medicine, Department of Medicine (D.C.D., D.R.), and Department of Obstetrics and Gynecology (A.K.N.), McGill University, Montreal, Quebec, Canada; Program in Infectious Diseases and Immunity in Global Health, McGill University Health Center, Montreal, Quebec, Canada (M.Y., J.S., D.C.D., D.R.); and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic (J.B.D.S., M.H., D.R.)
| | - Marian Hajduch
- Department of Human Genetics (M.Y., A.K.N., D.R.), Department of Pharmacology and Therapeutics (J.S.), Division of Experimental Medicine, Department of Medicine (D.C.D., D.R.), and Department of Obstetrics and Gynecology (A.K.N.), McGill University, Montreal, Quebec, Canada; Program in Infectious Diseases and Immunity in Global Health, McGill University Health Center, Montreal, Quebec, Canada (M.Y., J.S., D.C.D., D.R.); and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic (J.B.D.S., M.H., D.R.)
| | - Anna K Naumova
- Department of Human Genetics (M.Y., A.K.N., D.R.), Department of Pharmacology and Therapeutics (J.S.), Division of Experimental Medicine, Department of Medicine (D.C.D., D.R.), and Department of Obstetrics and Gynecology (A.K.N.), McGill University, Montreal, Quebec, Canada; Program in Infectious Diseases and Immunity in Global Health, McGill University Health Center, Montreal, Quebec, Canada (M.Y., J.S., D.C.D., D.R.); and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic (J.B.D.S., M.H., D.R.)
| | - Danuta Radzioch
- Department of Human Genetics (M.Y., A.K.N., D.R.), Department of Pharmacology and Therapeutics (J.S.), Division of Experimental Medicine, Department of Medicine (D.C.D., D.R.), and Department of Obstetrics and Gynecology (A.K.N.), McGill University, Montreal, Quebec, Canada; Program in Infectious Diseases and Immunity in Global Health, McGill University Health Center, Montreal, Quebec, Canada (M.Y., J.S., D.C.D., D.R.); and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic (J.B.D.S., M.H., D.R.)
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9
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Lymphocyte DNA methylation mediates genetic risk at shared immune-mediated disease loci. J Allergy Clin Immunol 2020; 145:1438-1451. [PMID: 31945409 PMCID: PMC7201180 DOI: 10.1016/j.jaci.2019.12.910] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 12/04/2019] [Accepted: 12/10/2019] [Indexed: 12/21/2022]
Abstract
Background Defining regulatory mechanisms through which noncoding risk variants influence the cell-mediated pathogenesis of immune-mediated disease (IMD) has emerged as a priority in the post–genome-wide association study era. Objectives With a focus on rheumatoid arthritis, we sought new insight into genetic mechanisms of adaptive immune dysregulation to help prioritize molecular pathways for targeting in this and related immune pathologies. Methods Whole-genome methylation and transcriptional data from isolated CD4+ T cells and B cells of more than 100 genotyped and phenotyped patients with inflammatory arthritis, all of whom were naive to immunomodulatory treatments, were obtained. Analysis integrated these comprehensive data with genome-wide association study findings across IMDs and other publicly available resources. Results We provide strong evidence that disease-associated DNA variants regulate cis-CpG methylation in CD4+ T and/or B cells at 37% RA loci. Using paired, cell-specific transcriptomic data and causal inference testing, we identify examples where site-specific DNA methylation in turn mediates gene expression, including FCRL3 in both cell types and ORMDL3/GSDMB, IL6ST/ANKRD55, and JAZF1 in CD4+ T cells. A number of genes regulated in this way highlight mechanisms common to RA and other IMDs including multiple sclerosis and asthma, in turn distinguishing them from osteoarthritis, a primarily degenerative disease. Finally, we corroborate the observed effects experimentally. Conclusions Our observations highlight important mechanisms of genetic risk in RA and the wider context of immune dysregulation. They confirm the utility of DNA methylation profiling as a tool for causal gene prioritization and, potentially, therapeutic targeting in complex IMD.
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10
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Qi C, Xu CJ, Koppelman GH. The role of epigenetics in the development of childhood asthma. Expert Rev Clin Immunol 2019; 15:1287-1302. [PMID: 31674254 DOI: 10.1080/1744666x.2020.1686977] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: The development of childhood asthma is caused by a combination of genetic factors and environmental exposures. Epigenetics describes mechanisms of (heritable) regulation of gene expression that occur without changes in DNA sequence. Epigenetics is strongly related to aging, is cell-type specific, and includes DNA methylation, noncoding RNAs, and histone modifications.Areas covered: This review summarizes recent epigenetic studies of childhood asthma in humans, which mostly involve studies of DNA methylation published in the recent five years. Environmental exposures, in particular cigarette smoking, have significant impact on epigenetic changes, but few of these epigenetic signals are also associated with asthma. Several asthma-associated genetic variants relate to DNA methylation. Epigenetic signals can be better understood by studying their correlation with gene expression, which revealed higher presence and activation of blood eosinophils in asthma. Strong associations of nasal methylation signatures and atopic asthma were identified, which were replicable across different populations.Expert commentary: Epigenetic markers have been strongly associated with asthma, and might serve as biomarker of asthma. The causal and longitudinal relationships between epigenetics and disease, and between environmental exposures and epigenetic changes need to be further investigated. Efforts should be made to understand cell-type-specific epigenetic mechanisms in asthma.
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Affiliation(s)
- Cancan Qi
- Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cheng-Jian Xu
- Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Gastroenterology, Hepatology and Endocrinology, CiiM, Centre for individualised infection medicine, A joint venture between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gerard H Koppelman
- Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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11
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James B, Milstien S, Spiegel S. ORMDL3 and allergic asthma: From physiology to pathology. J Allergy Clin Immunol 2019; 144:634-640. [PMID: 31376405 DOI: 10.1016/j.jaci.2019.07.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 01/10/2023]
Abstract
There is a strong genetic component to asthma, and numerous genome-wide association studies have identified ORM1 (yeast)-like protein 3 (ORMDL3) as a gene associated with asthma susceptibility. However, how ORMDL3 contributes to asthma pathogenesis and its physiologic functions is not well understood and a matter of great debate. This rostrum describes recent advances and new insights in understanding of the multifaceted functions of ORMDL3 in patients with allergic asthma. We also suggest a potential unifying paradigm and discuss molecular mechanisms for the pathologic functions of ORMDL3 in asthma related to its evolutionarily conserved role in regulation of sphingolipid homeostasis. Finally, we briefly survey the utility of sphingolipid metabolites as potential biomarkers for allergic asthma.
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Affiliation(s)
- Briana James
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Sheldon Milstien
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Va
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Va.
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12
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Everson TM, Zhang H, Lockett GA, Kaushal A, Forthofer M, Ewart SL, Burrows K, Relton CL, Sharp GC, Henderson AJ, Patil VK, Rezwan FI, Arshad SH, Holloway JW, Karmaus W. Epigenome-wide association study of asthma and wheeze characterizes loci within HK1. Allergy Asthma Clin Immunol 2019; 15:43. [PMID: 31367216 PMCID: PMC6657035 DOI: 10.1186/s13223-019-0356-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/12/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND To identify novel epigenetic markers of adolescent asthma and replicate findings in an independent cohort, then explore whether such markers are detectable at birth, predictive of early-life wheeze, and associated with gene expression in cord blood. METHODS We performed epigenome-wide screening with recursive random forest feature selection and internal validation in the IOW birth cohort. We then tested whether we could replicate these findings in the independent cohort ALSPAC and followed-up our top finding with children of the IOW cohort. RESULTS We identified 10 CpG sites associated with adolescent asthma at a 5% false discovery rate (IOW, n = 370), five of which exhibited evidence of associations in the replication study (ALSPAC, n = 720). One site, cg16658191, within HK1 displayed particularly strong associations after cellular heterogeneity adjustments in both cohorts (ORIOW = 0.17, 95% CI 0.04-0.57) (ORALSPAC = 0.57, 95% CI 0.38-0.87). Additionally, higher expression of HK1 (OR = 3.81, 95% CI 1.41-11.77) in cord blood was predictive of wheezing in infancy (n = 82). CONCLUSION We identified novel associations between asthma and wheeze with methylation at cg16658191 and the expression of HK1, which may serve as markers of, predictors of, and potentially etiologic factors involved in asthma and early life wheeze.
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Affiliation(s)
- Todd M. Everson
- 0000 0000 9075 106Xgrid.254567.7Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene Street, Columbia, SC 29208 USA ,0000 0001 0941 6502grid.189967.8Present Address: Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd, Atlanta, GA 30322 USA
| | - Hongmei Zhang
- 0000 0000 9560 654Xgrid.56061.34Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA
| | - Gabrielle A. Lockett
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK
| | - Akhilesh Kaushal
- 0000 0001 2160 926Xgrid.39382.33Center for Precision and Environmental Health, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030 USA
| | - Melinda Forthofer
- 0000 0000 9075 106Xgrid.254567.7Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene Street, Columbia, SC 29208 USA ,0000 0000 8598 2218grid.266859.6Present Address: Department of Public Health Sciences at the College of Health and Human Services, University of North Carolina Charlotte, 9201 University City Boulevard, Charlotte, NC 28223 USA
| | - Susan L. Ewart
- 0000 0001 2150 1785grid.17088.36Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI USA
| | - Kimberley Burrows
- 0000 0004 1936 7603grid.5337.2MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - Caroline L. Relton
- 0000 0004 1936 7603grid.5337.2MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - Gemma C. Sharp
- 0000 0004 1936 7603grid.5337.2MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - A. John Henderson
- 0000 0004 1936 7603grid.5337.2Avon Longitudinal Study of Parents and Children, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - Veeresh K. Patil
- grid.439564.9The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight UK
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK
| | - S. Hasan Arshad
- Clinical and Experimental Sciences Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK ,grid.439564.9The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight UK ,0000000103590315grid.123047.3NIHR Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton, UK
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK ,Clinical and Experimental Sciences Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK
| | - Wilfried Karmaus
- 0000 0000 9560 654Xgrid.56061.34Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA
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13
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Debeuf N, Zhakupova A, Steiner R, Van Gassen S, Deswarte K, Fayazpour F, Van Moorleghem J, Vergote K, Pavie B, Lemeire K, Hammad H, Hornemann T, Janssens S, Lambrecht BN. The ORMDL3 asthma susceptibility gene regulates systemic ceramide levels without altering key asthma features in mice. J Allergy Clin Immunol 2019; 144:1648-1659.e9. [PMID: 31330218 DOI: 10.1016/j.jaci.2019.06.041] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Genome-wide association studies in asthma have repeatedly identified single nucleotide polymorphisms in the ORM (yeast)-like protein isoform 3 (ORMDL3) gene across different populations. Although the ORM homologues in yeast are well-known inhibitors of sphingolipid synthesis, it is still unclear whether and how mammalian ORMDL3 regulates sphingolipid metabolism and whether altered sphingolipid synthesis would be causally related to asthma risk. OBJECTIVE We sought to examine the in vivo role of ORMDL3 in sphingolipid metabolism and allergic asthma. METHODS Ormdl3-LacZ reporter mice, gene-deficient Ormdl3-/- mice, and overexpressing Ormdl3Tg/wt mice were exposed to physiologically relevant aeroallergens, such as house dust mite (HDM) or Alternaria alternata, to induce experimental asthma. Mass spectrometry-based sphingolipidomics were performed, and airway eosinophilia, TH2 cytokine production, immunoglobulin synthesis, airway remodeling, and bronchial hyperreactivity were measured. RESULTS HDM challenge significantly increased levels of total sphingolipids in the lungs of HDM-sensitized mice compared with those in control mice. In Ormdl3Tg/wt mice the allergen-induced increase in lung ceramide levels was significantly reduced, whereas total sphingolipid levels were not affected. Conversely, in liver and serum, levels of total sphingolipids, including ceramides, were increased in Ormdl3-/- mice, whereas they were decreased in Ormdl3Tg/wt mice. This difference was independent of allergen exposure. Despite these changes, all features of asthma were identical between wild-type, Ormdl3Tg/wt, and Ormdl3-/- mice across several models of experimental asthma. CONCLUSION ORMDL3 regulates systemic ceramide levels, but genetically interfering with Ormdl3 expression does not result in altered experimental asthma.
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Affiliation(s)
- Nincy Debeuf
- Laboratory of Mucosal Immunology and Immunoregulation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Assem Zhakupova
- Institute of Clinical Chemistry, University and University Hospital Zurich, Zurich, Switzerland
| | - Regula Steiner
- Institute of Clinical Chemistry, University and University Hospital Zurich, Zurich, Switzerland
| | - Sofie Van Gassen
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Kim Deswarte
- Laboratory of Mucosal Immunology and Immunoregulation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Farzaneh Fayazpour
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Ghent, Belgium
| | - Justine Van Moorleghem
- Laboratory of Mucosal Immunology and Immunoregulation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Karl Vergote
- Laboratory of Mucosal Immunology and Immunoregulation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Benjamin Pavie
- VIB Bioimaging Core, VIB Center for Inflammation Research, Ghent, Belgium; Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kelly Lemeire
- Biomedical Molecular Biology, Ghent University, Ghent, Belgium; VIB Center for Inflammation Research, Ghent, Belgium
| | - Hamida Hammad
- Laboratory of Mucosal Immunology and Immunoregulation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University and University Hospital Zurich, Zurich, Switzerland
| | - Sophie Janssens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Ghent, Belgium
| | - Bart N Lambrecht
- Laboratory of Mucosal Immunology and Immunoregulation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
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14
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Miller M, Broide DH. Why Is ORMDL3 on Chromosome 17q21 Highly Linked to Asthma? Am J Respir Crit Care Med 2019; 199:404-406. [PMID: 30365391 DOI: 10.1164/rccm.201810-1941ed] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Marina Miller
- 1 Department of Medicine University of California San Diego La Jolla, California
| | - David H Broide
- 1 Department of Medicine University of California San Diego La Jolla, California
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15
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White SR, Laxman B, Naureckas ET, Hogarth DK, Solway J, Sperling AI, Ober C. Evidence for an IL-6-high asthma phenotype in asthmatic patients of African ancestry. J Allergy Clin Immunol 2019; 144:304-306.e4. [PMID: 31029772 DOI: 10.1016/j.jaci.2019.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/14/2019] [Accepted: 04/17/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Steven R White
- Department of Medicine, University of Chicago, Chicago, Ill.
| | | | | | - D Kyle Hogarth
- Department of Medicine, University of Chicago, Chicago, Ill
| | - Julian Solway
- Department of Medicine, University of Chicago, Chicago, Ill
| | | | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
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16
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den Dekker HT, Burrows K, Felix JF, Salas LA, Nedeljkovic I, Yao J, Rifas-Shiman SL, Ruiz-Arenas C, Amin N, Bustamante M, DeMeo DL, Henderson AJ, Howe CG, Hivert MF, Ikram MA, de Jongste JC, Lahousse L, Mandaviya PR, van Meurs JB, Pinart M, Sharp GC, Stolk L, Uitterlinden AG, Anto JM, Litonjua AA, Breton CV, Brusselle GG, Sunyer J, Smith GD, Relton CL, Jaddoe VWV, Duijts L. Newborn DNA-methylation, childhood lung function, and the risks of asthma and COPD across the life course. Eur Respir J 2019; 53:13993003.01795-2018. [PMID: 30765504 DOI: 10.1183/13993003.01795-2018] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/08/2019] [Indexed: 01/13/2023]
Abstract
RATIONALE We aimed to identify differentially methylated regions (DMRs) in cord blood DNA associated with childhood lung function, asthma and chronic obstructive pulmonary disease (COPD) across the life course. METHODS We meta-analysed epigenome-wide data of 1688 children from five cohorts to identify cord blood DMRs and their annotated genes, in relation to forced expiratory volume in 1 s (FEV1), FEV1/forced vital capacity (FVC) ratio and forced expiratory flow at 75% of FVC at ages 7-13 years. Identified DMRs were explored for associations with childhood asthma, adult lung function and COPD, gene expression and involvement in biological processes. RESULTS We identified 59 DMRs associated with childhood lung function, of which 18 were associated with childhood asthma and nine with COPD in adulthood. Genes annotated to the top 10 identified DMRs were HOXA5, PAOX, LINC00602, ABCA7, PER3, CLCA1, VENTX, NUDT12, PTPRN2 and TCL1A. Differential gene expression in blood was observed for 32 DMRs in childhood and 18 in adulthood. Genes related with 16 identified DMRs were associated with respiratory developmental or pathogenic pathways. INTERPRETATION Our findings suggest that the epigenetic status of the newborn affects respiratory health and disease across the life course.
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Affiliation(s)
- Herman T den Dekker
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,These authors contributed equally
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, Bristol, UK.,These authors contributed equally
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,These authors contributed equally
| | - Lucas A Salas
- ISGLobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Dept of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Ivana Nedeljkovic
- Dept of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jin Yao
- Dept of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sheryl L Rifas-Shiman
- Obesity Prevention Program, Dept of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Carlos Ruiz-Arenas
- ISGLobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - N Amin
- Dept of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mariona Bustamante
- ISGLobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - A John Henderson
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Caitlin G Howe
- Dept of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Marie-France Hivert
- Obesity Prevention Program, Dept of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - M Arfan Ikram
- Dept of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan C de Jongste
- Dept of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lies Lahousse
- Dept of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Pooja R Mandaviya
- Dept of Clinical Chemistry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Joyce B van Meurs
- Dept of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mariona Pinart
- ISGLobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Lisette Stolk
- Dept of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Netherlands Consortium for Healthy Ageing (NCHA), Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - André G Uitterlinden
- Dept of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Netherlands Consortium for Healthy Ageing (NCHA), Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Josep M Anto
- ISGLobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carrie V Breton
- Dept of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guy G Brusselle
- Dept of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Preventive Medicine, University of Southern California, Los Angeles, CA, USA.,Dept of Respiratory Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jordi Sunyer
- ISGLobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, UK School of Social and Community Medicine, University of Bristol, Bristol, UK.,These authors contributed equally
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Dept of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,These authors contributed equally
| | - Liesbeth Duijts
- Dept of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands .,Dept of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,These authors contributed equally
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17
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Kogan V, Millstein J, London SJ, Ober C, White SR, Naureckas ET, Gauderman WJ, Jackson DJ, Barraza-Villarreal A, Romieu I, Raby BA, Breton CV. Genetic-Epigenetic Interactions in Asthma Revealed by a Genome-Wide Gene-Centric Search. Hum Hered 2019; 83:130-152. [PMID: 30669148 PMCID: PMC7365350 DOI: 10.1159/000489765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES There is evidence to suggest that asthma pathogenesis is affected by both genetic and epigenetic variation independently, and there is some evidence to suggest that genetic-epigenetic interactions affect risk of asthma. However, little research has been done to identify such interactions on a genome-wide scale. The aim of this studies was to identify genes with genetic-epigenetic interactions associated with asthma. METHODS Using asthma case-control data, we applied a novel nonparametric gene-centric approach to test for interactions between multiple SNPs and CpG sites simultaneously in the vicinities of 18,178 genes across the genome. RESULTS Twelve genes, PF4, ATF3, TPRA1, HOPX, SCARNA18, STC1, OR10K1, UPK1B, LOC101928523, LHX6, CHMP4B, and LANCL1, exhibited statistically significant SNP-CpG interactions (false discovery rate = 0.05). Of these, three have previously been implicated in asthma risk (PF4, ATF3, and TPRA1). Follow-up analysis revealed statistically significant pairwise SNP-CpG interactions for several of these genes, including SCARNA18, LHX6, and LOC101928523 (p = 1.33E-04, 8.21E-04, 1.11E-03, respectively). CONCLUSIONS Joint effects of genetic and epigenetic variation may play an important role in asthma pathogenesis. Statistical methods that simultaneously account for multiple variations across chromosomal regions may be needed to detect these types of effects on a genome-wide scale.
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Affiliation(s)
- Vladimir Kogan
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Joshua Millstein
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA,
| | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, RTP, Research Triangle Park, North Carolina, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Steven R White
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - W James Gauderman
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Daniel J Jackson
- University of Wisconsin School of Medicine and Public Health, Madison, Illinois, USA
| | - Albino Barraza-Villarreal
- Department of Environmental Health, Population Health Center, National Institute of Public Health of Mexico, Cuernavaca, Mexico
| | - Isabelle Romieu
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, Lyon, France
| | - Benjamin A Raby
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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18
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Li P, Lang X, Xia S. Elevated expression of microRNA-378 in children with asthma aggravates airway remodeling by promoting the proliferation and apoptosis resistance of airway smooth muscle cells. Exp Ther Med 2018; 17:1529-1536. [PMID: 30783418 PMCID: PMC6364182 DOI: 10.3892/etm.2018.7141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 10/25/2018] [Indexed: 12/14/2022] Open
Abstract
The present study determined the expression of microRNA (miR)-378 in the peripheral blood and lung tissues of children with asthma, and investigated its effect and mechanism of action on the biological functions of airway smooth muscle cells. A total of 23 asthmatic children and 15 healthy children were included in the study. Peripheral blood and tissues were obtained from asthmatic children. Healthy children provided peripheral blood. Quantitative real-time polymerase chain reaction was used to determine the expression of miR-378. Airway smooth muscle cells were isolated and cultured in vitro. The cells were transfected with miR-378 mimics or miR-378 inhibitor. Following transfection, proliferation of the cells was determined using the CCK-8 assay. In addition, flow cytometry was used to detect the cell cycles and apoptosis of smooth muscle cells. Western blotting was performed to determine the expression of extracellular matrix proteins in smooth muscle cells. Furthermore, bioinformatics was used to predict potential target genes of miR-378 and their downstream signaling pathways. Results indicated that the expression of miR-378 in peripheral blood and lung tissues from asthmatic children was increased compared with that in healthy children. Serum from asthmatic children promoted the proliferation of smooth muscle cells in vitro by affecting the cell cycle, and enhanced apoptotic resistance of smooth muscle cells. Notably, overexpression of miR-378 increased the proliferation of smooth muscle cells by affecting the cell cycle, and this upregulated apoptotic resistance of smooth muscle cells and enhanced the expression of extracellular matrix-related proteins in smooth muscle cells. However, downregulation of miR-378 expression reversed the promoting effect of serum from asthmatic children on the biological functions of smooth muscle cells. These findings suggested that miR-378 possibly affects the proliferation, apoptosis and motility of airway smooth muscle cells via downstream signaling pathways. To conclude, the present study demonstrated that miR-378 expression was elevated in the peripheral blood and lung tissues from children with asthma. Furthermore, miR-378 promoted the biological functions of extracellular matrix-related proteins of smooth muscle cells, and possibly exerts its effect via its target genes through downstream signaling pathways.
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Affiliation(s)
- Peng Li
- Department of Pediatrics, Maternity and Child Health Care Hospital of Zibo City, Zibo, Shandong 255029, P.R. China
| | - Xufang Lang
- Department of Student Affairs, College of Nursing, Zibo Vocational Institute, Zibo, Shandong 255314, P.R. China
| | - Shungang Xia
- Department of Pediatrics, Maternity and Child Health Care Hospital of Zibo City, Zibo, Shandong 255029, P.R. China
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19
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Grayson MH, Feldman S, Prince BT, Patel PJ, Matsui EC, Apter AJ. Advances in asthma in 2017: Mechanisms, biologics, and genetics. J Allergy Clin Immunol 2018; 142:1423-1436. [PMID: 30213625 DOI: 10.1016/j.jaci.2018.08.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 02/07/2023]
Abstract
This review summarizes some of the most significant advances in asthma research over the past year. We first focus on novel discoveries in the mechanism of asthma development and exacerbation. This is followed by a discussion of potential new biomarkers, including the use of radiographic markers of disease. Several new biologics have become available to the clinician in the past year, and we summarize these advances and how they can influence the clinical delivery of asthma care. After this, important findings in the genetics of asthma and heterogeneity in phenotypes of the disease are explored, as is the role the environment plays in shaping the development and exacerbation of asthma. Finally, we conclude with a discussion of advances in health literacy and how they will affect asthma care.
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Affiliation(s)
- Mitchell H Grayson
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio.
| | - Scott Feldman
- Section of Allergy and Immunology, Division of Pulmonary Allergy Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pa
| | - Benjamin T Prince
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio
| | - Priya J Patel
- Section of Allergy and Immunology, Division of Pulmonary Allergy Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pa
| | - Elizabeth C Matsui
- Department of Population Health, Dell Medical School, University of Texas-Austin, Austin, Tex
| | - Andrea J Apter
- Section of Allergy and Immunology, Division of Pulmonary Allergy Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pa
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20
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Mørkve Knudsen T, Rezwan FI, Jiang Y, Karmaus W, Svanes C, Holloway JW. Transgenerational and intergenerational epigenetic inheritance in allergic diseases. J Allergy Clin Immunol 2018; 142:765-772. [PMID: 30040975 PMCID: PMC6167012 DOI: 10.1016/j.jaci.2018.07.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 01/07/2023]
Abstract
It has become clear that early life (including in utero exposures) is a key window of vulnerability during which environmental exposures can alter developmental trajectories and initiate allergic disease development. However, recent evidence suggests that there might be additional windows of vulnerability to environmental exposures in the parental generation before conception or even in previous generations. There is evidence suggesting that information of prior exposures can be transferred across generations, and experimental animal models suggest that such transmission can be conveyed through epigenetic mechanisms. Although the molecular mechanisms of intergenerational and transgenerationational epigenetic transmission have yet to be determined, the realization that environment before conception can alter the risks of allergic diseases has profound implications for the development of public health interventions to prevent disease. Future research in both experimental models and in multigenerational human cohorts is needed to better understand the role of intergenerational and transgenerational effects in patients with asthma and allergic disease. This will provide the knowledge basis for a new approach to efficient intervention strategies aimed at reducing the major public health challenge of these conditions.
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Affiliation(s)
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, Tenn
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, Tenn
| | - Cecilie Svanes
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway; Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
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21
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Davis D, Kannan M, Wattenberg B. Orm/ORMDL proteins: Gate guardians and master regulators. Adv Biol Regul 2018; 70:3-18. [PMID: 30193828 DOI: 10.1016/j.jbior.2018.08.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 12/22/2022]
Abstract
Sphingolipids comprise a diverse family of lipids that perform multiple functions in both structure of cellular membranes and intra- and inter-cellular signaling. The diversity of this family is generated by an array of enzymes that produce individual classes and molecular species of family members and enzymes which catabolize those lipids for recycling pathways. However, all of these lipids begin their lives with a single step, the condensation of an amino acid, almost always serine, and a fatty acyl-CoA, almost always the 16-carbon, saturated fatty acid, palmitate. The enzyme complex that accomplishes this condensation is serine palmitoyltransferase (SPT), a membrane-bound component of the endoplasmic reticulum. This places SPT in the unique position of regulating the production of the entire sphingolipid pool. Understanding how SPT activity is regulated is currently a central focus in the field of sphingolipid biology. In this review we examine the regulation of SPT activity by a set of small, membrane-bound proteins of the endoplasmic reticulum, the Orms (in yeast) and ORMDLs (in vertebrates). We discuss what is known about how these proteins act as homeostatic regulators by monitoring cellular levels of sphingolipid, but also how the Orms/ORMDLs regulate SPT in response to other stimuli. Finally, we discuss the intriguing connection between one of the mammalian ORMDL isoforms, ORMDL3, and the pervasive pulmonary disease, asthma, in humans.
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Affiliation(s)
- Deanna Davis
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Muthukumar Kannan
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Binks Wattenberg
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA.
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