101
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Heijink IH, Kuchibhotla VNS, Roffel MP, Maes T, Knight DA, Sayers I, Nawijn MC. Epithelial cell dysfunction, a major driver of asthma development. Allergy 2020; 75:1902-1917. [PMID: 32460363 PMCID: PMC7496351 DOI: 10.1111/all.14421] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Airway epithelial barrier dysfunction is frequently observed in asthma and may have important implications. The physical barrier function of the airway epithelium is tightly interwoven with its immunomodulatory actions, while abnormal epithelial repair responses may contribute to remodelling of the airway wall. We propose that abnormalities in the airway epithelial barrier play a crucial role in the sensitization to allergens and pathogenesis of asthma. Many of the identified susceptibility genes for asthma are expressed in the airway epithelium, supporting the notion that events at the airway epithelial surface are critical for the development of the disease. However, the exact mechanisms by which the expression of epithelial susceptibility genes translates into a functionally altered response to environmental risk factors of asthma are still unknown. Interactions between genetic factors and epigenetic regulatory mechanisms may be crucial for asthma susceptibility. Understanding these mechanisms may lead to identification of novel targets for asthma intervention by targeting the airway epithelium. Moreover, exciting new insights have come from recent studies using single‐cell RNA sequencing (scRNA‐Seq) to study the airway epithelium in asthma. This review focuses on the role of airway epithelial barrier function in the susceptibility to develop asthma and novel insights in the modulation of epithelial cell dysfunction in asthma.
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Affiliation(s)
- Irene H. Heijink
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Pulmonology University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Virinchi N. S. Kuchibhotla
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan NSW Australia
| | - Mirjam P. Roffel
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Respiratory Medicine Laboratory for Translational Research in Obstructive Pulmonary Diseases Ghent University Hospital Ghent University Ghent Belgium
| | - Tania Maes
- Department of Respiratory Medicine Laboratory for Translational Research in Obstructive Pulmonary Diseases Ghent University Hospital Ghent University Ghent Belgium
| | - Darryl A. Knight
- School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan NSW Australia
- UBC Providence Health Care Research Institute Vancouver BC Canada
- Department of Anesthesiology, Pharmacology and Therapeutics University of British Columbia Vancouver BC Canada
| | - Ian Sayers
- Division of Respiratory Medicine National Institute for Health Research Nottingham Biomedical Research Centre University of Nottingham Biodiscovery Institute University of Nottingham Nottingham UK
| | - Martijn C. Nawijn
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
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102
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Wang Y, Shi P, Chen Q, Huang Z, Zou D, Zhang J, Gao X, Lin Z. Mitochondrial ROS promote macrophage pyroptosis by inducing GSDMD oxidation. J Mol Cell Biol 2020; 11:1069-1082. [PMID: 30860577 PMCID: PMC6934151 DOI: 10.1093/jmcb/mjz020] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/10/2019] [Accepted: 03/08/2019] [Indexed: 01/03/2023] Open
Abstract
Disrupted mitochondrial membrane potential (MMP) and reactive oxygen species (ROS) generation are often associated with macrophage pyroptosis. It remains unclear how these forms of mitochondrial dysfunction relate to inflammasome activation and gasdermin-D (Gsdmd) cleavage, two central steps of the pyroptotic process. Here, we also found MMP collapse and ROS generation induced by Nlrp3 inflammasome activation as previous studies reported. The elimination of ROS alleviated the cleavage of Gsdmd, suggesting that Gsdmd cleavage occurs downstream of ROS release. Consistent with this result, hydrogen peroxide treatment augmented the cleavage of Gsdmd by caspase-1. Indeed, four amino acid residues of Gsdmd were oxidized under oxidative stress in macrophages. The efficiency of Gsdmd cleavage by inflammatory caspase-1 was dramatically reduced when oxidative modification was blocked by mutation of these amino acid residues. These results demonstrate that Gsdmd oxidation serves as a de novo mechanism by which mitochondrial ROS promote Nlrp3 inflammasome-dependent pyroptotic cell death.
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Affiliation(s)
- Yufang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Peiliang Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Qin Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Zan Huang
- Jiangsu Province Key Laboratory of Gastrointestinal Nutrition and Animal Health, Nanjing Agriculture University, Nanjing 210095, China
| | - Dayuan Zou
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Jingzi Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Xiang Gao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Zhaoyu Lin
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Hepatopancreatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
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103
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Chen Q, Shi P, Wang Y, Zou D, Wu X, Wang D, Hu Q, Zou Y, Huang Z, Ren J, Lin Z, Gao X. GSDMB promotes non-canonical pyroptosis by enhancing caspase-4 activity. J Mol Cell Biol 2020; 11:496-508. [PMID: 30321352 DOI: 10.1093/jmcb/mjy056] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/08/2018] [Accepted: 10/13/2018] [Indexed: 12/11/2022] Open
Abstract
Gasdermin B (GSDMB) has been reported to be associated with immune diseases in humans, but the detailed molecular mechanisms remain unsolved. The N-terminus of GSDMB by itself, unlike other gasdermin family proteins, does not induce cell death. Here, we show that GSDMB is highly expressed in the leukocytes of septic shock patients, which is associated with increased release of the gasdermin D (GSDMD) N-terminus. GSDMB expression and the accumulation of the N-terminal fragment of GSDMD are induced by the activation of the non-canonical pyroptosis pathway in a human monocyte cell line. The downregulation of GSDMB alleviates the cleavage of GSDMD and cell death. Consistently, the overexpression of GSDMB promotes GSDMD cleavage, accompanied by increased LDH release. We further found that GSDMB promotes caspase-4 activity, which is required for the cleavage of GSDMD in non-canonical pyroptosis, by directly binding to the CARD domain of caspase-4. Our study reveals a GSDMB-mediated novel regulatory mechanism for non-canonical pyroptosis and suggests a potential new strategy for the treatment of inflammatory diseases.
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Affiliation(s)
- Qin Chen
- State Key Laboratory of Pharmaceutical Biotechnology and Nanjing Drum Tower Hospital, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Peiliang Shi
- State Key Laboratory of Pharmaceutical Biotechnology and Nanjing Drum Tower Hospital, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Yufang Wang
- State Key Laboratory of Pharmaceutical Biotechnology and Nanjing Drum Tower Hospital, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Dayuan Zou
- State Key Laboratory of Pharmaceutical Biotechnology and Nanjing Drum Tower Hospital, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Xiuwen Wu
- Department of Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Dingyu Wang
- State Key Laboratory of Pharmaceutical Biotechnology and Nanjing Drum Tower Hospital, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Qiongyuan Hu
- Department of Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yujie Zou
- State Key Laboratory of Pharmaceutical Biotechnology and Nanjing Drum Tower Hospital, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Zan Huang
- State Key Laboratory of Pharmaceutical Biotechnology and Nanjing Drum Tower Hospital, Model Animal Research Center, Nanjing University, Nanjing, China.,Jiangsu Province Key Laboratory of Gastrointestinal Nutrition and Animal Health, Nanjing Agriculture University, Nanjing, China
| | - Jianan Ren
- Department of Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhaoyu Lin
- State Key Laboratory of Pharmaceutical Biotechnology and Nanjing Drum Tower Hospital, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Xiang Gao
- State Key Laboratory of Pharmaceutical Biotechnology and Nanjing Drum Tower Hospital, Model Animal Research Center, Nanjing University, Nanjing, China
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104
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Zheng Z, Deng W, Lou X, Bai Y, Wang J, Zeng H, Gong S, Liu X. Gasdermins: pore-forming activities and beyond. Acta Biochim Biophys Sin (Shanghai) 2020; 52:467-474. [PMID: 32294153 DOI: 10.1093/abbs/gmaa016] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/28/2020] [Indexed: 11/13/2022] Open
Abstract
Gasdermins (GSDMs) belong to a protein superfamily that is found only in vertebrates and consists of GSDMA, GSDMB, GSDMC, GSDMD, DFNA5 (a.k.a. GSDME) and DFNB59 (a.k.a. Pejvakin (PJVK)) in humans. Except for DFNB59, all members of the GSDM superfamily contain a conserved two-domain structure (N-terminal and C-terminal domains) and share an autoinhibitory mechanism. When the N-terminal domain of these GSDMs is released, it possesses pore-forming activity that causes inflammatory death associated with the loss of cell membrane integrity and release of inflammatory mediators. It has also been found that spontaneous mutations occurring in the genes of GSDMs have been associated with the development of certain autoimmune disorders, as well as cancers. Here, we review the current knowledge of the expression profile and regulation of GSDMs and the important roles of this protein family in inflammatory cell death, tumorigenesis and other related diseases.
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Affiliation(s)
- Zengzhang Zheng
- The Joint Center for Infection and Immunity between Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, 510623, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wanyan Deng
- The Joint Center for Infection and Immunity between Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, 510623, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiwen Lou
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Bai
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junhong Wang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Huasong Zeng
- The Joint Center for Infection and Immunity between Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, 510623, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sitang Gong
- The Joint Center for Infection and Immunity between Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, 510623, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xing Liu
- The Joint Center for Infection and Immunity between Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, 510623, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
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105
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Stuart WD, Guo M, Fink-Baldauf IM, Coleman AM, Clancy JP, Mall MA, Lim FY, Brewington JJ, Maeda Y. CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions. NAR Genom Bioinform 2020; 2:lqaa036. [PMID: 32500120 PMCID: PMC7252574 DOI: 10.1093/nargab/lqaa036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 04/24/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies have identified lung disease-associated loci; however, the functions of such loci are not well understood in part because the majority of such loci are located at non-coding regions. Hi-C, ChIP-seq and eQTL data predict potential roles (e.g. enhancer) of such loci; however, they do not elucidate the molecular function. To determine whether these loci function as gene-regulatory regions, CRISPR interference (CRISPRi; CRISPR/dCas9-KRAB) has been recently used. Here, we applied CRISPRi along with Hi-C, ChIP-seq and eQTL to determine the functional roles of loci established as highly associated with asthma, cystic fibrosis (CF), chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Notably, Hi-C, ChIP-seq and eQTL predicted that non-coding regions located at chromosome 19q13 or chromosome 17q21 harboring single-nucleotide polymorphisms (SNPs) linked to asthma/CF/COPD and chromosome 11p15 harboring an SNP linked to IPF interact with nearby genes and function as enhancers; however, CRISPRi indicated that the regions with rs1800469, rs2241712, rs12603332 and rs35705950, but not others, regulate the expression of nearby genes (single or multiple genes). These data indicate that CRISPRi is useful to precisely determine the roles of non-coding regions harboring lung disease-associated loci as to whether they function as gene-regulatory regions at a genomic level.
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Affiliation(s)
- William D Stuart
- Division of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Minzhe Guo
- Division of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Iris M Fink-Baldauf
- Division of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Alan M Coleman
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.,Cincinnati Fetal Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John P Clancy
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.,Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marcus A Mall
- Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, 13353, Germany.,Berlin Institute of Health, Berlin, 10178, Germany.,German Center for Lung Research, Berlin, 13353, Germany
| | - Foong-Yen Lim
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.,Cincinnati Fetal Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John J Brewington
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.,Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yutaka Maeda
- Division of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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106
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Abstract
Immune cells use a variety of membrane-disrupting proteins [complement, perforin, perforin-2, granulysin, gasdermins, mixed lineage kinase domain-like pseudokinase (MLKL)] to induce different kinds of death of microbes and host cells, some of which cause inflammation. After activation by proteolytic cleavage or phosphorylation, these proteins oligomerize, bind to membrane lipids, and disrupt membrane integrity. These membrane disruptors play a critical role in both innate and adaptive immunity. Here we review our current knowledge of the functions, specificity, activation, and regulation of membrane-disrupting immune proteins and what is known about the mechanisms behind membrane damage, the structure of the pores they form, how the cells expressing these lethal proteins are protected, and how cells targeted for destruction can sometimes escape death by repairing membrane damage.
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Affiliation(s)
- Xing Liu
- Center for Microbes, Development and Health; Key Laboratory of Molecular Virology and Immunology; Institut Pasteur of Shanghai; Chinese Academy of Sciences, Shanghai 200031, China;
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA;
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107
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Gasdermin family: a promising therapeutic target for cancers and inflammation-driven diseases. J Cell Commun Signal 2020; 14:293-301. [PMID: 32236886 DOI: 10.1007/s12079-020-00564-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
This review focuses on current advances in researches of gasdermin family. The distinctive expression patterns and biological roles of members in this family were discussed. Most of them exhibit pore-forming activity on cell membranes and are executors for programmed cell death with cytokines release, and play roles in cancers and inflammation-driven diseases. Therefore, they can be used as potential therapeutic targets to treat related diseases.
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108
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Maiorino E, Baek SH, Guo F, Zhou X, Kothari PH, Silverman EK, Barabási AL, Weiss ST, Raby BA, Sharma A. Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. Nat Commun 2020; 11:811. [PMID: 32041952 PMCID: PMC7010776 DOI: 10.1038/s41467-020-14600-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 01/17/2020] [Indexed: 12/21/2022] Open
Abstract
The molecular and clinical features of a complex disease can be influenced by other diseases affecting the same individual. Understanding disease-disease interactions is therefore crucial for revealing shared molecular mechanisms among diseases and designing effective treatments. Here we introduce Flow Centrality (FC), a network-based approach to identify the genes mediating the interaction between two diseases in a protein-protein interaction network. We focus on asthma and COPD, two chronic respiratory diseases that have been long hypothesized to share common genetic determinants and mechanisms. We show that FC highlights potential mediator genes between the two diseases, and observe similar outcomes when applying FC to 66 additional pairs of related diseases. Further, we perform in vitro perturbation experiments on a widely replicated asthma gene, GSDMB, showing that FC identifies candidate mediators of the interactions between GSDMB and COPD-associated genes. Our results indicate that FC predicts promising gene candidates for further study of disease-disease interactions.
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Affiliation(s)
- Enrico Maiorino
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Network Science Institute, Center for Complex Network Research, Department of Physics, Northeastern University, Boston, MA, USA.
| | - Seung Han Baek
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Feng Guo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Parul H Kothari
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Albert-László Barabási
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Network Science Institute, Center for Complex Network Research, Department of Physics, Northeastern University, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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109
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Structural Insight of Gasdermin Family Driving Pyroptotic Cell Death. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1172:189-205. [DOI: 10.1007/978-981-13-9367-9_9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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110
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Wu J, Lin S, Wan B, Velani B, Zhu Y. Pyroptosis in Liver Disease: New Insights into Disease Mechanisms. Aging Dis 2019; 10:1094-1108. [PMID: 31595205 PMCID: PMC6764727 DOI: 10.14336/ad.2019.0116] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/16/2019] [Indexed: 12/12/2022] Open
Abstract
There has been increasing interest in pyroptosis as a novel form of pro-inflammatory programmed cell death. The mechanism of pyroptosis is significantly different from other forms of cell death in its morphological and biochemical features. Pyroptosis is characterized by the activation of two different types of caspase enzymes—caspase-1 and caspase-4/5/11, and by the occurrence of a proinflammatory cytokine cascade and an immune response. Pyroptosis participates in the immune defense mechanisms against intracellular bacterial infections. On the other hand, excessive inflammasome activation can induce sterile inflammation and eventually cause some diseases, such as acute or chronic hepatitis and liver fibrosis. The mechanism and biological significance of this novel form of cell death in different liver diseases will be evaluated in this review. Specifically, we will focus on the role of pyroptosis in alcoholic and non-alcoholic fatty liver disease, as well as in liver failure. Finally, the therapeutic implications of pyroptosis in liver diseases will be discussed.
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Affiliation(s)
- Jiali Wu
- 1Liver research center of the First Affiliated Hospital of Fujian Medical University, Fujian 350005, China
| | - Su Lin
- 1Liver research center of the First Affiliated Hospital of Fujian Medical University, Fujian 350005, China
| | - Bo Wan
- 2Faculty of Life Sciences and Medicine, King's College London, London SE1 1UL, United Kingdom
| | - Bharat Velani
- 3Basildon and Thurrock University Hospitals NHS Foundation Trust, Nethermayne, Basildon, Essex SS16 5NL, United Kingdom
| | - Yueyong Zhu
- 1Liver research center of the First Affiliated Hospital of Fujian Medical University, Fujian 350005, China
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111
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Maeda K, Caldez MJ, Akira S. Innate immunity in allergy. Allergy 2019; 74:1660-1674. [PMID: 30891811 PMCID: PMC6790574 DOI: 10.1111/all.13788] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/26/2019] [Accepted: 03/10/2019] [Indexed: 12/13/2022]
Abstract
Innate immune system quickly responds to invasion of microbes and foreign substances through the extracellular and intracellular sensing receptors, which recognize distinctive molecular and structural patterns. The recognition of innate immune receptors leads to the induction of inflammatory and adaptive immune responses by activating downstream signaling pathways. Allergy is an immune-related disease and results from a hypersensitive immune response to harmless substances in the environment. However, less is known about the activation of innate immunity during exposure to allergens. New insights into the innate immune system by sensors and their signaling cascades provide us with more important clues and a framework for understanding allergy disorders. In this review, we will focus on recent advances in the innate immune sensing system.
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Affiliation(s)
- Kazuhiko Maeda
- Laboratory of Host Defense, The World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC) Osaka University Osaka Japan
| | - Matias J. Caldez
- Laboratory of Host Defense, The World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC) Osaka University Osaka Japan
| | - Shizuo Akira
- Laboratory of Host Defense, The World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC) Osaka University Osaka Japan
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112
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Yu XH, He M, Zheng XR, Wang X, Kuang J. [Levels of airway inflammatory mediators in peripheral blood in infants and young children with wheezing]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2019; 21:861-867. [PMID: 31506143 PMCID: PMC7390249 DOI: 10.7499/j.issn.1008-8830.2019.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To examine the levels of airway inflammatory mediators in peripheral blood in infants and young children with wheezing and to study the possible pathogenesis of wheezing from the aspects of T helper cell 1 (Th1)/T helper cell 2 (Th2) imbalance and airway inflammation. METHODS A total of 50 children aged 1 month to 3 years with an acute wheezing episode were enrolled as the wheezing group, and 25 age-matched healthy infants were enrolled as the healthy control group. According to the number of wheezing episodes, the wheezing group was divided into a first-episode group (n=25) and a recurrent wheezing (number of episodes ≥2) group (n=25). According to the presence or absence of high-risk factors for asthma, the wheezing group was divided into a high-risk factor group (n=22) and a non-high-risk factor group (n=28). According to the results of pathogen detection, the wheezing group was divided into a positive pathogen group (n=23) and a negative pathogen group (n=27). Levels of interleukin-2 (IL-2), interleukin-4 (IL-4), interleukin-5 (IL-5), interleukin-13 (IL-13), transforming growth factor-β1 (TGF-β1), and total IgE (TIgE) in peripheral blood were measured for each group. For children with wheezing, eosinophil (EOS) count in peripheral blood was measured, and related samples were collected for respiratory pathogen detection. RESULTS The wheezing group had significantly higher levels of IL-4, IL-5, IL-13, TGF-β1, and TIgE in peripheral blood than the healthy control group (P<0.05). There were no significant differences in the levels of IL-2, IL-4, IL-5, IL-13, TGF-β1, and TIgE in peripheral blood between the first-episode and recurrent wheezing groups, between the high-risk factor and non-high-risk factor groups, and between the positive pathogen and negative pathogen groups (P>0.05). The correlation analysis showed that in children with wheezing, EOS count was positively correlated with IL-4 level (P<0.01), IL-4 level was positively correlated with IL-5 and IL-13 levels (P<0.01), IL-5 level was positively correlated with IL-13 level (P<0.01), and IL-2 level was positively correlated with TGF-β1 level (P<0.05). CONCLUSIONS Th1/Th2 imbalance with a predominance of Th2 is observed in infants and young children with wheezing. IL-4, IL-5, IL-13, TGF-β1, and IgE are involved in the pathogenesis of wheezing in these children. Airway inflammation is also observed in these children with wheezing, but it is not associated with the number of wheezing episodes, presence or absence of high-risk factors for asthma, or results of pathogen detection.
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Affiliation(s)
- Xiao-He Yu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha 410008, China.
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Willis-Owen SAG, Cookson WOC, Moffatt MF. The Genetics and Genomics of Asthma. Annu Rev Genomics Hum Genet 2019; 19:223-246. [PMID: 30169121 DOI: 10.1146/annurev-genom-083117-021651] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Asthma is a common, clinically heterogeneous disease with strong evidence of heritability. Progress in defining the genetic underpinnings of asthma, however, has been slow and hampered by issues of inconsistency. Recent advances in the tools available for analysis-assaying transcription, sequence variation, and epigenetic marks on a genome-wide scale-have substantially altered this landscape. Applications of such approaches are consistent with heterogeneity at the level of causation and specify patterns of commonality with a wide range of alternative disease traits. Looking beyond the individual as the unit of study, advances in technology have also fostered comprehensive analysis of the human microbiome and its varied roles in health and disease. In this article, we consider the implications of these technological advances for our current understanding of the genetics and genomics of asthma.
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Affiliation(s)
- Saffron A G Willis-Owen
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; , ,
| | - William O C Cookson
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; , ,
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; , ,
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Abstract
PURPOSE OF REVIEW This article reviews the progress in the search for the genetic determinants of severe asthma. RECENT FINDINGS Twin studies estimate that approximately 25% of the phenotypic variability in asthma severity is determined by genetic factors, with the remainder determined by nongenetic factors including environmental and psychosocial factors, behavioral traits, and comorbidities. Most genetic association studies of asthma severity performed to date are underpowered and not designed to clearly distinguish asthma severity variants from asthma susceptibility variants. However, the most recent genome-wide asthma severity association study, conducted in more than 57 000 individuals, demonstrated significant associations for 25 loci, including three not previously associated with asthma: GATA3, MUC5AC, and KIAA1109. Of these, the MUC5AC association was restricted to cohorts that included moderate-to-severe (but not mild) asthma. Additional insights from rare monogenic disorders that can present as severe asthma include recognition that loss-of-function variants in the filaggrin gene known to cause ichthyosis vulgaris are consistently associated with more severe asthma outcomes. Other notable loci of interest include RAD50-IL13 on chromosome 5q and the ORMDL3-GSDMB locus on chromosome 17q21. SUMMARY Severe asthma is a polygenic trait. Future research should explore the role of rare genetic variation and gene-by-environment interaction.
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Hur GY, Broide DH. Genes and Pathways Regulating Decline in Lung Function and Airway Remodeling in Asthma. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2019; 11:604-621. [PMID: 31332973 PMCID: PMC6658410 DOI: 10.4168/aair.2019.11.5.604] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/15/2019] [Accepted: 04/19/2019] [Indexed: 12/14/2022]
Abstract
Asthma is a common disorder of the airways characterized by airway inflammation and by decline in lung function and airway remodeling in a subset of asthmatics. Airway remodeling is characterized by structural changes which include airway smooth muscle hypertrophy/hyperplasia, subepithelial fibrosis due to thickening of the reticular basement membrane, mucus metaplasia of the epithelium, and angiogenesis. Epidemiologic studies suggest that both genetic and environmental factors may contribute to decline in lung function and airway remodeling in a subset of asthmatics. Environmental factors include respiratory viral infection-triggered asthma exacerbations, and tobacco smoke. There is also evidence that several asthma candidate genes may contribute to decline in lung function, including ADAM33, PLAUR, VEGF, IL13, CHI3L1, TSLP, GSDMB, TGFB1, POSTN, ESR1 and ARG2. In addition, mediators or cytokines, including cysteinyl leukotrienes, matrix metallopeptidase-9, interleukin-33 and eosinophil expression of transforming growth factor-β, may contribute to airway remodeling in asthma. Although increased airway smooth muscle is associated with reduced lung function (i.e. forced expiratory volume in 1 second) in asthma, there have been few long-term studies to determine how individual pathologic features of airway remodeling contribute to decline in lung function in asthma. Clinical studies with inhibitors of individual gene products, cytokines or mediators are needed in asthmatic patients to identify their individual role in decline in lung function and/or airway remodeling.
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Affiliation(s)
- Gyu Young Hur
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea.,Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - David H Broide
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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116
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Shrine N, Portelli MA, John C, Soler Artigas M, Bennett N, Hall R, Lewis J, Henry AP, Billington CK, Ahmad A, Packer RJ, Shaw D, Pogson ZEK, Fogarty A, McKeever TM, Singapuri A, Heaney LG, Mansur AH, Chaudhuri R, Thomson NC, Holloway JW, Lockett GA, Howarth PH, Djukanovic R, Hankinson J, Niven R, Simpson A, Chung KF, Sterk PJ, Blakey JD, Adcock IM, Hu S, Guo Y, Obeidat M, Sin DD, van den Berge M, Nickle DC, Bossé Y, Tobin MD, Hall IP, Brightling CE, Wain LV, Sayers I. Moderate-to-severe asthma in individuals of European ancestry: a genome-wide association study. THE LANCET. RESPIRATORY MEDICINE 2019; 7:20-34. [PMID: 30552067 PMCID: PMC6314966 DOI: 10.1016/s2213-2600(18)30389-8] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Few genetic studies that focus on moderate-to-severe asthma exist. We aimed to identity novel genetic variants associated with moderate-to-severe asthma, see whether previously identified genetic variants for all types of asthma contribute to moderate-to-severe asthma, and provide novel mechanistic insights using expression analyses in patients with asthma. METHODS In this genome-wide association study, we used a two-stage case-control design. In stage 1, we genotyped patient-level data from two UK cohorts (the Genetics of Asthma Severity and Phenotypes [GASP] initiative and the Unbiased BIOmarkers in PREDiction of respiratory disease outcomes [U-BIOPRED] project) and used data from the UK Biobank to collect patient-level genomic data for cases and controls of European ancestry in a 1:5 ratio. Cases were defined as having moderate-to-severe asthma if they were taking appropriate medication or had been diagnosed by a doctor. Controls were defined as not having asthma, rhinitis, eczema, allergy, emphysema, or chronic bronchitis as diagnosed by a doctor. For stage 2, an independent cohort of cases and controls (1:5) was selected from the UK Biobank only, with no overlap with stage 1 samples. In stage 1 we undertook a genome-wide association study of moderate-to-severe asthma, and in stage 2 we followed up independent variants that reached the significance threshold of p less than 1 × 10-6 in stage 1. We set genome-wide significance at p less than 5 × 10-8. For novel signals, we investigated their effect on all types of asthma (mild, moderate, and severe). For all signals meeting genome-wide significance, we investigated their effect on gene expression in patients with asthma and controls. FINDINGS We included 5135 cases and 25 675 controls for stage 1, and 5414 cases and 21 471 controls for stage 2. We identified 24 genome-wide significant signals of association with moderate-to-severe asthma, including several signals in innate or adaptive immune-response genes. Three novel signals were identified: rs10905284 in GATA3 (coded allele A, odds ratio [OR] 0·90, 95% CI 0·88-0·93; p=1·76 × 10-10), rs11603634 in the MUC5AC region (coded allele G, OR 1·09, 1·06-1·12; p=2·32 × 10-8), and rs560026225 near KIAA1109 (coded allele GATT, OR 1·12, 1·08-1·16; p=3·06 × 10-9). The MUC5AC signal was not associated with asthma when analyses included mild asthma. The rs11603634 G allele was associated with increased expression of MUC5AC mRNA in bronchial epithelial brush samples via proxy SNP rs11602802; (p=2·50 × 10-5) and MUC5AC mRNA was increased in bronchial epithelial samples from patients with severe asthma (in two independent analyses, p=0·039 and p=0·022). INTERPRETATION We found substantial shared genetic architecture between mild and moderate-to-severe asthma. We also report for the first time genetic variants associated with the risk of developing moderate-to-severe asthma that regulate mucin production. Finally, we identify candidate causal genes in these loci and provide increased insight into this difficult to treat population. FUNDING Asthma UK, AirPROM, U-BIOPRED, UK Medical Research Council, and Rosetrees Trust.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Michael A Portelli
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Catherine John
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Neil Bennett
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Robert Hall
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Jon Lewis
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Amanda P Henry
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Charlotte K Billington
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Azaz Ahmad
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Richard J Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Dominick Shaw
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Zara E K Pogson
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
| | - Andrew Fogarty
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
| | - Tricia M McKeever
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
| | - Amisha Singapuri
- Institute for Lung Health, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK; Glenfield Hospital, Leicester, UK
| | - Liam G Heaney
- Centre for Infection and Immunity, Queen's University of Belfast, Belfast, UK
| | - Adel H Mansur
- Respiratory Medicine, Birmingham Heartlands Hospital and University of Birmingham, Birmingham, UK
| | - Rekha Chaudhuri
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Neil C Thomson
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - John W Holloway
- Human Development and Health, Clinical and Experimental Sciences, Faculty of Medicine and National Institute of Health Biomedical Research Centre, Southampton, University of Southampton, Southampton, UK
| | - Gabrielle A Lockett
- Human Development and Health, Clinical and Experimental Sciences, Faculty of Medicine and National Institute of Health Biomedical Research Centre, Southampton, University of Southampton, Southampton, UK
| | - Peter H Howarth
- Human Development and Health, Clinical and Experimental Sciences, Faculty of Medicine and National Institute of Health Biomedical Research Centre, Southampton, University of Southampton, Southampton, UK
| | - Ratko Djukanovic
- Human Development and Health, Clinical and Experimental Sciences, Faculty of Medicine and National Institute of Health Biomedical Research Centre, Southampton, University of Southampton, Southampton, UK
| | - Jenny Hankinson
- Division of Infection Immunity and Respiratory Medicine, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation Trust, Manchester, UK
| | - Robert Niven
- Division of Infection Immunity and Respiratory Medicine, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation Trust, Manchester, UK
| | - Angela Simpson
- Division of Infection Immunity and Respiratory Medicine, The University of Manchester, Manchester Academic Health Science Centre, and Manchester University NHS Foundation Trust, Manchester, UK
| | - Kian Fan Chung
- The National Heart and Lung Institute, Imperial College, London, UK
| | - Peter J Sterk
- Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - John D Blakey
- Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Ian M Adcock
- The National Heart and Lung Institute, Imperial College, London, UK
| | - Sile Hu
- Data Science Institute, Imperial College, London, UK
| | - Yike Guo
- Data Science Institute, Imperial College, London, UK
| | - Maen Obeidat
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, Vancouver, BC, Canada
| | - Don D Sin
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, Vancouver, BC, Canada; Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen Research Institute for Asthma and COPD Research Institute, Groningen, Netherlands
| | | | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Ian P Hall
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Christopher E Brightling
- Institute for Lung Health, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, University of Leicester, Leicester, UK; Glenfield Hospital, Leicester, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Ian Sayers
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK.
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Panganiban RA, Sun M, Dahlin A, Park HR, Kan M, Himes BE, Mitchel JA, Iribarren C, Jorgenson E, Randell SH, Israel E, Tantisira K, Shore S, Park JA, Weiss ST, Wu AC, Lu Q. A functional splice variant associated with decreased asthma risk abolishes the ability of gasdermin B to induce epithelial cell pyroptosis. J Allergy Clin Immunol 2018; 142:1469-1478.e2. [PMID: 29330013 PMCID: PMC6037620 DOI: 10.1016/j.jaci.2017.11.040] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 11/12/2017] [Accepted: 11/22/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Genetic variants in the chromosomal region 17q21 are consistently associated with asthma. However, mechanistic studies have not yet linked any of the associated variants to a function that could influence asthma, and as a result, the identity of the asthma gene(s) remains elusive. OBJECTIVES We sought to identify and characterize functional variants in the 17q21 locus. METHODS We used the Exome Aggregation Consortium browser to identify coding (amino acid-changing) variants in the 17q21 locus. We obtained asthma association measures for these variants in both the Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort (16,274 cases and 38,269 matched controls) and the EVE Consortium study (5,303 asthma cases and 12,560 individuals). Gene expression and protein localization were determined by quantitative RT-PCR and fluorescence immunostaining, respectively. Molecular and cellular studies were performed to determine the functional effects of coding variants. RESULTS Two coding variants (rs2305480 and rs11078928) of the gasdermin B (GSDMB) gene in the 17q21 locus were associated with lower asthma risk in both GERA (odds ratio, 0.92; P = 1.01 × 10-6) and EVE (odds ratio, 0.85; joint PEVE = 1.31 × 10-13). In GERA, rs11078928 had a minor allele frequency (MAF) of 0.45 in unaffected (nonasthmatic) controls and 0.43 in asthma cases. For European Americans in EVE, the MAF of rs2305480 was 0.45 for controls and 0.39 for cases; for all EVE subjects, the MAF was 0.32 for controls and 0.27 for cases. GSDMB is highly expressed in differentiated airway epithelial cells, including the ciliated cells. We found that, when the GSDMB protein is cleaved by inflammatory caspase-1 to release its N-terminal fragment, potent pyroptotic cell death is induced. The splice variant rs11078928 deletes the entire exon 6, which encodes 13 amino acids in the critical N-terminus, and abolishes the pyroptotic activity of the GSDMB protein. CONCLUSIONS Our study identified a functional asthma variant in the GSDMB gene of the 17q21 locus and implicates GSDMB-mediated epithelial cell pyroptosis in pathogenesis.
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Affiliation(s)
- Ronald A Panganiban
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Maoyun Sun
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Hae-Ryung Park
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer A Mitchel
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Center, University of North Carolina, Chapel Hill, NC
| | - Elliot Israel
- Asthma Research Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Stephanie Shore
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Jin-Ah Park
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Ann Chen Wu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School, Boston, Mass
| | - Quan Lu
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass.
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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: 53] [Impact Index Per Article: 8.8] [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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Miller M, Vuong C, Garcia MF, Rosenthal P, Das S, Weng N, Pham A, Kim YJ, Broide DH. Does reduced zona pellucida binding protein 2 (ZPBP2) expression on chromosome 17q21 protect against asthma? J Allergy Clin Immunol 2018; 142:706-709.e4. [PMID: 29709669 PMCID: PMC6078789 DOI: 10.1016/j.jaci.2018.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/09/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022]
Affiliation(s)
- Marina Miller
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - Christine Vuong
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | | | - Peter Rosenthal
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - Sudipta Das
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - Ning Weng
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - Alexa Pham
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - Yu Jin Kim
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - David H Broide
- Department of Medicine, University of California San Diego, La Jolla, Calif.
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Feng S, Fox D, Man SM. Mechanisms of Gasdermin Family Members in Inflammasome Signaling and Cell Death. J Mol Biol 2018; 430:3068-3080. [PMID: 29990470 DOI: 10.1016/j.jmb.2018.07.002] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/25/2018] [Accepted: 07/04/2018] [Indexed: 12/16/2022]
Abstract
The Gasdermin (GSDM) family consists of Gasdermin A (GSDMA), Gasdermin B (GSDMB), Gasdermin C (GSDMC), Gasdermin D (GSDMD), Gasdermin E (GSDME) and Pejvakin (PJVK). GSDMD is activated by inflammasome-associated inflammatory caspases. Cleavage of GSDMD by human or mouse caspase-1, human caspase-4, human caspase-5, and mouse caspase-11 liberates the N-terminal effector domain from the C-terminal inhibitory domain. The N-terminal domain oligomerizes in the cell membrane and forms a pore of 10-16 nm in diameter, through which substrates of a smaller diameter, such as interleukin-1β and interleukin-18, are secreted. The increasing abundance of membrane pores ultimately leads to membrane rupture and pyroptosis, releasing the entire cellular content. Other than GSDMD, the N-terminal domain of all GSDMs, with the exception of PJVK, have the ability to form pores. There is evidence to suggest that GSDMB and GSDME are cleaved by apoptotic caspases. Here, we review the mechanistic functions of GSDM proteins with respect to their expression and signaling profile in the cell, with more focused discussions on inflammasome activation and cell death.
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Affiliation(s)
- Shouya Feng
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Daniel Fox
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Si Ming Man
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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Tliba O, Panettieri RA. Paucigranulocytic asthma: Uncoupling of airway obstruction from inflammation. J Allergy Clin Immunol 2018; 143:1287-1294. [PMID: 29928921 DOI: 10.1016/j.jaci.2018.06.008] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/17/2018] [Accepted: 06/01/2018] [Indexed: 01/01/2023]
Abstract
Among patients with asthma, heterogeneity exists regarding the pattern of airway inflammation and response to treatment, prompting the necessity of recognizing specific phenotypes. Based on the analysis of inflammatory cell counts in induced sputum, asthmatic patients can be classified into 4 unique phenotypes: eosinophilic asthma, neutrophilic asthma, mixed granulocytic asthma, and paucigranulocytic asthma (PGA). PGA is an asthma phenotype with no evidence of increased numbers of eosinophils or neutrophils in sputum or blood and in which anti-inflammatory therapies are ineffective at controlling symptoms. Although underinvestigated, PGA is the most common asthma phenotype in patients with stable asthma. However, PGA is sometimes underestimated because of the exclusive reliance on induced sputum cell counts, which are variable among cohorts of studies, prompting the necessity of developing improved biomarkers. Importantly, investigators have reported that inhaled corticosteroids had a limited effect on airway inflammatory markers in patients with PGA and therefore defining PGA as a potentially "steroid-insensitive" phenotype that requires exploration of alternative therapies. PGA manifests as an uncoupling of airway obstruction from airway inflammation that can be driven by structural changes within the airways, such as airway smooth muscle tissue hypertrophy. Animal models provide evidence that processes evoking airway hyperresponsiveness and airway smooth muscle thickening occur independent from inflammation and might be a consequence of a loss of negative homeostatic processes. Collectively, further understanding of PGA with a focus on the characterization, prevalence, clinical significance, and pathobiology derived from animal studies will likely provide precision therapies that will improve PGA clinical outcomes.
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Affiliation(s)
- Omar Tliba
- Rutgers Institute for Translational Medicine & Science, Robert Wood Johnson School of Medicine, Rutgers, State University of New Jersey, New Brunswick, NJ
| | - Reynold A Panettieri
- Rutgers Institute for Translational Medicine & Science, Robert Wood Johnson School of Medicine, Rutgers, State University of New Jersey, New Brunswick, NJ.
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122
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Emdin CA, Khera AV, Chaffin M, Klarin D, Natarajan P, Aragam K, Haas M, Bick A, Zekavat SM, Nomura A, Ardissino D, Wilson JG, Schunkert H, McPherson R, Watkins H, Elosua R, Bown MJ, Samani NJ, Baber U, Erdmann J, Gupta N, Danesh J, Chasman D, Ridker P, Denny J, Bastarache L, Lichtman JH, D'Onofrio G, Mattera J, Spertus JA, Sheu WHH, Taylor KD, Psaty BM, Rich SS, Post W, Rotter JI, Chen YDI, Krumholz H, Saleheen D, Gabriel S, Kathiresan S. Analysis of predicted loss-of-function variants in UK Biobank identifies variants protective for disease. Nat Commun 2018; 9:1613. [PMID: 29691411 PMCID: PMC5915445 DOI: 10.1038/s41467-018-03911-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/21/2018] [Indexed: 02/02/2023] Open
Abstract
Less than 3% of protein-coding genetic variants are predicted to result in loss of protein function through the introduction of a stop codon, frameshift, or the disruption of an essential splice site; however, such predicted loss-of-function (pLOF) variants provide insight into effector transcript and direction of biological effect. In >400,000 UK Biobank participants, we conduct association analyses of 3759 pLOF variants with six metabolic traits, six cardiometabolic diseases, and twelve additional diseases. We identified 18 new low-frequency or rare (allele frequency < 5%) pLOF variant-phenotype associations. pLOF variants in the gene GPR151 protect against obesity and type 2 diabetes, in the gene IL33 against asthma and allergic disease, and in the gene IFIH1 against hypothyroidism. In the gene PDE3B, pLOF variants associate with elevated height, improved body fat distribution and protection from coronary artery disease. Our findings prioritize genes for which pharmacologic mimics of pLOF variants may lower risk for disease.
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Affiliation(s)
- Connor A Emdin
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Amit V Khera
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Mark Chaffin
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Derek Klarin
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Krishna Aragam
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Mary Haas
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Alexander Bick
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Seyedeh M Zekavat
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
- Department of Computational Biology & Bioinformatics, Yale Medical School, Yale University, New Haven, MA, 06510, USA
| | - Akihiro Nomura
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Diego Ardissino
- Division of Cardiology, Azienda Ospedaliero-Universitaria di Parma, Parma, 43121, Italy
- Associazione per lo Studio Della Trombosi in Cardiologia, Pavia, 27100, Italy
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, Deutsches Zentrum für Herz-Kreislauf-Forschung, München, 80333, Germany
| | - Ruth McPherson
- University of Ottawa Heart Institute, Ottawa, ON, K1Y4W7, Canada
| | - Hugh Watkins
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Oxford, OX1 2JD, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 2JD, UK
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics, Hospital del Mar Research Institute, Barcelona, 08003, Spain
- CIBER Enfermedades Cardiovasculares (CIBERCV), Barcelona, 28029, Spain
- Facultat de Medicina, Universitat de Vic-Central de Cataluña, Barcelona, VIC, 08500, Spain
| | - Matthew J Bown
- Department of Cardiovascular Sciences, University of Leicester, and NIHR Leicester Biomedical Research Centre, Leicester, LE1 7RH, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, and NIHR Leicester Biomedical Research Centre, Leicester, LE1 7RH, UK
| | - Usman Baber
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - Jeanette Erdmann
- Institute for Integrative and Experimental Genomics, University of Lübeck, Lübeck, 23562, Germany
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - John Danesh
- Department of Public Health and Primary Care, Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, CB2 0SR, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- National Institute of Health Research Blood and Transplant; Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Daniel Chasman
- Center for Cardiovascular Disease Prevention, Brigham and Women's Hospital, Boston, 02115, USA
| | - Paul Ridker
- Center for Cardiovascular Disease Prevention, Brigham and Women's Hospital, Boston, 02115, USA
| | - Joshua Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Judith H Lichtman
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Gail D'Onofrio
- Department of Emergency Medicine, Yale University, New Haven, CT, 06520, USA
| | - Jennifer Mattera
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, 06510, USA
| | - John A Spertus
- Department of Biomedical & Saint Luke's Mid America Heart Institute and the Health Informatics, Division of Endocrinology and Metabolism, University of Missouri-Kansas City, Kansas City, MO, 64110, USA
| | - Wayne H-H Sheu
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, 40705, Taiwan
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, LABioMed and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, 90095, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, 98195, WA, USA
- Cardiovascular Health Research Unit, Kaiser Permanente Washington Health Research Institute, 98101, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Wendy Post
- Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, LABioMed and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, 90095, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, LABioMed and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, 90095, USA
| | - Harlan Krumholz
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, 06510, USA
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, 74800, Pakistan
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stacey Gabriel
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Sekar Kathiresan
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Department of Medicine, Massachusetts General Hospital, Cardiology Division, Harvard Medical School, Boston, MA, 02114, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, 02142, USA.
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123
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DeBoever C, Tanigawa Y, Lindholm ME, McInnes G, Lavertu A, Ingelsson E, Chang C, Ashley EA, Bustamante CD, Daly MJ, Rivas MA. Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study. Nat Commun 2018; 9:1612. [PMID: 29691392 PMCID: PMC5915386 DOI: 10.1038/s41467-018-03910-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/21/2018] [Indexed: 02/08/2023] Open
Abstract
Protein-truncating variants can have profound effects on gene function and are critical for clinical genome interpretation and generating therapeutic hypotheses, but their relevance to medical phenotypes has not been systematically assessed. Here, we characterize the effect of 18,228 protein-truncating variants across 135 phenotypes from the UK Biobank and find 27 associations between medical phenotypes and protein-truncating variants in genes outside the major histocompatibility complex. We perform phenome-wide analyses and directly measure the effect in homozygous carriers, commonly referred to as “human knockouts,” across medical phenotypes for genes implicated as being protective against disease or associated with at least one phenotype in our study. We find several genes with strong pleiotropic or non-additive effects. Our results illustrate the importance of protein-truncating variants in a variety of diseases. Protein-truncating variants (PTVs) are predicted to significantly affect a gene’s function and, thus, human traits. Here, DeBoever et al. systematically analyze PTVs in more than 300,000 individuals across 135 phenotypes and identify 27 associations between PTVs and medical conditions.
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Affiliation(s)
- Christopher DeBoever
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Yosuke Tanigawa
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | | | - Greg McInnes
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Adam Lavertu
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Erik Ingelsson
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chris Chang
- Grail, Inc., 1525 O'Brien Drive, Menlo Park, CA, 94025, USA
| | - Euan A Ashley
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Mark J Daly
- Analytical and Translational Genetics Unit, Boston, MA, 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, 02142, MA, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
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124
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Kanagaratham C, Chiwara V, Ho B, Moussette S, Youssef M, Venuto D, Jeannotte L, Bourque G, de Sanctis JB, Radzioch D, Naumova AK. Loss of the zona pellucida-binding protein 2 (Zpbp2) gene in mice impacts airway hypersensitivity and lung lipid metabolism in a sex-dependent fashion. Mamm Genome 2018. [PMID: 29536159 DOI: 10.1007/s00335-018-9743-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The human chromosomal region 17q12-q21 is one of the best replicated genome-wide association study loci for childhood asthma. The associated SNPs span a large genomic interval that includes several protein-coding genes. Here, we tested the hypothesis that the zona pellucida-binding protein 2 (ZPBP2) gene residing in this region contributes to asthma pathogenesis using a mouse model. We tested the lung phenotypes of knock-out (KO) mice that carry a deletion of the Zpbp2 gene. The deletion attenuated airway hypersensitivity (AHR) in female, but not male, mice in the absence of allergic sensitization. Analysis of the lipid profiles of their lungs showed that female, but not male, KO mice had significantly lower levels of sphingosine-1-phosphate (S1P), very long-chain ceramides (VLCCs), and higher levels of long-chain ceramides compared to wild-type controls. Furthermore, in females, lung resistance following methacholine challenge correlated with lung S1P levels (Pearson correlation coefficient 0.57) suggesting a link between reduced AHR in KO females, Zpbp2 deletion, and S1P level regulation. In livers, spleens and blood plasma, however, VLCC, S1P, and sphingosine levels were reduced in both KO females and males. We also find that the Zpbp2 deletion was associated with gain of methylation in the adjacent DNA regions. Thus, we demonstrate that the mouse ortholog of ZPBP2 has a role in controlling AHR in female mice. Our data also suggest that Zpbp2 may act through regulation of ceramide metabolism. These findings highlight the importance of phospholipid metabolism for sexual dimorphism in AHR.
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Affiliation(s)
| | - Victoria Chiwara
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Bianca Ho
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sanny Moussette
- The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mina Youssef
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - David Venuto
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Lucie Jeannotte
- Département de Biologie moléculaire, Biochimie medicale & Pathologie, Faculté de médecine, Université Laval, Québec, QC, Canada.,Centre de recherche sur le cancer de l'Université Laval, CRCHU de Québec-Université Laval, L'Hôtel-Dieu de Québec, Québec, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Juan Bautista de Sanctis
- Institute of Immunology, Faculty of Medicine, Universidad Central de Venezuela, Sabana Grande, Caracas, Venezuela
| | - Danuta Radzioch
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program (IDIGH), The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Anna K Naumova
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,The Research Institute of the McGill University Health Centre, Montreal, QC, Canada. .,Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada.
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125
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Rajput C, Walsh MP, Eder BN, Metitiri EE, Popova AP, Hershenson MB. Rhinovirus infection induces distinct transcriptome profiles in polarized human macrophages. Physiol Genomics 2018. [PMID: 29521598 DOI: 10.1152/physiolgenomics.00122.2017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Infections with rhinovirus (RV) cause asthma exacerbations. Recent studies suggest that macrophages play a role in asthmatic airway inflammation and the innate immune response to RV infection. Macrophages exhibit phenotypes based on surface markers and gene expression. We hypothesized that macrophage polarization state alters gene expression in response to RV infection. Cells were derived from human peripheral blood derived monocytes. M1 and M2 polarization was carried out by using IFN-γ and IL-4, respectively, and RNA was extracted for Affymetrix Human Gene ST2.1 exon arrays. Selected genes were validated by quantitative (q)PCR. Treatment of nonactivated (M0) macrophages with IFN-γ and IL-4 induced the expression of 252 and 153 distinct genes, respectively, including previously-identified M1 and M2 markers. RV infection of M0 macrophages induced upregulation of 232 genes; pathway analysis showed significant overrepresentation of genes involved in IFN-α/β signaling and cytokine signaling in the immune system. RV infection induced differential expression of 195 distinct genes in M1-like macrophages but only seven distinct genes in M2-like-polarized cells. In a secondary analysis, comparison between M0-, RV-infected, and M1-like-polarized, RV-infected macrophages revealed differential expression of 227 genes including those associated with asthma and its exacerbation. qPCR demonstrated increased expression of CCL8, CXCL10, TNFSF10, TNFSF18, IL6, NOD2, and GSDMD and reduced expression of VNN1, AGO1, and AGO2. Together, these data show that, in contrast to M2-like-polarized macrophages, gene expression of M1-like macrophages is highly regulated by RV.
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Affiliation(s)
- Charu Rajput
- Departments of Pediatrics and Communicable Diseases, University of Michigan Medical School , Ann Arbor, Michigan
| | - Megan P Walsh
- Department of Epidemiology, University of Michigan School of Public Health , Ann Arbor, MI
| | - Breanna N Eder
- Departments of Pediatrics and Communicable Diseases, University of Michigan Medical School , Ann Arbor, Michigan
| | - Ediri E Metitiri
- Departments of Pediatrics and Communicable Diseases, University of Michigan Medical School , Ann Arbor, Michigan
| | - Antonia P Popova
- Departments of Pediatrics and Communicable Diseases, University of Michigan Medical School , Ann Arbor, Michigan
| | - Marc B Hershenson
- Departments of Pediatrics and Communicable Diseases, University of Michigan Medical School , Ann Arbor, Michigan.,Department of Molecular and Integrative Physiology, University of Michigan Medical School , Ann Arbor, Michigan
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126
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A decade of research on the 17q12-21 asthma locus: Piecing together the puzzle. J Allergy Clin Immunol 2018; 142:749-764.e3. [PMID: 29307657 PMCID: PMC6172038 DOI: 10.1016/j.jaci.2017.12.974] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 12/20/2022]
Abstract
Chromosome 17q12–21 remains the most highly replicated and significant asthma locus. Genotypes in the core region defined by the first genome-wide association study correlate with expression of 2 genes, ORM1-like 3 (ORMDL3) and gasdermin B (GSDMB), making these prime candidate asthma genes, although recent studies have implicated gasdermin A (GSDMA) distal to and post-GPI attachment to proteins 3 (PGAP3) proximal to the core region as independent loci. We review 10 years of studies on the 17q12–21 locus and suggest that genotype-specific risks for asthma at the proximal and distal loci are not specific to early-onset asthma and mediated by PGAP3, ORMDL3, and/or GSDMA expression. We propose that the weak and inconsistent associations of 17q single nucleotide polymorphisms with asthma in African Americans is due to the high frequency of some 17q alleles, the breakdown of linkage disequilibrium on African-derived chromosomes, and possibly different early-life asthma endotypes in these children. Finally, the inconsistent association between asthma and gene expression levels in blood or lung cells from older children and adults suggests that genotype effects may mediate asthma risk or protection during critical developmental windows and/or in response to relevant exposures in early life. Thus studies of young children and ethnically diverse populations are required to fully understand the relationship between genotype and asthma phenotype and the gene regulatory architecture at this locus. (J Allergy Clin Immunol 2018;142:749–64.)
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127
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Vicente CT, Revez JA, Ferreira MAR. Lessons from ten years of genome-wide association studies of asthma. Clin Transl Immunology 2017; 6:e165. [PMID: 29333270 PMCID: PMC5750453 DOI: 10.1038/cti.2017.54] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/10/2017] [Accepted: 10/31/2017] [Indexed: 12/13/2022] Open
Abstract
Twenty-five genome-wide association studies (GWAS) of asthma were published between 2007 and 2016, the largest with a sample size of 157242 individuals. Across these studies, 39 genetic variants in low linkage disequilibrium (LD) with each other were reported to associate with disease risk at a significance threshold of P<5 × 10−8, including 31 in populations of European ancestry. Results from analyses of the UK Biobank data (n=380 503) indicate that at least 28 of the 31 associations reported in Europeans represent true-positive findings, collectively explaining 2.5% of the variation in disease liability (median of 0.06% per variant). We identified 49 transcripts as likely target genes of the published asthma risk variants, mostly based on LD with expression quantitative trait loci (eQTL). Of these genes, 16 were previously implicated in disease pathophysiology by functional studies, including TSLP, TNFSF4, ADORA1, CHIT1 and USF1. In contrast, at present, there is limited or no functional evidence directly implicating the remaining 33 likely target genes in asthma pathophysiology. Some of these genes have a known function that is relevant to allergic disease, including F11R, CD247, PGAP3, AAGAB, CAMK4 and PEX14, and so could be prioritized for functional follow-up. We conclude by highlighting three areas of research that are essential to help translate GWAS findings into clinical research or practice, namely validation of target gene predictions, understanding target gene function and their role in disease pathophysiology and genomics-guided prioritization of targets for drug development.
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Affiliation(s)
| | - Joana A Revez
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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128
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Unno H, Miller M, Rosenthal P, Beppu A, Das S, Broide DH. Activating transcription factor 6α (ATF6α) regulates airway hyperreactivity, smooth muscle proliferation, and contractility. J Allergy Clin Immunol 2017; 141:439-442.e4. [PMID: 28958904 DOI: 10.1016/j.jaci.2017.07.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/18/2017] [Accepted: 07/26/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Hirotoshi Unno
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - Marina Miller
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - Peter Rosenthal
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - Andrew Beppu
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - Sudipta Das
- Department of Medicine, University of California San Diego, La Jolla, Calif
| | - David H Broide
- Department of Medicine, University of California San Diego, La Jolla, Calif.
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129
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Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis. Proc Natl Acad Sci U S A 2017; 114:10642-10647. [PMID: 28928145 DOI: 10.1073/pnas.1708194114] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recent findings have revealed that the protein gasdermin D (GSDMD) plays key roles in cell pyroptosis. GSDMD binds lipids and forms pore structures to induce pyroptosis upon microbial infection and associated danger signals. However, detailed structural information for GSDMD remains unknown. Here, we report the crystal structure of the C-terminal domain of human GSDMD (GSDMD-C) at 2.64-Å resolution. The first loop on GSDMD-C inserts into the N-terminal domain (GSDMD-N), which helps stabilize the conformation of the full-length GSDMD. Substitution of this region by a short linker sequence increased levels of cell death. Mutants F283A and F283R can increase protein heterogeneity in vitro and are capable of undergoing cell pyroptosis in 293T cells. The small-angle X-ray-scattering envelope of human GSDMD is consistent with the modeled GSDMD structure and mouse GSDMA3 structure, which suggests that GSDMD adopts an autoinhibited conformation in solution. The positive potential surface of GSDMD-N covered by GSDMD-C is exposed after being released from the autoinhibition state and can form high-order oligomers via a charge-charge interaction. Furthermore, by mapping different regions of GSDMD, we determined that one short segment is sufficient to kill bacteria in vitro and can efficiently inhibit cell growth in Escherichia coli and Mycobacterium Smegmatis These findings reveal that GSDMD-C acts as an auto-inhibition executor and GSDMD-N could form pore structures via a charge-charge interaction upon cleavage by caspases during cell pyroptosis.
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Twardziok M, Schröder PC, Krusche J, Casaca VI, Illi S, Böck A, Loss GJ, Kabesch M, Toncheva AA, Roduit C, Depner M, Genuneit J, Renz H, Roponen M, Weber J, Braun-Fahrländer C, Riedler J, Lauener R, Vuitton DA, Dalphin JC, Pekkanen J, von Mutius E, Schaub B, Hyvärinen A, Karvonen AM, Kirjavainen PV, Remes S, Kaulek V, Dalphin ML, Ege M, Pfefferle PI, Doekes G. Asthmatic farm children show increased CD3 +CD8 low T-cells compared to non-asthmatic farm children. Clin Immunol 2017; 183:285-292. [PMID: 28917722 DOI: 10.1016/j.clim.2017.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/28/2017] [Accepted: 09/12/2017] [Indexed: 11/15/2022]
Affiliation(s)
- Monika Twardziok
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Paul C Schröder
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Johanna Krusche
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany; Member of German Center for Lung Research, DZL, LMU Munich, Germany
| | - Vera I Casaca
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Sabina Illi
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Andreas Böck
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Georg J Loss
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany; University of California, San Diego, School of Medicine, Department of Pediatrics, CA, USA
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Antoaneta A Toncheva
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Caroline Roduit
- Zurich University Children's Hospital, Zurich, Switzerland; Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland and Christine Kühne-Center for Allergy Research and Education, St. Gallen, Switzerland
| | - Martin Depner
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany
| | - Jon Genuneit
- Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Harald Renz
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany; Member of German Center for Lung Research, DZL, LMU Munich, Germany
| | - Marjut Roponen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Juliane Weber
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | | | | | - Roger Lauener
- Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland and Christine Kühne-Center for Allergy Research and Education, St. Gallen, Switzerland
| | | | | | - Juha Pekkanen
- Department of Public health, University of Helsinki, Helsinki, Finland; Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
| | - Erika von Mutius
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany; Member of German Center for Lung Research, DZL, LMU Munich, Germany
| | - Bianca Schaub
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany; Member of German Center for Lung Research, DZL, LMU Munich, Germany.
| | | | - Anne Hyvärinen
- Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
| | - Anne M Karvonen
- Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
| | - Pirkka V Kirjavainen
- Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
| | - Sami Remes
- Kuopio University Hospital, Department of Paediatrics, Kuopio, Finland
| | - Vincent Kaulek
- University Hospital of Besançon, University of Franche-Comté, Besançon, France
| | - Marie-Laure Dalphin
- University Hospital of Besançon, University of Franche-Comté, Besançon, France
| | - Markus Ege
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany; Member of German Center for Lung Research, DZL, LMU Munich, Germany
| | - Petra I Pfefferle
- Institute of Laboratory Medicine, Philipps University Marburg, Marburg, Germany; Member of German Center for Lung Research, DZL, LMU Munich, Germany
| | - Gert Doekes
- Utrecht University, Institut for Risk Assessment Sciences (IRAS), Devision of Environmental Epidemiology, Utrecht, Netherlands
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131
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Kovacs SB, Miao EA. Gasdermins: Effectors of Pyroptosis. Trends Cell Biol 2017; 27:673-684. [PMID: 28619472 PMCID: PMC5565696 DOI: 10.1016/j.tcb.2017.05.005] [Citation(s) in RCA: 782] [Impact Index Per Article: 111.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 12/20/2022]
Abstract
Pyroptosis is a form of lytic programmed cell death initiated by inflammasomes, which detect cytosolic contamination or perturbation. This drives activation of caspase-1 or caspase-11/4/5, which cleave gasdermin D, separating its N-terminal pore-forming domain (PFD) from the C-terminal repressor domain (RD). The PFD oligomerizes to form large pores in the membrane that drive swelling and membrane rupture. Gasdermin D is one of six (in humans) gasdermin family members; several other gasdermins have also been shown to form pores that cause pyroptosis after cleavage to activate their PFDs. One of these, gasdermin E, is activated by caspase-3 cleavage. We review our current understanding of pyroptosis as well as current knowledge of the gasdermin family.
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Affiliation(s)
- Stephen B Kovacs
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, and Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Edward A Miao
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, and Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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132
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Das S, Miller M, Broide DH. Chromosome 17q21 Genes ORMDL3 and GSDMB in Asthma and Immune Diseases. Adv Immunol 2017; 135:1-52. [PMID: 28826527 DOI: 10.1016/bs.ai.2017.06.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chromosome 17q21 contains a cluster of genes including ORMDL3 and GSDMB, which have been highly linked to asthma in genome-wide association studies. ORMDL3 is localized to the endoplasmic reticulum and regulates downstream pathways including sphingolipids, metalloproteases, remodeling genes, and chemokines. ORMDL3 inhibits serine palmitoyl-CoA transferase, the rate-limiting enzyme for sphingolipid biosynthesis. In addition, ORMDL3 activates the ATF6α branch of the unfolded protein response which regulates SERCA2b and IL-6, pathways of potential importance to asthma. The SNP-linking chromosome 17q21 to asthma is associated with increased ORMDL3 and GSDMB expression. Mice expressing either increased levels of human ORMDL3, or human GSDMB, have an asthma phenotype characterized by increased airway responsiveness and increased airway remodeling (increased smooth muscle and fibrosis) in the absence of airway inflammation. GSDMB regulates expression of 5-LO and TGF-β1 which are known pathways involved in the pathogenesis of asthma. GSDMB is one of four members of the GSDM family (GSDMA, GSDMB, GSDMC, and GSDMD). GSDMD (located on chromosome 8q24 and not linked to asthma) has emerged as a key mediator of pyroptosis. GSDMD is a key component of the NLPR3 inflammasome and is required for its activation. GSDMD undergoes proteolytic cleavage by caspase-1 to release its N-terminal fragment, which in turn mediates pyroptosis and IL-1β secretion. Chromosome 17q21 has not only been linked to asthma but also to type 1 diabetes, inflammatory bowel disease, and primary biliary cirrhosis suggesting that future insights into the biology of genes located in this region will increase our understanding of these diseases.
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Affiliation(s)
- Sudipta Das
- University of California, San Diego, CA, United States
| | - Marina Miller
- University of California, San Diego, CA, United States
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133
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Himes BE, Ortega VE. Making progress toward understanding the genetic architecture of asthma in the most affected US ethnic group. Eur Respir J 2017; 49:49/5/1700329. [PMID: 28461304 DOI: 10.1183/13993003.00329-2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Blanca E Himes
- Dept of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Victor E Ortega
- Center for Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
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134
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Liu X, Lieberman J. A Mechanistic Understanding of Pyroptosis: The Fiery Death Triggered by Invasive Infection. Adv Immunol 2017; 135:81-117. [PMID: 28826530 DOI: 10.1016/bs.ai.2017.02.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Immune cells and skin and mucosal epithelial cells recognize invasive microbes and other signs of danger to sound alarms that recruit responder cells and initiate an immediate "innate" immune response. An especially powerful alarm is triggered by cytosolic sensors of invasive infection that assemble into multimolecular complexes, called inflammasomes, that activate the inflammatory caspases, leading to maturation and secretion of proinflammatory cytokines and pyroptosis, an inflammatory death of the infected cell. Work in the past year has defined the molecular basis of pyroptosis. Activated inflammatory caspases cleave Gasdermin D (GSDMD), a cytosolic protein in immune antigen-presenting cells and epithelia. Cleavage separates the autoinhibitory C-terminal fragment from the active N-terminal fragment, which moves to the cell membrane, binds to lipids on the inside of the cell membrane, and oligomerizes to form membrane pores that disrupt cell membrane integrity, causing death and leakage of small molecules, including the proinflammatory cytokines and GSDMD itself. GSDMD also binds to cardiolipin on bacterial membranes and kills the very bacteria that activate the inflammasome. GSDMD belongs to a family of poorly studied gasdermins, expressed in the skin and mucosa, which can also form membrane pores. Spontaneous mutations that disrupt the binding of the N- and C-terminal domains of other gasdermins are associated with alopecia and asthma. Here, we review recent studies that identified the roles of the inflammasome, inflammatory caspases, and GSDMD in pyroptosis and highlight some of the outstanding questions about their roles in innate immunity, control of infection, and sepsis.
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Affiliation(s)
- Xing Liu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States.
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135
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Cardamone G, Paraboschi EM, Rimoldi V, Duga S, Soldà G, Asselta R. The Characterization of GSDMB Splicing and Backsplicing Profiles Identifies Novel Isoforms and a Circular RNA That Are Dysregulated in Multiple Sclerosis. Int J Mol Sci 2017; 18:ijms18030576. [PMID: 28272342 PMCID: PMC5372592 DOI: 10.3390/ijms18030576] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/20/2017] [Accepted: 03/01/2017] [Indexed: 01/08/2023] Open
Abstract
Abnormalities in alternative splicing (AS) are emerging as recurrent features in autoimmune diseases (AIDs). In particular, a growing body of evidence suggests the existence of a pathogenic association between a generalized defect in splicing regulatory genes and multiple sclerosis (MS). Moreover, several studies have documented an unbalance in alternatively-spliced isoforms in MS patients possibly contributing to the disease etiology. In this work, using a combination of PCR-based techniques (reverse-transcription (RT)-PCR, fluorescent-competitive, real-time, and digital RT-PCR assays), we investigated the alternatively-spliced gene encoding Gasdermin B, GSDMB, which was repeatedly associated with susceptibility to asthma and AIDs. The in-depth characterization of GSDMB AS and backsplicing profiles led us to the identification of an exonic circular RNA (ecircRNA) as well as of novel GSDMB in-frame and out-of-frame isoforms. The non-productive splicing variants were shown to be downregulated by the nonsense-mediated mRNA decay (NMD) in human cell lines, suggesting that GSDMB levels are significantly modulated by NMD. Importantly, both AS isoforms and the identified ecircRNA were significantly dysregulated in peripheral blood mononuclear cells of relapsing-remitting MS patients compared to controls, further supporting the notion that aberrant RNA metabolism is a characteristic feature of the disease.
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Affiliation(s)
- Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
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136
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Chao KL, Kulakova L, Herzberg O. Gene polymorphism linked to increased asthma and IBD risk alters gasdermin-B structure, a sulfatide and phosphoinositide binding protein. Proc Natl Acad Sci U S A 2017; 114:E1128-E1137. [PMID: 28154144 PMCID: PMC5321033 DOI: 10.1073/pnas.1616783114] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The exact function of human gasdermin-B (GSDMB), which regulates differentiation and growth of epithelial cells, is yet to be elucidated. In human epidermal growth factor receptor 2 (HER2)-positive breast cancer, GSDMB gene amplification and protein overexpression indicate a poor response to HER2-targeted therapy. Genome-wide association studies revealed a correlation between GSDMB SNPs and an increased susceptibility to Crohn's disease, ulcerative colitis, and asthma. The N- and C-terminal domains of all gasdermins possess lipid-binding and regulatory activities, respectively. Inflammatory caspases cleave gasdermin-D in the interdomain linker but not GSDMB. The cleaved N-terminal domain binds phosphoinositides and cardiolipin, forms membrane-disrupting pores, and executes pyroptosis. We show that both full-length GSDMB and the N-terminal domain bind to nitrocellulose membranes immobilized with phosphoinositides or sulfatide, but not with cardiolipin. In addition, the GSDMB N-terminal domain binds liposomes containing sulfatide. The crystal structure of the GSDMB C-terminal domain reveals the structural impact of the amino acids encoded by SNPs that are linked to asthma and inflammatory bowel disease (IBD). A loop that carries the polymorphism amino acids corresponding to healthy individuals (Gly299:Pro306) exhibits high conformational flexibility, whereas the loop carrying amino acids found in individuals with increased disease risk (Arg299:Ser306) exhibits a well-defined conformation and higher positive surface charge. Apoptotic executioner caspase-3, -6, and -7, but not the inflammatory caspases, cleave GSDMB at 88DNVD91 within the N-terminal domain. Selective sulfatide binding may indicate possible function for GSDMB in the cellular sulfatide transport.
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Affiliation(s)
- Kinlin L Chao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Liudmila Kulakova
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850;
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742
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137
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Affiliation(s)
- Xing Liu
- Program in Cellular and Molecular Medicine Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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