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Murano H, Inoue S, Hashidate-Yoshida T, Shindou H, Shimizu T, Otaki Y, Minegishi Y, Kitaoka T, Futakuchi M, Igarashi A, Nishiwaki M, Nemoto T, Sato M, Kobayashi M, Sato K, Hanawa T, Miyazaki O, Watanabe M. Lysophospholipid Acyltransferase 9 Promotes Emphysema Formation via Platelet-activating Factor. Am J Respir Cell Mol Biol 2024; 70:482-492. [PMID: 38377392 DOI: 10.1165/rcmb.2023-0253oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/20/2024] [Indexed: 02/22/2024] Open
Abstract
Cigarette smoking is known to be the leading cause of chronic obstructive pulmonary disease (COPD). However, the detailed mechanisms have not been elucidated. PAF (platelet-activating factor), a potent inflammatory mediator, is involved in the pathogenesis of various respiratory diseases such as bronchial asthma and COPD. We focused on LPLAT9 (lysophospholipid acyltransferase 9), a biosynthetic enzyme of PAF, in the pathogenesis of COPD. LPLAT9 gene expression was observed in excised COPD lungs and single-cell RNA sequencing data of alveolar macrophages (AMs). LPLAT9 was predominant and upregulated in AMs, particularly monocyte-derived AMs, in patients with COPD. To identify the function of LPLAT9/PAF in AMs in the pathogenesis of COPD, we exposed systemic LPLAT9-knockout (LPALT9-/-) mice to cigarette smoke (CS). CS increased the number of AMs, especially the monocyte-derived fraction, which secreted MMP12 (matrix metalloprotease 12). Also, CS augmented LPLAT9 phosphorylation/activation on macrophages and, subsequently, PAF synthesis in the lung. The LPLAT9-/- mouse lung showed reduced PAF production after CS exposure. Intratracheal PAF administration accumulated AMs by increasing MCP1 (monocyte chemoattractant protein-1). After CS exposure, AM accumulation and subsequent pulmonary emphysema, a primary pathologic change of COPD, were reduced in LPALT9-/- mice compared with LPLAT9+/+ mice. Notably, these phenotypes were again worsened by LPLAT9+/+ bone marrow transplantation in LPALT9-/- mice. Thus, CS-induced LPLAT9 activation in monocyte-derived AMs aggravated pulmonary emphysema via PAF-induced further accumulation of AMs. These results suggest that PAF synthesized by LPLAT9 has an important role in the pathogenesis of COPD.
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Affiliation(s)
- Hiroaki Murano
- Department of Cardiology, Pulmonology, and Nephrology and
- Department of Lipid Life Science and
| | - Sumito Inoue
- Department of Cardiology, Pulmonology, and Nephrology and
| | | | - Hideo Shindou
- Department of Lipid Life Science and
- Department of Medical Lipid Science, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; and
| | - Takao Shimizu
- Department of Lipid Signaling Project, National Center for Global Health and Medicine, Tokyo, Japan
- Institute of Microbial Chemistry, Tokyo, Japan
| | - Yoichiro Otaki
- Department of Cardiology, Pulmonology, and Nephrology and
| | | | - Takumi Kitaoka
- Department of Pathology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Mitsuru Futakuchi
- Department of Pathology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Akira Igarashi
- Department of Cardiology, Pulmonology, and Nephrology and
| | | | - Takako Nemoto
- Department of Cardiology, Pulmonology, and Nephrology and
| | - Masamichi Sato
- Department of Cardiology, Pulmonology, and Nephrology and
| | - Maki Kobayashi
- Department of Cardiology, Pulmonology, and Nephrology and
| | - Kento Sato
- Department of Cardiology, Pulmonology, and Nephrology and
| | | | - Osamu Miyazaki
- Department of Cardiology, Pulmonology, and Nephrology and
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Mijač S, Banić I, Genc AM, Lipej M, Turkalj M. The Effects of Environmental Exposure on Epigenetic Modifications in Allergic Diseases. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:110. [PMID: 38256371 PMCID: PMC10820670 DOI: 10.3390/medicina60010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Allergic diseases are one of the most common chronic conditions and their prevalence is on the rise. Environmental exposure, primarily prenatal and early life influences, affect the risk for the development and specific phenotypes of allergic diseases via epigenetic mechanisms. Exposure to pollutants, microorganisms and parasites, tobacco smoke and certain aspects of diet are known to drive epigenetic changes that are essential for immune regulation (e.g., the shift toward T helper 2-Th2 cell polarization and decrease in regulatory T-cell (Treg) differentiation). DNA methylation and histone modifications can modify immune programming related to either pro-allergic interleukin 4 (IL-4), interleukin 13 (IL-13) or counter-regulatory interferon γ (IFN-γ) production. Differential expression of small non-coding RNAs has also been linked to the risk for allergic diseases and associated with air pollution. Certain exposures and associated epigenetic mechanisms play a role in the susceptibility to allergic conditions and specific clinical manifestations of the disease, while others are thought to have a protective role against the development of allergic diseases, such as maternal and early postnatal microbial diversity, maternal helminth infections and dietary supplementation with polyunsaturated fatty acids and vitamin D. Epigenetic mechanisms are also known to be involved in mediating the response to common treatment in allergic diseases, for example, changes in histone acetylation of proinflammatory genes and in the expression of certain microRNAs are associated with the response to inhaled corticosteroids in asthma. Gaining better insight into the epigenetic regulation of allergic diseases may ultimately lead to significant improvements in the management of these conditions, earlier and more precise diagnostics, optimization of current treatment regimes, and the implementation of novel therapeutic options and prevention strategies in the near future.
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Affiliation(s)
- Sandra Mijač
- Department of Medical Research, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia; (S.M.); (A.-M.G.)
| | - Ivana Banić
- Department of Medical Research, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia; (S.M.); (A.-M.G.)
- Department of Innovative Diagnostics, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia
| | - Ana-Marija Genc
- Department of Medical Research, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia; (S.M.); (A.-M.G.)
| | - Marcel Lipej
- IT Department, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia;
| | - Mirjana Turkalj
- Department of Pediatric Allergy and Pulmonology, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia;
- Faculty of Medicine, J.J. Strossmayer University of Osijek, J. Huttlera 4, HR-31000 Osijek, Croatia
- Faculty of Medicine, Catholic University of Croatia, Ilica 242, HR-10000 Zagreb, Croatia
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3
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Xu Z, Forno E, Sun Y, Manni ML, Han YY, Kim S, Yue M, Vonk JM, Kersten ETM, Acosta-Perez E, Canino G, Koppelman GH, Chen W, Celedón JC. Nasal epithelial gene expression and total IgE in children and adolescents with asthma. J Allergy Clin Immunol 2024; 153:122-131. [PMID: 37742934 PMCID: PMC10842443 DOI: 10.1016/j.jaci.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Little is known about nasal epithelial gene expression and total IgE in youth. OBJECTIVE We aimed to identify genes whose nasal epithelial expression differs by total IgE in youth, and group them into modules that could be mapped to airway epithelial cell types. METHODS We conducted a transcriptome-wide association study of total IgE in 469 Puerto Ricans aged 9 to 20 years who participated in the Epigenetic Variation and Childhood Asthma in Puerto Ricans study, separately in all subjects and in those with asthma. We then attempted to replicate top findings for each analysis using data from 3 cohorts. Genes with a Benjamini-Hochberg-adjusted P value of less than .05 in the Epigenetic Variation and Childhood Asthma in Puerto Ricans study and a P value of less than .05 in the same direction of association in 1 or more replication cohort were considered differentially expressed genes (DEGs). DEGs for total IgE in subjects with asthma were further dissected into gene modules using coexpression analysis, and such modules were mapped to specific cell types in airway epithelia using public single-cell RNA-sequencing data. RESULTS A higher number of DEGs for total IgE were identified in subjects with asthma (n = 1179 DEGs) than in all subjects (n = 631 DEGs). In subjects with asthma, DEGs were mapped to 11 gene modules. The top module for positive correlation with total IgE was mapped to myoepithelial and mucus secretory cells in lower airway epithelia and was regulated by IL-4, IL5, IL-13, and IL-33. Within this module, hub genes included CDH26, FETUB, NTRK2, CCBL1, CST1, and CST2. Furthermore, an enrichment analysis showed overrepresentation of genes in signaling pathways for synaptogenesis, IL-13, and ferroptosis, supporting interactions between interleukin- and acetylcholine-induced responses. CONCLUSIONS Our findings for nasal epithelial gene expression support neuroimmune coregulation of total IgE in youth with asthma.
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Affiliation(s)
- Zhongli Xu
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa; School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Yidan Sun
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Michelle L Manni
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Yueh Ying Han
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Soyeon Kim
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Molin Yue
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Judith M Vonk
- GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands; Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elin T M Kersten
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Edna Acosta-Perez
- Behavioral Sciences Research Institute of Puerto Rico, University of Puerto Rico, San Juan, Puerto Rico
| | - Glorisa Canino
- Behavioral Sciences Research Institute of Puerto Rico, University of Puerto Rico, San Juan, Puerto Rico; Department of Pediatrics, Medical Science Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Wei Chen
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Juan C Celedón
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa.
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Valentine WJ, Shimizu T, Shindou H. Lysophospholipid acyltransferases orchestrate the compositional diversity of phospholipids. Biochimie 2023; 215:24-33. [PMID: 37611890 DOI: 10.1016/j.biochi.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/14/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Lysophospholipid acyltransferases (LPLATs), in concert with glycerol-3-phosphate acyltransferases (GPATs) and phospholipase A1/2s, orchestrate the compositional diversity of the fatty chains in membrane phospholipids. Fourteen LPLAT enzymes which come from two distinct families, AGPAT and MBOAT, have been identified, and in this mini-review we provide an overview of their roles in de novo and remodeling pathways of membrane phospholipid biosynthesis. Recently new nomenclature for LPLATs has been introduced (LPLATx, where x is a number 1-14), and we also give an overview of key biological functions that have been discovered for LPLAT1-14, revealed primarily through studies of LPLAT-gene-deficient mice as well as by linkages to various human diseases.
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Affiliation(s)
- William J Valentine
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, 187-8502, Japan.
| | - Takao Shimizu
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Tokyo, 162-8655, Japan; Institute of Microbial Chemistry, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Hideo Shindou
- Department of Lipid Life Science, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Tokyo, 162-8655, Japan; Department of Lipid Medical Science, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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5
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Johansson Å, Andreassen OA, Brunak S, Franks PW, Hedman H, Loos RJ, Meder B, Melén E, Wheelock CE, Jacobsson B. Precision medicine in complex diseases-Molecular subgrouping for improved prediction and treatment stratification. J Intern Med 2023; 294:378-396. [PMID: 37093654 PMCID: PMC10523928 DOI: 10.1111/joim.13640] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Complex diseases are caused by a combination of genetic, lifestyle, and environmental factors and comprise common noncommunicable diseases, including allergies, cardiovascular disease, and psychiatric and metabolic disorders. More than 25% of Europeans suffer from a complex disease, and together these diseases account for 70% of all deaths. The use of genomic, molecular, or imaging data to develop accurate diagnostic tools for treatment recommendations and preventive strategies, and for disease prognosis and prediction, is an important step toward precision medicine. However, for complex diseases, precision medicine is associated with several challenges. There is a significant heterogeneity between patients of a specific disease-both with regards to symptoms and underlying causal mechanisms-and the number of underlying genetic and nongenetic risk factors is often high. Here, we summarize precision medicine approaches for complex diseases and highlight the current breakthroughs as well as the challenges. We conclude that genomic-based precision medicine has been used mainly for patients with highly penetrant monogenic disease forms, such as cardiomyopathies. However, for most complex diseases-including psychiatric disorders and allergies-available polygenic risk scores are more probabilistic than deterministic and have not yet been validated for clinical utility. However, subclassifying patients of a specific disease into discrete homogenous subtypes based on molecular or phenotypic data is a promising strategy for improving diagnosis, prediction, treatment, prevention, and prognosis. The availability of high-throughput molecular technologies, together with large collections of health data and novel data-driven approaches, offers promise toward improved individual health through precision medicine.
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Affiliation(s)
- Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala university, Sweden
| | - Ole A. Andreassen
- NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopment Research, University of Oslo, Oslo, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, DK-2200 Copenhagen, Denmark
| | - Paul W. Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Department of Clinical Science, Lund University, Sweden
- Novo Nordisk Foundation, Denmark
| | - Harald Hedman
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Ruth J.F. Loos
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Charles Bronfman Institute for Personalized Medicine at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Meder
- Precision Digital Health, Cardiogenetics Center Heidelberg, Department of Cardiology, University Of Heidelberg, Germany
| | - Erik Melén
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm
- Sachś Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Craig E Wheelock
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Obstetrics and Gynaecology, Sahlgrenska University Hospital, Göteborg, Sweden
- Department of Genetics and Bioinformatics, Domain of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
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6
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Recto K, Kachroo P, Huan T, Van Den Berg D, Lee GY, Bui H, Lee DH, Gereige J, Yao C, Hwang SJ, Joehanes R, Weiss ST, O'Connor GT, Levy D, DeMeo DL. Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma. EBioMedicine 2023; 95:104758. [PMID: 37598461 PMCID: PMC10462855 DOI: 10.1016/j.ebiom.2023.104758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Identifying novel epigenetic signatures associated with serum immunoglobulin E (IgE) may improve our understanding of molecular mechanisms underlying asthma and IgE-mediated diseases. METHODS We performed an epigenome-wide association study using whole blood from Framingham Heart Study (FHS; n = 3,471, 46% females) participants and validated results using the Childhood Asthma Management Program (CAMP; n = 674, 39% females) and the Genetic Epidemiology of Asthma in Costa Rica Study (CRA; n = 787, 41% females). Using the closest gene to each IgE-associated CpG, we highlighted biologically plausible pathways underlying IgE regulation and analyzed the transcription patterns linked to IgE-associated CpGs (expression quantitative trait methylation loci; eQTMs). Using prior UK Biobank summary data from genome-wide association studies of asthma and allergy, we performed Mendelian randomization (MR) for causal inference testing using the IgE-associated CpGs from FHS with methylation quantitative trait loci (mQTLs) as instrumental variables. FINDINGS We identified 490 statistically significant differentially methylated CpGs associated with IgE in FHS, of which 193 (39.3%) replicated in CAMP and CRA (FDR < 0.05). Gene ontology analysis revealed enrichment in pathways related to transcription factor binding, asthma, and other immunological processes. eQTM analysis identified 124 cis-eQTMs for 106 expressed genes (FDR < 0.05). MR in combination with drug-target analysis revealed CTSB and USP20 as putatively causal regulators of IgE levels (Bonferroni adjusted P < 7.94E-04) that can be explored as potential therapeutic targets. INTERPRETATION By integrating eQTM and MR analyses in general and clinical asthma populations, our findings provide a deeper understanding of the multidimensional inter-relations of DNA methylation, gene expression, and IgE levels. FUNDING US NIH/NHLBI grants: P01HL132825, K99HL159234. N01-HC-25195 and HHSN268201500001I.
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Affiliation(s)
- Kathryn Recto
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Priyadarshini Kachroo
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA 02115, USA
| | - Tianxiao Huan
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - David Van Den Berg
- University of Southern California Methylation Characterization Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Gha Young Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Helena Bui
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Dong Heon Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Jessica Gereige
- Boston University School of Medicine, Pulmonary Center, Boston, MA 02118, USA
| | - Chen Yao
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Shih-Jen Hwang
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Roby Joehanes
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Scott T Weiss
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA 02115, USA
| | - George T O'Connor
- The Framingham Heart Study, Framingham, MA 01702, USA; Boston University School of Medicine, Pulmonary Center, Boston, MA 02118, USA
| | - Daniel Levy
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA.
| | - Dawn L DeMeo
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA 02115, USA.
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7
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Wise SK, Damask C, Roland LT, Ebert C, Levy JM, Lin S, Luong A, Rodriguez K, Sedaghat AR, Toskala E, Villwock J, Abdullah B, Akdis C, Alt JA, Ansotegui IJ, Azar A, Baroody F, Benninger MS, Bernstein J, Brook C, Campbell R, Casale T, Chaaban MR, Chew FT, Chambliss J, Cianferoni A, Custovic A, Davis EM, DelGaudio JM, Ellis AK, Flanagan C, Fokkens WJ, Franzese C, Greenhawt M, Gill A, Halderman A, Hohlfeld JM, Incorvaia C, Joe SA, Joshi S, Kuruvilla ME, Kim J, Klein AM, Krouse HJ, Kuan EC, Lang D, Larenas-Linnemann D, Laury AM, Lechner M, Lee SE, Lee VS, Loftus P, Marcus S, Marzouk H, Mattos J, McCoul E, Melen E, Mims JW, Mullol J, Nayak JV, Oppenheimer J, Orlandi RR, Phillips K, Platt M, Ramanathan M, Raymond M, Rhee CS, Reitsma S, Ryan M, Sastre J, Schlosser RJ, Schuman TA, Shaker MS, Sheikh A, Smith KA, Soyka MB, Takashima M, Tang M, Tantilipikorn P, Taw MB, Tversky J, Tyler MA, Veling MC, Wallace D, Wang DY, White A, Zhang L. International consensus statement on allergy and rhinology: Allergic rhinitis - 2023. Int Forum Allergy Rhinol 2023; 13:293-859. [PMID: 36878860 DOI: 10.1002/alr.23090] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/11/2022] [Accepted: 09/13/2022] [Indexed: 03/08/2023]
Abstract
BACKGROUND In the 5 years that have passed since the publication of the 2018 International Consensus Statement on Allergy and Rhinology: Allergic Rhinitis (ICAR-Allergic Rhinitis 2018), the literature has expanded substantially. The ICAR-Allergic Rhinitis 2023 update presents 144 individual topics on allergic rhinitis (AR), expanded by over 40 topics from the 2018 document. Originally presented topics from 2018 have also been reviewed and updated. The executive summary highlights key evidence-based findings and recommendation from the full document. METHODS ICAR-Allergic Rhinitis 2023 employed established evidence-based review with recommendation (EBRR) methodology to individually evaluate each topic. Stepwise iterative peer review and consensus was performed for each topic. The final document was then collated and includes the results of this work. RESULTS ICAR-Allergic Rhinitis 2023 includes 10 major content areas and 144 individual topics related to AR. For a substantial proportion of topics included, an aggregate grade of evidence is presented, which is determined by collating the levels of evidence for each available study identified in the literature. For topics in which a diagnostic or therapeutic intervention is considered, a recommendation summary is presented, which considers the aggregate grade of evidence, benefit, harm, and cost. CONCLUSION The ICAR-Allergic Rhinitis 2023 update provides a comprehensive evaluation of AR and the currently available evidence. It is this evidence that contributes to our current knowledge base and recommendations for patient evaluation and treatment.
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Affiliation(s)
- Sarah K Wise
- Otolaryngology-HNS, Emory University, Atlanta, Georgia, USA
| | - Cecelia Damask
- Otolaryngology-HNS, Private Practice, University of Central Florida, Lake Mary, Florida, USA
| | - Lauren T Roland
- Otolaryngology-HNS, Washington University, St. Louis, Missouri, USA
| | - Charles Ebert
- Otolaryngology-HNS, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Joshua M Levy
- Otolaryngology-HNS, Emory University, Atlanta, Georgia, USA
| | - Sandra Lin
- Otolaryngology-HNS, University of Wisconsin, Madison, Wisconsin, USA
| | - Amber Luong
- Otolaryngology-HNS, McGovern Medical School of the University of Texas, Houston, Texas, USA
| | - Kenneth Rodriguez
- Otolaryngology-HNS, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Ahmad R Sedaghat
- Otolaryngology-HNS, University of Cincinnati, Cincinnati, Ohio, USA
| | - Elina Toskala
- Otolaryngology-HNS, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | | | - Baharudin Abdullah
- Otolaryngology-HNS, Universiti Sains Malaysia, Kubang, Kerian, Kelantan, Malaysia
| | - Cezmi Akdis
- Immunology, Infectious Diseases, Swiss Institute of Allergy and Asthma Research, Davos, Switzerland
| | - Jeremiah A Alt
- Otolaryngology-HNS, University of Utah, Salt Lake City, Utah, USA
| | | | - Antoine Azar
- Allergy/Immunology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Fuad Baroody
- Otolaryngology-HNS, University of Chicago, Chicago, Illinois, USA
| | | | | | - Christopher Brook
- Otolaryngology-HNS, Harvard University, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Raewyn Campbell
- Otolaryngology-HNS, Macquarie University, Sydney, NSW, Australia
| | - Thomas Casale
- Allergy/Immunology, University of South Florida College of Medicine, Tampa, Florida, USA
| | - Mohamad R Chaaban
- Otolaryngology-HNS, Cleveland Clinic, Case Western Reserve University, Cleveland, Ohio, USA
| | - Fook Tim Chew
- Allergy/Immunology, Genetics, National University of Singapore, Singapore, Singapore
| | - Jeffrey Chambliss
- Allergy/Immunology, University of Texas Southwestern, Dallas, Texas, USA
| | - Antonella Cianferoni
- Allergy/Immunology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Anne K Ellis
- Allergy/Immunology, Queens University, Kingston, ON, Canada
| | | | - Wytske J Fokkens
- Otorhinolaryngology, Amsterdam University Medical Centres, Amsterdam, Netherlands
| | | | - Matthew Greenhawt
- Allergy/Immunology, Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Amarbir Gill
- Otolaryngology-HNS, University of Michigan, Ann Arbor, Michigan, USA
| | - Ashleigh Halderman
- Otolaryngology-HNS, University of Texas Southwestern, Dallas, Texas, USA
| | - Jens M Hohlfeld
- Respiratory Medicine, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Hannover Medical School, German Center for Lung Research, Hannover, Germany
| | | | - Stephanie A Joe
- Otolaryngology-HNS, University of Illinois Chicago, Chicago, Illinois, USA
| | - Shyam Joshi
- Allergy/Immunology, Oregon Health and Science University, Portland, Oregon, USA
| | | | - Jean Kim
- Otolaryngology-HNS, Johns Hopkins University, Baltimore, Maryland, USA
| | - Adam M Klein
- Otolaryngology-HNS, Emory University, Atlanta, Georgia, USA
| | - Helene J Krouse
- Otorhinolaryngology Nursing, University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Edward C Kuan
- Otolaryngology-HNS, University of California Irvine, Orange, California, USA
| | - David Lang
- Allergy/Immunology, Cleveland Clinic, Cleveland, Ohio, USA
| | | | | | - Matt Lechner
- Otolaryngology-HNS, University College London, Barts Health NHS Trust, London, UK
| | - Stella E Lee
- Otolaryngology-HNS, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Victoria S Lee
- Otolaryngology-HNS, University of Illinois Chicago, Chicago, Illinois, USA
| | - Patricia Loftus
- Otolaryngology-HNS, University of California San Francisco, San Francisco, California, USA
| | - Sonya Marcus
- Otolaryngology-HNS, Stony Brook University, Stony Brook, New York, USA
| | - Haidy Marzouk
- Otolaryngology-HNS, State University of New York Upstate, Syracuse, New York, USA
| | - Jose Mattos
- Otolaryngology-HNS, University of Virginia, Charlottesville, Virginia, USA
| | - Edward McCoul
- Otolaryngology-HNS, Ochsner Clinic, New Orleans, Louisiana, USA
| | - Erik Melen
- Pediatric Allergy, Karolinska Institutet, Stockholm, Sweden
| | - James W Mims
- Otolaryngology-HNS, Wake Forest University, Winston Salem, North Carolina, USA
| | - Joaquim Mullol
- Otorhinolaryngology, Hospital Clinic Barcelona, Barcelona, Spain
| | - Jayakar V Nayak
- Otolaryngology-HNS, Stanford University, Palo Alto, California, USA
| | - John Oppenheimer
- Allergy/Immunology, Rutgers, State University of New Jersey, Newark, New Jersey, USA
| | | | - Katie Phillips
- Otolaryngology-HNS, University of Cincinnati, Cincinnati, Ohio, USA
| | - Michael Platt
- Otolaryngology-HNS, Boston University, Boston, Massachusetts, USA
| | | | | | - Chae-Seo Rhee
- Rhinology/Allergy, Seoul National University Hospital and College of Medicine, Seoul, Korea
| | - Sietze Reitsma
- Otolaryngology-HNS, University of Amsterdam, Amsterdam, Netherlands
| | - Matthew Ryan
- Otolaryngology-HNS, University of Texas Southwestern, Dallas, Texas, USA
| | - Joaquin Sastre
- Allergy, Fundacion Jiminez Diaz, University Autonoma de Madrid, Madrid, Spain
| | - Rodney J Schlosser
- Otolaryngology-HNS, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Theodore A Schuman
- Otolaryngology-HNS, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Marcus S Shaker
- Allergy/Immunology, Dartmouth Geisel School of Medicine, Lebanon, New Hampshire, USA
| | - Aziz Sheikh
- Primary Care, University of Edinburgh, Edinburgh, Scotland
| | - Kristine A Smith
- Otolaryngology-HNS, University of Utah, Salt Lake City, Utah, USA
| | - Michael B Soyka
- Otolaryngology-HNS, University of Zurich, University Hospital of Zurich, Zurich, Switzerland
| | - Masayoshi Takashima
- Otolaryngology-HNS, Houston Methodist Academic Institute, Houston, Texas, USA
| | - Monica Tang
- Allergy/Immunology, University of California San Francisco, San Francisco, California, USA
| | | | - Malcolm B Taw
- Integrative East-West Medicine, University of California Los Angeles, Westlake Village, California, USA
| | - Jody Tversky
- Allergy/Immunology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Matthew A Tyler
- Otolaryngology-HNS, University of Minnesota, Minneapolis, Minnesota, USA
| | - Maria C Veling
- Otolaryngology-HNS, University of Texas Southwestern, Dallas, Texas, USA
| | - Dana Wallace
- Allergy/Immunology, Nova Southeastern University, Ft. Lauderdale, Florida, USA
| | - De Yun Wang
- Otolaryngology-HNS, National University of Singapore, Singapore, Singapore
| | - Andrew White
- Allergy/Immunology, Scripps Clinic, San Diego, California, USA
| | - Luo Zhang
- Otolaryngology-HNS, Beijing Tongren Hospital, Beijing, China
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8
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Hu J, Xu X, Li J, Jiang Y, Hong X, Rexrode KM, Wang G, Hu FB, Zhang H, Karmaus WJ, Wang X, Liang L. Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts. Clin Epigenetics 2023; 15:51. [PMID: 36966332 PMCID: PMC10040137 DOI: 10.1186/s13148-023-01442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 02/06/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND The mother-child inheritance of DNA methylation (DNAm) variations could contribute to the inheritance of disease susceptibility across generations. However, no study has investigated patterns of mother-child associations in DNAm at the genome-wide scale. It remains unknown whether there are sex differences in mother-child DNAm associations. RESULTS Using genome-wide DNAm profiling data (721,331 DNAm sites, including 704,552 on autosomes and 16,779 on the X chromosome) of 396 mother-newborn pairs (54.5% male) from the Boston Birth Cohort, we found significant sex differences in mother-newborn correlations in genome-wide DNAm patterns (Spearman's rho = 0.91-0.98; p = 4.0 × 10-8), with female newborns having stronger correlations. Sex differences in correlations were attenuated but remained significant after excluding X-chromosomal DNAm sites (Spearman's rho = 0.91-0.98; p = 0.035). Moreover, 89,267 DNAm sites (12.4% of all analyzed, including 88,051 [12.5% of analyzed] autosomal and 1,216 [7.2% of analyzed] X-chromosomal sites) showed significant mother-newborn associations in methylation levels, and the top autosomal DNAm sites had high heritability than the genome-wide background (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.92). Additionally, significant interactions between newborn sex and methylation levels were observed for 11 X-chromosomal and 4 autosomal DNAm sites that were mapped to genes that have been associated with sex-specific disease/traits or early development (e.g., EFHC2, NXY, ADCYAP1R1, and BMP4). Finally, 18,769 DNAm sites (14,482 [77.2%] on the X chromosome) showed mother-newborn differences in methylation levels that were significantly associated with newborn sex, and the top autosomal DNAm sites had relatively small heritability (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.23). These DNAm sites were mapped to 2,532 autosomal genes and 978 X-chromosomal genes with significant enrichment in pathways involved in neurodegenerative and psychological diseases, development, neurophysiological process, immune response, and sex-specific cancers. Replication analysis in the Isle of Wight birth cohort yielded consistent results. CONCLUSION In two independent birth cohorts, we demonstrated strong mother-newborn correlations in whole blood DNAm on both autosomes and ChrX, and such correlations vary substantially by sex. Future studies are needed to examine to what extent our findings contribute to developmental origins of pediatric and adult diseases with well-observed sex differences.
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Affiliation(s)
- Jie Hu
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Xin Xu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Jun Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiumei Hong
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kathryn M Rexrode
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guoying Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried J Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiaobin Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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9
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Recto KA, Huan T, Lee DH, Lee GY, Gereige J, Yao C, Hwang SJ, Joehanes R, Kelly RS, Lasky-Su J, O’Connor G, Levy D. Transcriptome-wide association study of circulating IgE levels identifies novel targets for asthma and allergic diseases. Front Immunol 2023; 14:1080071. [PMID: 36793728 PMCID: PMC9922991 DOI: 10.3389/fimmu.2023.1080071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
Measurement of circulating immunoglobulin E (IgE) concentration is helpful for diagnosing and treating asthma and allergic diseases. Identifying gene expression signatures associated with IgE might elucidate novel pathways for IgE regulation. To this end, we performed a discovery transcriptome-wide association study to identify differentially expressed genes associated with circulating IgE levels in whole-blood derived RNA from 5,345 participants in the Framingham Heart Study across 17,873 mRNA gene-level transcripts. We identified 216 significant transcripts at a false discovery rate <0.05. We conducted replication using the meta-analysis of two independent external studies: the Childhood Asthma Management Program (n=610) and the Genetic Epidemiology of Asthma in Costa Rica Study (n=326); we then reversed the discovery and replication cohorts, which revealed 59 significant genes that replicated in both directions. Gene ontology analysis revealed that many of these genes were implicated in immune function pathways, including defense response, inflammatory response, and cytokine production. Mendelian randomization (MR) analysis revealed four genes (CLC, CCDC21, S100A13, and GCNT1) as putatively causal (p<0.05) regulators of IgE levels. GCNT1 (beta=1.5, p=0.01)-which is a top result in the MR analysis of expression in relation to asthma and allergic diseases-plays a role in regulating T helper type 1 cell homing, lymphocyte trafficking, and B cell differentiation. Our findings build upon prior knowledge of IgE regulation and provide a deeper understanding of underlying molecular mechanisms. The IgE-associated genes that we identified-particularly those implicated in MR analysis-can be explored as promising therapeutic targets for asthma and IgE-related diseases.
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Affiliation(s)
- Kathryn A. Recto
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Tianxiao Huan
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Dong Heon Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Gha Young Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Jessica Gereige
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States
| | - Chen Yao
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Shih-Jen Hwang
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Roby Joehanes
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
| | - Rachel S. Kelly
- Brigham and Women’s Hospital, Channing Division of Network Medicine, Boston, MA, United States
| | - Jessica Lasky-Su
- Brigham and Women’s Hospital, Channing Division of Network Medicine, Boston, MA, United States
| | - George O’Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA, United States
| | - Daniel Levy
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
- The Framingham Heart Study, Framingham, MA, United States
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10
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Hussain SRA, Grayson MH. Chronic allergy signaling: is it all stressed-out mitochondria? Fac Rev 2022; 11:37. [PMID: 36644297 PMCID: PMC9816874 DOI: 10.12703/r/11-37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Allergic diseases in general, and chronic allergic inflammation in particular, are on the rise in the United States and other developed countries. The idea of chronic allergic disease as a chronic type 2 immune response has been around for several decades. However, data suggest that other mechanisms may be important in chronic disease. Therefore, we believe it is time for a paradigm shift in understanding the mechanistic causes of disease symptoms in these diseases. In this review, we have avoided the classic canonical pathways and focused on the emerging idea that oxidative stress, changes in immuno-metabolism, mitochondrial dysfunction, and epigenetic changes (particularly microRNA profile) may be working concurrently or synergistically to potentiate allergic disease symptoms. Furthermore, we have addressed how the epidemic of obesity exacerbates allergic disease via the dysregulation of the aforementioned factors.
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Affiliation(s)
- Syed-Rehan A Hussain
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children’s Hospital - The Ohio State University College of Medicine, Columbus, OH, USA
- Center for Clinical and Translational Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
- mailto:
| | - Mitchell H Grayson
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children’s Hospital - The Ohio State University College of Medicine, Columbus, OH, USA
- Center for Clinical and Translational Research, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
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11
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Wjst M. Exome variants associated with asthma and allergy. Sci Rep 2022; 12:21028. [PMID: 36470944 PMCID: PMC9722654 DOI: 10.1038/s41598-022-24960-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
The mutational spectrum of asthma and allergy associated genes is not known although recent biobank based exome sequencing studies included these traits. We therefore conducted a secondary analysis of exome data from 281,104 UK Biobank samples for association of mostly rare variants with asthma, allergic rhinitis and atopic dermatitis. Variants of interest (VOI) were tabulated, shared genes annotated and compared to earlier genome-wide SNP association studies (GWAS), whole genome sequencing, exome and bisulfit sequencing studies. 354 VOI were significantly associated with asthma, allergic rhinitis and atopic dermatitis. They cluster mainly in two large regions on chromosome 6 and 17. After exclusion of the variants associated with atopic dermatitis and redundant variants, 321 unique VOI remain in 122 unique genes. 30 genes are shared among the 87 genes with increased and the 65 genes with decreased risk for allergic disease. 85% of genes identified earlier by common GWAS SNPs are not replicated here. Most identified genes are located in interferon ɣ and IL33 signaling pathway. These genes include already known but also new pharmacological targets, including the IL33 receptor ST2/IL1RL1, as well as TLR1, ALOX15, GSDMA, BTNL2, IL13 and IKZF3. Future pharmacological studies will need to included these VOI for stratification of the study population paving the way to individualized treatment.
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Affiliation(s)
- Matthias Wjst
- Institute of Lung Health and Immunity (LHI), Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, München, Germany. .,Institut für KI und Informatik in der Medizin, Lehrstuhl für Medizinische Informatik, Klinikum Rechts der Isar, Grillparzerstr. 18, 81675, München, Germany.
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12
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Shen Y, Zhang N, Yang Y, Hong S, Bachert C. Local Immunoglobulin E in nasal polyps: Role and modulation. Front Immunol 2022; 13:961503. [PMID: 36159836 PMCID: PMC9492990 DOI: 10.3389/fimmu.2022.961503] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/19/2022] [Indexed: 11/29/2022] Open
Abstract
In the airway, IgE is traditionally regarded as a key mediator in allergic diseases, such as AR and allergic asthma. However, growing evidence demonstrates the importance of local IgE in airway inflammatory diseases, irrespective of the presence of allergy. In this review, we discuss the most recent evidence for IgE in chronic rhinosinusitis with nasal polyps(CRSwNP), including the local IgE’s characteristics, the modulation of its synthesis, and its function. The levels of local IgE are significantly elevated in polyps independently of IgE serum levels and atopic status. Local IgE, which is correlated with type 2 inflammation, is polyclonal and functional. IgE is produced by active B cells and is dependent on the class switch recombination(CSR). In NPs, this process is triggered by not only allergens but also microbial colonization, especially the superantigen- Staphylococcus aureus. The production of local IgE is modulated by lymphocytes(such as Tfh, ILC2s, iTreg), cytokines(such as IL-4, IL-13, IFN-γ, TGF-β, IL-2, IL-21), transcription factors, and B cell-intrinsic factor. Due to the central role of IgE in NPs, it is regarded as an ideal target for therapy and has been proved to be clinically successful. Based on this knowledge, we believe that exploring the trigger and regulatory factors for the activation of local B cells and CSR to IgE will provide more valuable information for us to recognize the pathological mechanisms of local IgE and offer the possible option for new therapeutic targets of nasal polyps.
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Affiliation(s)
- Yang Shen
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Nan Zhang
- Upper Airways Research Laboratory, Department of Otorhinolaryngology, Ghent University, Ghent, Belgium
| | - Yucheng Yang
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Suling Hong
- Department of Otorhinolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Claus Bachert
- Upper Airways Research Laboratory, Department of Otorhinolaryngology, Ghent University, Ghent, Belgium
- Division of Otorhinolaryngology Diseases, Department of Clinical Sciences, Intervention and Technology (CLINTEC), Karolinska Institute, Stockholm, Sweden
- *Correspondence: Claus Bachert,
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13
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Peng G, Xi Y, Bellini C, Pham K, Zhuang ZW, Yan Q, Jia M, Wang G, Lu L, Tang MS, Zhao H, Wang H. Nicotine dose-dependent epigenomic-wide DNA methylation changes in the mice with long-term electronic cigarette exposure. Am J Cancer Res 2022; 12:3679-3692. [PMID: 36119846 PMCID: PMC9442002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/16/2022] [Indexed: 04/20/2023] Open
Abstract
Epigenomic-wide DNA methylation profiling holds the potential to reflect both electronic cigarette exposure-associated risks and individual poor health outcomes. However, a systemic study in animals or humans is still lacking. Using the Infinium Mouse Methylation BeadChip, we examined the DNA methylation status of white blood cells in male ApoE-/- mice after 14 weeks of electronic cigarette exposure with the InExpose system (2 hr/day, 5 days/week, 50% PG and 50% VG) with low (6 mg/ml) and high (36 mg/ml) nicotine concentrations. Our results indicate that electronic cigarette aerosol inhalation induces significant alteration of 8,985 CpGs in a dose-dependent manner (FDR<0.05); 7,389 (82.2%) of the CpG sites are annotated with known genes. Among the top 6 significant CpG sites (P-value<1e-8), 4 CpG sites are located in the known genes, and most (3/5) of these genes have been related to cigarette smoking. The other two CpGs are close to/associated with the Phc2 gene that was recently linked to smoking in a transcriptome-wide associations study. Furthermore, the gene set enrichment analysis highlights the activation of MAPK and 4 cardiomyocyte/cardiomyopathy-related signaling pathways (including adrenergic signaling in cardiomyocytes and arrhythmogenic right ventricular cardiomyopathy) following repeated electronic cigarette use. The MAPK pathway activation correlates well with our finding of increased cytokine mRNA expression after electronic cigarette exposure in the same batch of mice. Interestingly, two pathways related to mitochondrial activities, namely mitochondrial gene expression and mitochondrial translation, are also activated after electronic cigarette exposure. Elucidating the relationship between these pathways and the increased circulating mitochondrial DNA observed here will provide further insight into the cell-damaging effects of prolonged inhalation of e-cigarette aerosols.
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Affiliation(s)
- Gang Peng
- Department of Biostatistics, Yale University School of Public HealthNew Haven, USA
| | - Yibo Xi
- Department of Pathology, Yale University School of MedicineNew Haven, USA
| | - Chiara Bellini
- Department of Bioengineering, College of Engineering, Northeastern UniversityUSA
| | - Kien Pham
- Department of Pathology, Yale University School of MedicineNew Haven, USA
| | - Zhen W Zhuang
- Department of Cardiovascular Medicine, Yale University School of MedicineNew Haven, USA
| | - Qin Yan
- Department of Pathology, Yale University School of MedicineNew Haven, USA
| | - Man Jia
- Department of Pathology, Yale University School of MedicineNew Haven, USA
| | - Guilin Wang
- Department of Genetics, Yale University School of MedicineNew Haven, USA
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale University School of Public HealthNew Haven, USA
| | - Moon-Shong Tang
- Department of Environmental Medicine, New York University School of MedicineNew York, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale University School of Public HealthNew Haven, USA
| | - He Wang
- Department of Pathology, Yale University School of MedicineNew Haven, USA
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14
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Sharma S, Yang IV, Schwartz DA. Epigenetic regulation of immune function in asthma. J Allergy Clin Immunol 2022; 150:259-265. [PMID: 35717251 PMCID: PMC9378596 DOI: 10.1016/j.jaci.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 12/13/2022]
Abstract
Asthma is a common complex respiratory disease characterized by chronic airway inflammation and partially reversible airflow obstruction resulting from genetic and environmental determinants. Because epigenetic marks influence gene expression and can be modified by both environmental exposures and genetic variation, they are increasingly recognized as relevant to the pathogenesis of asthma and may be a key link between environmental exposures and asthma susceptibility. Unlike changes to DNA sequence, epigenetic signatures are dynamic and reversible, creating an opportunity for not only therapeutic targets but may serve as biomarkers to follow disease course and identify molecular subtypes in heterogeneous diseases such as asthma. In this review, we will examine the relationship between asthma and 3 key epigenetic processes that modify gene expression: DNA methylation, modification of histone tails, and noncoding RNAs. In addition to presenting a comprehensive assessment of the existing epigenetic studies focusing on immune regulation in asthma, we will discuss future directions for epigenetic investigation in allergic airway disease.
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Affiliation(s)
- Sunita Sharma
- Divisions of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo.
| | - Ivana V Yang
- Divisions of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo; Divisions of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - David A Schwartz
- Divisions of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
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15
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O'Donnell VB. New appreciation for an old pathway: the Lands Cycle moves into new arenas in health and disease. Biochem Soc Trans 2022; 50:1-11. [PMID: 35225335 PMCID: PMC9022965 DOI: 10.1042/bst20210579] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 02/08/2023]
Abstract
The Lands Pathway is a fundamental biochemical process named for its discovery by William EM Lands and revealed in a series of seminal papers published in the Journal of Biological Chemistry between 1958-65. It describes the selective placement in phospholipids of acyl chains, by phospholipid acyltransferases. This pathway has formed a core component of our knowledge of phospholipid and also diglyceride metabolism in mammalian tissues for over 60 years now. Our understanding of how the Lands pathways are enzymatically mediated via large families of related gene products that display both substrate and tissue specificity has grown exponentially since. Recent studies building on this are starting to reveal key roles for the Lands pathway in specific scenarios, in particular inflammation, immunity and inflammation. This review will cover the Lands cycle from historical perspectives first, then present new information on how this important cycle forms a central regulatory node connecting fatty acyl and phospholipid metabolism and how its altered regulation may present new opportunities for therapeutic intervention in human disease.
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Affiliation(s)
- Valerie B. O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4SN, U.K
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16
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Abstract
The prevalence of allergic diseases such as asthma is globally increasing, posing threat to the life quality of the affected population. Genome-wide association studies (GWAS) suggest that genetic variations only account for a small proportion of immunoglobulin E (IgE)-mediated type I hypersensitivity. Recently, epigenetics has gained attention as an approach to further understand the missing heritability and underpinning mechanisms of allergic diseases. Furthermore, epigenetic regulation allows the evaluation of the interaction between an individual's genetic predisposition and their environmental exposures. This chapter summarizes several large-scale epigenome-wide association studies (EWAS) on asthma and other allergic diseases and draws a blueprint for future analysis and research direction.
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Affiliation(s)
- Yale Jiang
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA.
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Bermick J, Schaller M. Epigenetic regulation of pediatric and neonatal immune responses. Pediatr Res 2022; 91:297-327. [PMID: 34239066 DOI: 10.1038/s41390-021-01630-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Epigenetic regulation of transcription is a collective term that refers to mechanisms known to regulate gene transcription without changing the underlying DNA sequence. These mechanisms include DNA methylation and histone tail modifications which influence chromatin accessibility, and microRNAs that act through post-transcriptional gene silencing. Epigenetics is known to regulate a variety of biological processes, and the role of epigtenetics in immunity and immune-mediated diseases is becoming increasingly recognized. While DNA methylation is the most widely studied, each of these systems play an important role in the development and maintenance of appropriate immune responses. There is clear evidence that epigenetic mechanisms contribute to developmental stage-specific immune responses in a cell-specific manner. There is also mounting evidence that prenatal exposures alter epigenetic profiles and subsequent immune function in exposed offspring. Early life exposures that are associated with poor long-term health outcomes also appear to impact immune specific epigenetic patterning. Finally, each of these epigenetic mechanisms contribute to the pathogenesis of a wide variety of diseases that manifest during childhood. This review will discuss each of these areas in detail. IMPACT: Epigenetics, including DNA methylation, histone tail modifications, and microRNA expression, dictate immune cell phenotypes. Epigenetics influence immune development and subsequent immune health. Prenatal, perinatal, and postnatal exposures alter immune cell epigenetic profiles and subsequent immune function. Numerous pediatric-onset diseases have an epigenetic component. Several successful strategies for childhood diseases target epigenetic mechanisms.
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Affiliation(s)
- Jennifer Bermick
- Department of Pediatrics, Division of Neonatology, University of Iowa, Iowa City, IA, USA. .,Iowa Inflammation Program, University of Iowa, Iowa City, IA, USA.
| | - Matthew Schaller
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Florida, Gainesville, FL, USA
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18
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The Vista of Application of Specific Anaphylaxis Accurate Diagnosis Based on DNA Single-Nucleotide Methylation Sites. CONTRAST MEDIA & MOLECULAR IMAGING 2021; 2021:8202068. [PMID: 34908915 PMCID: PMC8635942 DOI: 10.1155/2021/8202068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/21/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
Anaphylaxis has rapidly spread around the world in the last several decades. Environmental factors seem to play a major role, and epigenetic marks, especially DNA methylation, get more attention. We discussed several GEO opening data classifications with TOP 100 specific methylation region values (normalized M-values on line) by machine learning, which are remarkable to classify specific anaphylaxis after monoallergen exposure. Then, we sequenced the whole-genome DNA methylation of six people (3 wormwood monoallergen atopic rhinitis patients and 3 normal-immune people) during the pollen season and analyzed the difference of the single nucleotide and DNA region. The results' divergences were obvious (the differential single nucleotides were mostly distributed in nongene regions but the differential DNA regions of GWAS, on the other hand), which may have caused most single nucleotides to be concealed in the regions' sequences. Therefore, we suggest that we should conduct more “pragmatic” and directly find special single-nucleotide changes after exposure to atopic allergens instead of complex correlativity. It is possible to try to use DNA methylation marks to accurately diagnose anaphylaxis and form a machine learning classification based on the single methylated CpGs.
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19
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Valentine WJ, Yanagida K, Kawana H, Kono N, Noda NN, Aoki J, Shindou H. Update and nomenclature proposal for mammalian lysophospholipid acyltransferases which create membrane phospholipid diversity. J Biol Chem 2021; 298:101470. [PMID: 34890643 PMCID: PMC8753187 DOI: 10.1016/j.jbc.2021.101470] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
The diversity of glycerophospholipid species in cellular membranes is immense and affects various biological functions. Glycerol-3-phosphate acyltransferases (GPATs) and lysophospholipid acyltransferases (LPLATs), in concert with phospholipase A1/2s enzymes, contribute to this diversity via selective esterification of fatty acyl chains at the sn-1 or sn-2 positions of membrane phospholipids. These enzymes are conserved across all kingdoms, and in mammals four GPATs of the 1-acylglycerol-3-phosphate O-acyltransferase (AGPAT) family and at least 14 LPLATs, either of the AGPAT or the membrane-bound O-acyltransferase (MBOAT) families, have been identified. Here we provide an overview of the biochemical and biological activities of these mammalian enzymes, including their predicted structures, involvements in human diseases, and essential physiological roles as revealed by gene-deficient mice. Recently, the nomenclature used to refer to these enzymes has generated some confusion due to the use of multiple names to refer to the same enzyme and instances of the same name being used to refer to completely different enzymes. Thus, this review proposes a more uniform LPLAT enzyme nomenclature, as well as providing an update of recent advances made in the study of LPLATs, continuing from our JBC mini review in 2009.
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Affiliation(s)
- William J Valentine
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Tokyo 162-8655, Japan; Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo, 187-8502, Japan
| | - Keisuke Yanagida
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Tokyo 162-8655, Japan
| | - Hiroki Kawana
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, Tokyo 141-0021, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideo Shindou
- Department of Lipid Signaling, National Center for Global Health and Medicine (NCGM), Shinjuku-ku, Tokyo 162-8655, Japan; Department of Lipid Medical Science, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
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20
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Xu CJ, Scheltema NM, Qi C, Vedder R, Klein LBC, Nibbelke EE, van der Ent CK, Bont LJ, Koppelman GH. Infant RSV immunoprophylaxis changes nasal epithelial DNA methylation at 6 years of age. Pediatr Pulmonol 2021; 56:3822-3831. [PMID: 34473906 DOI: 10.1002/ppul.25643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) infection has been associated with childhood wheeze and asthma, and potential mechanisms include persistent epigenetic effects. METHODS In the randomized, placebo-controlled MAKI trial, 429 preterm infants randomly received RSV immunoprophylaxis with palivizumab or placebo during their first RSV season. Children were followed until age 6 for asthma evaluation. DNA methylation in cells obtained by nasal brushes at age 6 was measured by Illumina MethylationEPIC array. RESULTS RSV immunoprophylaxis in infancy had a significant impact on global methylation patterns in nasal cells at age 6. The first principal component (PC) related to the immunoprophylaxis intervention was enriched for the pathway "detection of chemical stimulus involved in sensory perception of smell" and "T cell differentiation." Subsequent analysis of these PCs indicated an effect of RSV immunoprophylaxis on cell type composition of nasal brushed cells. Three CpG sites, cg18040241, cg08243963, and cg19555973 which are annotated to genes GLB1L2, SC5D, and BPIFB1, were differentially methylated at genome-wide significance, but were not associated with asthma. CONCLUSION The study provides the first proof of concept that RSV immunoprophylaxis during infancy has long-term effects on nasal epigenetic signatures at age 6, relating to host sensory perception, epidermal growth factor receptor signaling, and adaptive immune responses.
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Affiliation(s)
- Cheng-Jian Xu
- Centre for Individualised Infection Medicine, CiiM, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Research Group of Bioinformatics and Computational Genomics, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nienke M Scheltema
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Cancan Qi
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,GRIAC Research Institute Groningen, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Rolf Vedder
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Laura B C Klein
- Department of Molecular Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Elisabeth E Nibbelke
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
| | - Louis J Bont
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands.,Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,GRIAC Research Institute Groningen, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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21
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Dietary Fibers: Effects, Underlying Mechanisms and Possible Role in Allergic Asthma Management. Nutrients 2021; 13:nu13114153. [PMID: 34836408 PMCID: PMC8621630 DOI: 10.3390/nu13114153] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 12/13/2022] Open
Abstract
The prevalence of asthma is increasing, but the cause remains under debate. Research currently focuses on environmental and dietary factors that may impact the gut-lung axis. Dietary fibers are considered to play a crucial role in supporting diversity and activity of the microbiome, as well as immune homeostasis in the gut and lung. This review discusses the current state of knowledge on how dietary fibers and their bacterial fermentation products may affect the pathophysiology of allergic asthma. Moreover, the impact of dietary fibers on early type 2 asthma management, as shown in both pre-clinical and clinical studies, is described. Short-chain fatty acids, fiber metabolites, modulate host immunity and might reduce the risk of allergic asthma development. Underlying mechanisms include G protein-coupled receptor activation and histone deacetylase inhibition. These results are supported by studies in mice, children and adults with allergic asthma. Fibers might also exert direct effects on the immune system via yet to be elucidated mechanisms. However, the effects of specific types of fiber, dosages, duration of treatment, and combination with probiotics, need to be explored. There is an urgent need to further valorize the potential of specific dietary fibers in prevention and treatment of allergic asthma by conducting more large-scale dietary intervention trials.
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22
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Barišić A, Stanković A, Stojković L, Pereza N, Ostojić S, Peterlin A, Peterlin B, Vraneković J. Maternal LINE-1 DNA Methylation in Early Spontaneous Preterm Birth. Biol Res Nurs 2021; 24:85-93. [PMID: 34727781 DOI: 10.1177/10998004211043571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite considerable effort aimed at decreasing the incidence of spontaneous preterm birth (SPTB), it remains the leading cause of infant mortality and morbidity. The aim of this study was to evaluate maternal LINE-1 DNA methylation (DNAm), along with DNMT polymorphisms and factors proposed to modulate DNAm, in patients who delivered early preterm. This case-control study included women who delivered spontaneously early preterm (23-336/7 weeks of gestation), and control women. DNAm was analyzed in peripheral blood lymphocytes by quantification of LINE-1 DNAm using the MethyLight method. There was no significant difference in LINE-1 DNAm between patients with early PTB and controls. Among the investigated predictors, only the history of previous PTB was significantly associated with LINE-1 DNAm in PTB patients (β = -0.407; R2 = 0.131; p = 0.011). The regression analysis showed the effect of DNMT3B rs1569686 TT+TG genotypes on LINE-1 DNAm in patients with familial PTB (β = -0.524; R2 = 0.275; p = 0.037). Our findings suggest novel associations of maternal LINE-1 DNA hypomethylation with DNMT3B rs1569686 T allele. These results also contribute to the understanding of a complex (epi)genetic and environmental relationship underlying the early PTB.
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Affiliation(s)
- Anita Barišić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Aleksandra Stanković
- Department for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Serbia
| | - Ljiljana Stojković
- Department for Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences-National Institute of the Republic of Serbia, University of Belgrade, Serbia
| | - Nina Pereza
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Saša Ostojić
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ana Peterlin
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Center Ljubljana, Slovenia
| | - Jadranka Vraneković
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
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23
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Soliai MM, Kato A, Helling BA, Stanhope CT, Norton JE, Naughton KA, Klinger AI, Thompson EE, Clay SM, Kim S, Celedón JC, Gern JE, Jackson DJ, Altman MC, Kern RC, Tan BK, Schleimer RP, Nicolae DL, Pinto JM, Ober C. Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus. Genome Med 2021; 13:157. [PMID: 34629083 PMCID: PMC8504130 DOI: 10.1186/s13073-021-00967-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/10/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified thousands of variants associated with asthma and other complex diseases. However, the functional effects of most of these variants are unknown. Moreover, GWASs do not provide context-specific information on cell types or environmental factors that affect specific disease risks and outcomes. To address these limitations, we used an upper airway epithelial cell (AEC) culture model to assess transcriptional and epigenetic responses to rhinovirus (RV), an asthma-promoting pathogen, and provide context-specific functional annotations to variants discovered in GWASs of asthma. METHODS Genome-wide genetic, gene expression, and DNA methylation data in vehicle- and RV-treated upper AECs were collected from 104 individuals who had a diagnosis of airway disease (n=66) or were healthy participants (n=38). We mapped cis expression and methylation quantitative trait loci (cis-eQTLs and cis-meQTLs, respectively) in each treatment condition (RV and vehicle) in AECs from these individuals. A Bayesian test for colocalization between AEC molecular QTLs and adult onset asthma and childhood onset asthma GWAS SNPs, and a multi-ethnic GWAS of asthma, was used to assign the function to variants associated with asthma. We used Mendelian randomization to demonstrate DNA methylation effects on gene expression at asthma colocalized loci. RESULTS Asthma and allergic disease-associated GWAS SNPs were specifically enriched among molecular QTLs in AECs, but not in GWASs from non-immune diseases, and in AEC eQTLs, but not among eQTLs from other tissues. Colocalization analyses of AEC QTLs with asthma GWAS variants revealed potential molecular mechanisms of asthma, including QTLs at the TSLP locus that were common to both the RV and vehicle treatments and to both childhood onset and adult onset asthma, as well as QTLs at the 17q12-21 asthma locus that were specific to RV exposure and childhood onset asthma, consistent with clinical and epidemiological studies of these loci. CONCLUSIONS This study provides evidence of functional effects for asthma risk variants in AECs and insight into RV-mediated transcriptional and epigenetic response mechanisms that modulate genetic effects in the airway and risk for asthma.
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Affiliation(s)
- Marcus M Soliai
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
| | - Atsushi Kato
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Britney A Helling
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | - James E Norton
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Aiko I Klinger
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Emma E Thompson
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Selene M Clay
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Soyeon Kim
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, USA
| | - Robert C Kern
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bruce K Tan
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Robert P Schleimer
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dan L Nicolae
- Department of Statistics, University of Chicago, Chicago, IL, USA
| | - Jayant M Pinto
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Carole Ober
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
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24
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Suhre K, Zaghlool S. Connecting the epigenome, metabolome and proteome for a deeper understanding of disease. J Intern Med 2021; 290:527-548. [PMID: 33904619 DOI: 10.1111/joim.13306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/26/2022]
Abstract
Epigenome-wide association studies (EWAS) identify genes that are dysregulated by the studied clinical endpoints, thereby indicating potential new diagnostic biomarkers, drug targets and therapy options. Combining EWAS with deep molecular phenotyping, such as approaches enabled by metabolomics and proteomics, allows further probing of the underlying disease-associated pathways. For instance, methylation of the TXNIP gene is associated robustly with prevalent type 2 diabetes and further with metabolites that are short-term markers of glycaemic control. These associations reflect TXNIP's function as a glucose uptake regulator by interaction with the major glucose transporter GLUT1 and suggest that TXNIP methylation can be used as a read-out for the organism's exposure to glucose stress. Another case is the association between DNA methylation of the AHRR and F2RL3 genes with smoking and a protein that is involved in the reprogramming of the bronchial epithelium. These examples show that associations between DNA methylation and intermediate molecular traits can open new windows into how the body copes with physiological challenges. This knowledge, if carefully interpreted, may indicate novel therapy options and, together with monitoring of the methylation state of specific methylation sites, may in the future allow the early diagnosis of impending disease. It is essential for medical practitioners to recognize the potential that this field holds in translating basic research findings to clinical practice. In this review, we present recent advances in the field of EWAS with metabolomics and proteomics and discuss both the potential and the challenges of translating epigenetic associations, with deep molecular phenotypes, to biomedical applications.
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Affiliation(s)
- K Suhre
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
| | - S Zaghlool
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
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25
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Could the Epigenetics of Eosinophils in Asthma and Allergy Solve Parts of the Puzzle? Int J Mol Sci 2021; 22:ijms22168921. [PMID: 34445627 PMCID: PMC8396248 DOI: 10.3390/ijms22168921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics is a field of study investigating changes in gene expression that do not alter the DNA sequence. These changes are often influenced by environmental or social factors and are reversible. Epigenetic mechanisms include DNA methylation, histone modification, and noncoding RNA. Understanding the role of these epigenetic mechanisms in human diseases provides useful information with regard to disease severity and development. Several studies have searched for the epigenetic mechanisms that regulate allergies and asthma; however, only few studies have used samples of eosinophil, a proinflammatory cell type known to be largely recruited during allergic or asthmatic inflammation. Such studies would enable us to better understand the factors that influence the massive recruitment of eosinophils during allergic and asthmatic symptoms. In this review, we sought to summarize different studies that aimed to discover differential patterns of histone modifications, DNA methylation, and noncoding RNAs in eosinophil samples of individuals with certain diseases, with a particular focus on those with asthma or allergic diseases.
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26
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Komlósi ZI, van de Veen W, Kovács N, Szűcs G, Sokolowska M, O'Mahony L, Akdis M, Akdis CA. Cellular and molecular mechanisms of allergic asthma. Mol Aspects Med 2021; 85:100995. [PMID: 34364680 DOI: 10.1016/j.mam.2021.100995] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/21/2022]
Abstract
Asthma is a chronic disease of the airways, which affects more than 350 million people worldwide. It is the most common chronic disease in children, affecting at least 30 million children and young adults in Europe. Asthma is a complex, partially heritable disease with a marked heterogeneity. Its development is influenced both by genetic and environmental factors. The most common, as well as the most well characterized subtype of asthma is allergic eosinophilic asthma, which is characterized by a type 2 airway inflammation. The prevalence of asthma has substantially increased in industrialized countries during the last 60 years. The mechanisms underpinning this phenomenon are incompletely understood, however increased exposure to various environmental pollutants probably plays a role. Disease inception is thought to be enabled by a disadvantageous shift in the balance between protective and harmful lifestyle and environmental factors, including exposure to protective commensal microbes versus infection with pathogens, collectively leading to airway epithelial cell damage and disrupted barrier integrity. Epithelial cell-derived cytokines are one of the main drivers of the type 2 immune response against innocuous allergens, ultimately leading to infiltration of lung tissue with type 2 T helper (TH2) cells, type 2 innate lymphoid cells (ILC2s), M2 macrophages and eosinophils. This review outlines the mechanisms responsible for the orchestration of type 2 inflammation and summarizes the novel findings, including but not limited to dysregulated epithelial barrier integrity, alarmin release and innate lymphoid cell stimulation.
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Affiliation(s)
- Zsolt I Komlósi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary.
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Nóra Kovács
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary; Lung Health Hospital, Munkácsy Mihály Str. 70, 2045, Törökbálint, Hungary
| | - Gergő Szűcs
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary; Department of Pulmonology, Semmelweis University, Tömő Str. 25-29, 1083, Budapest, Hungary
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Liam O'Mahony
- Department of Medicine and School of Microbiology, APC Microbiome Ireland, University College Cork, Ireland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
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27
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Benincasa G, DeMeo DL, Glass K, Silverman EK, Napoli C. Epigenetics and pulmonary diseases in the horizon of precision medicine: a review. Eur Respir J 2021; 57:13993003.03406-2020. [PMID: 33214212 DOI: 10.1183/13993003.03406-2020] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
Epigenetic mechanisms represent potential molecular routes which could bridge the gap between genetic background and environmental risk factors contributing to the pathogenesis of pulmonary diseases. In patients with COPD, asthma and pulmonary arterial hypertension (PAH), there is emerging evidence of aberrant epigenetic marks, mainly including DNA methylation and histone modifications which directly mediate reversible modifications to the DNA without affecting the genomic sequence. Post-translational events and microRNAs can be also regulated epigenetically and potentially participate in disease pathogenesis. Thus, novel pathogenic mechanisms and putative biomarkers may be detectable in peripheral blood, sputum, nasal and buccal swabs or lung tissue. Besides, DNA methylation plays an important role during the early phases of fetal development and may be impacted by environmental exposures, ultimately influencing an individual's susceptibility to COPD, asthma and PAH later in life. With the advances in omics platforms and the application of computational biology tools, modelling the epigenetic variability in a network framework, rather than as single molecular defects, provides insights into the possible molecular pathways underlying the pathogenesis of COPD, asthma and PAH. Epigenetic modifications may have clinical applications as noninvasive biomarkers of pulmonary diseases. Moreover, combining molecular assays with network analysis of epigenomic data may aid in clarifying the multistage transition from a "pre-disease" to "disease" state, with the goal of improving primary prevention of lung diseases and its subsequent clinical management.We describe epigenetic mechanisms known to be associated with pulmonary diseases and discuss how network analysis could improve our understanding of lung diseases.
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Affiliation(s)
- Giuditta Benincasa
- Dept of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Dawn L DeMeo
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine and the Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Claudio Napoli
- Dept of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Naples, Italy .,Clinical Dept of Internal and Specialty Medicine (DAI), University Hospital (AOU), University of Campania "Luigi Vanvitelli", Naples, Italy
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28
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Abstract
OBJECTIVES Recent evidence from the fields of microbiology and immunology, as well as a small number of human sepsis studies, suggest that epigenetic regulation may play a central role in the pathogenesis of sepsis. The term "epigenetics" refers to regulatory mechanisms that control gene expression but are not related to changes in DNA sequence. These include DNA methylation, histone modifications, and regulation of transcription via non-coding RNAs. Epigenetic modifications, occurring in response to external stressors, lead to changes in gene expression, and thus lie at the intersection between genetics and the environment. In this review, we examine data from in vitro studies, animal studies, and the existing human sepsis studies in epigenetics to demonstrate that epigenetic mechanisms are likely central to the pathogenesis of sepsis and that epigenetic therapies may have potential in the treatment of sepsis and its associated organ failures. DATA SOURCES Online search of published scientific literature via Pubmed using the term "epigenetics" in combination with the terms "sepsis", "infection", "bacterial infection", "viral infection", "critical illness", "acute respiratory distress syndrome", and "acute lung injury". STUDY SELECTION Articles were chosen for inclusion based on their relevance to sepsis, acute inflammation, sepsis-related immune suppression, and sepsis-related organ failure. Reference lists were reviewed to identify additional relevant articles. DATA EXTRACTION Relevant data was extracted and synthesized for narrative review. DATA SYNTHESIS Epigenetic regulation is a key determinant of gene expression in sepsis. At the onset of infection, host-pathogen interactions often result in epigenetic alterations to host cells that favor pathogen survival. In parallel, the host inflammatory response is characterized by epigenetic modifications in key regulatory genes, including tumor necrosis factor and interleukin-1β. In human sepsis patients, multiple epigenetic modifying enzymes show differential expression in early sepsis, suggesting a role for epigenetics in coordinating the response to infection. In the later stages of sepsis, epigenetic modifications accompany endotoxin tolerance and the immune-suppressed state. In animal models, treatment with epigenetic modifiers can mitigate the effects of sepsis and improve survival as well as reverse sepsis-associated organ injury. CONCLUSIONS Epigenetic modifications are associated with key phases of sepsis, from the host-pathogen interaction, to acute inflammation, to immune suppression. Epigenetic markers show promise in the diagnosis and prognosis of sepsis and epigenetic modifying agents show promise as therapeutic tools in animal models of sepsis. Human studies in the area of epigenetics are sorely lacking and should be a priority for sepsis researchers.
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Han L, Kaushal A, Zhang H, Kadalayil L, Duan J, Holloway JW, Karmaus W, Banerjee P, Tsai SF, Wen HJ, Arshad SH, Wang SL. DNA Methylation at Birth is Associated with Childhood Serum Immunoglobulin E Levels. Epigenet Insights 2021; 14:25168657211008108. [PMID: 33870089 PMCID: PMC8024453 DOI: 10.1177/25168657211008108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/25/2020] [Indexed: 01/09/2023] Open
Abstract
Immunoglobulin E (IgE) is known to play an important role in allergic diseases. Epigenetic traits acquired due to modification of deoxyribonucleic acid (DNA) methylation (DNAm) in early life may have phenotypic consequences through their role in transcriptional regulation with relevance to the developmental origins of diseases including allergy. However, epigenome-scale studies on the longitudinal association of cord blood DNAm with IgE over time are lacking. Our study aimed to examine the association of DNAm at birth with childhood serum IgE levels during early life. Genome-scale DNAm and total serum IgE measured at birth, 5, 8, and 11 years of children in the Taiwan Maternal and Infant Cohort Study were included in the study in the discovery stage. Linear mixed models were implemented to assess the association between cord blood DNAm at ~310K 5′-cytosine-phosphate-guanine-3′ (CpG) sites with repeated IgE measurements, adjusting for cord blood IgE. Identified statistically significant CpGs (at a false discovery rate, FDR, of 0.05) were further tested in an independent replication cohort, the Isle of Wight (IoW) birth cohort. We mapped replicated CpGs to genes and conducted gene ontology analysis using ToppFun to identify significantly enriched pathways and biological processes of the genes. Cord blood DNAm of 273 CpG sites were significantly (FDR = 0.05) associated with IgE levels longitudinally. Among the identified CpGs available in both cohorts (184 CpGs), 92 CpGs (50%) were replicated in the IoW in terms of consistency in direction of associations between DNA methylation and IgE levels later in life, and 16 of the 92 CpGs showed statistically significant associations (P < .05). Gene ontology analysis identified 4 pathways (FDR = 0.05). The identified 16 CpG sites had the potential to serve as epigenetic markers associated with later IgE production, beneficial to allergic disease prevention and intervention.
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Affiliation(s)
- Luhang Han
- Department of Mathematical Sciences, University of Memphis, Memphis, TN, USA
| | | | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN, USA
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jiasong Duan
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN, USA
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.,Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, University of Memphis, Memphis, TN, USA
| | - Pratik Banerjee
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL, USA
| | - Shih-Fen Tsai
- Division of Environmental Health and Occupational Medicine, National Health Research Institutes, Miaoli
| | - Hui-Ju Wen
- Division of Environmental Health and Occupational Medicine, National Health Research Institutes, Miaoli
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,David Hide Asthma and Allergy Research Centre, St Mary's Hospital, Newport, Isle of Wight, UK
| | - Shu-Li Wang
- Division of Environmental Health and Occupational Medicine, National Health Research Institutes, Miaoli.,School of Public Health, National Defense Medical Center, Taipei.,Department of Public Health, China Medical University, Taichung
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30
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Tyler SR, Chun Y, Ribeiro VM, Grishina G, Grishin A, Hoffman GE, Do AN, Bunyavanich S. Merged Affinity Network Association Clustering: Joint multi-omic/clinical clustering to identify disease endotypes. Cell Rep 2021; 35:108975. [PMID: 33852839 PMCID: PMC8195153 DOI: 10.1016/j.celrep.2021.108975] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/25/2021] [Accepted: 03/18/2021] [Indexed: 12/21/2022] Open
Abstract
Although clinical and laboratory data have long been used to guide medical practice, this information is rarely integrated with multi-omic data to identify endotypes. We present Merged Affinity Network Association Clustering (MANAclust), a coding-free, automated pipeline enabling integration of categorical and numeric data spanning clinical and multi-omic profiles for unsupervised clustering to identify disease subsets. Using simulations and real-world data from The Cancer Genome Atlas, we demonstrate that MANAclust’s feature selection algorithms are accurate and outperform competitors. We also apply MANAclust to a clinically and multi-omically phenotyped asthma cohort. MANAclust identifies clinically and molecularly distinct clusters, including heterogeneous groups of “healthy controls” and viral and allergy-driven subsets of asthmatic subjects. We also find that subjects with similar clinical presentations have disparate molecular profiles, highlighting the need for additional testing to uncover asthma endotypes. This work facilitates data-driven personalized medicine through integration of clinical parameters with multi-omics. MANAclust is freely available at https://bitbucket.org/scottyler892/manaclust/src/master/. Clinical data commonly used in medical practice are underutilized in multi-omic analyses to identify disease endotypes. Tyler et al. present a python package called Merged Affinity Network Association Clustering (MANAclust) that automatically processes and integrates categorical and numeric data types, facilitating the inclusion of clinical data in multi-omic endotyping efforts.
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Affiliation(s)
- Scott R Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Victoria M Ribeiro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anh N Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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31
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Winkley K, Koseva B, Banerjee D, Cheung W, Selvarangan R, Pastinen T, Grundberg E. High-resolution epigenome analysis in nasal samples derived from children with respiratory viral infections reveals striking changes upon SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.09.21253155. [PMID: 33758880 PMCID: PMC7987039 DOI: 10.1101/2021.03.09.21253155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background DNA methylation patterns of the human genome can be modified by environmental stimuli and provide dense information on gene regulatory circuitries. We studied genome-wide DNA methylation in nasal samples from infants (<6 months) applying whole-genome bisulfite sequencing (WGBS) to characterize epigenome response to 10 different respiratory viral infections including SARS-CoV-2. Results We identified virus-specific differentially methylated regions (vDMR) with human metapneumovirus (hMPV) and SARS-CoV-2 followed by Influenza B (Flu B) causing the weakest vs. strongest epigenome response with 496 vs. 78541 and 14361 vDMR, respectively. We found a strong replication rate of FluB (52%) and SARS-CoV-2 (42%) vDMR in independent samples indicating robust epigenome perturbation upon infection. Among the FluB and SARS-CoV-2 vDMRs, around 70% were hypomethylated and significantly enriched among epithelial cell-specific regulatory elements whereas the hypermethylated vDMRs for these viruses mapped more frequently to immune cell regulatory elements, especially those of the myeloid lineage. The hypermethylated vDMRs were also enriched among genes and genetic loci in monocyte activation pathways and monocyte count. Finally, we perform single-cell RNA-sequencing characterization of nasal mucosa in response to these two viruses to functionally analyze the epigenome perturbations. Which supports the trends we identified in methylation data and highlights and important role for monocytes. Conclusions All together, we find evidence indicating genetic predisposition to innate immune response upon a respiratory viral infection. Our genome-wide monitoring of infant viral response provides first catalogue of associated host regulatory elements. Assessing epigenetic variation in individual patients may reveal evidence for viral triggers of childhood disease.
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Affiliation(s)
- Konner Winkley
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Boryana Koseva
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Dithi Banerjee
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Warren Cheung
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Tomi Pastinen
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, Missouri, US
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32
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Fiuza BSD, Fonseca HF, Meirelles PM, Marques CR, da Silva TM, Figueiredo CA. Understanding Asthma and Allergies by the Lens of Biodiversity and Epigenetic Changes. Front Immunol 2021; 12:623737. [PMID: 33732246 PMCID: PMC7957070 DOI: 10.3389/fimmu.2021.623737] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Exposure to different organisms (bacteria, mold, virus, protozoan, helminths, among others) can induce epigenetic changes affecting the modulation of immune responses and consequently increasing the susceptibility to inflammatory diseases. Epigenomic regulatory features are highly affected during embryonic development and are responsible for the expression or repression of different genes associated with cell development and targeting/conducting immune responses. The well-known, "window of opportunity" that includes maternal and post-natal environmental exposures, which include maternal infections, microbiota, diet, drugs, and pollutant exposures are of fundamental importance to immune modulation and these events are almost always accompanied by epigenetic changes. Recently, it has been shown that these alterations could be involved in both risk and protection of allergic diseases through mechanisms, such as DNA methylation and histone modifications, which can enhance Th2 responses and maintain memory Th2 cells or decrease Treg cells differentiation. In addition, epigenetic changes may differ according to the microbial agent involved and may even influence different asthma or allergy phenotypes. In this review, we discuss how exposure to different organisms, including bacteria, viruses, and helminths can lead to epigenetic modulations and how this correlates with allergic diseases considering different genetic backgrounds of several ancestral populations.
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Affiliation(s)
| | | | - Pedro Milet Meirelles
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia em Estudos Interdisciplinares e Transdisciplinares em Ecologia e Evolução (IN-TREE), Salvador, Brazil
| | - Cintia Rodrigues Marques
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista, Brazil
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33
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Proctor NK, Ertan-Bolelli T, Bolelli K, Taylor EW, Chiu NHL, Bowen JP. Towards a Better Understanding of Computational Models for Predicting DNA Methylation Effects at the Molecular Level. Curr Top Med Chem 2021; 20:901-909. [PMID: 32101127 DOI: 10.2174/1568026620666200226110019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 12/24/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022]
Abstract
Human DNA is a very sensitive macromolecule and slight changes in the structure of DNA can have disastrous effects on the organism. When nucleotides are modified, or changed, the resulting DNA sequence can lose its information, if it is part of a gene, or it can become a problem for replication and repair. Human cells can regulate themselves by using a process known as DNA methylation. This methylation is vitally important in cell differentiation and expression of genes. When the methylation is uncontrolled, however, or does not occur in the right place, serious pathophysiological consequences may result. Excess methylation causes changes in the conformation of the DNA double helix. The secondary structure of DNA is highly dependent upon the sequence. Therefore, if the sequence changes slightly the secondary structure can change as well. These slight changes will then cause the doublestranded DNA to be more open and available in some places where large adductions can come in and react with the DNA base pairs. Computer models have been used to simulate a variety of biological processes including protein function and binding, and there is a growing body of evidence that in silico methods can shed light on DNA methylation. Understanding the anomeric effect that contributes to the structural and conformational flexibility of furanose rings through a combination of quantum mechanical and experimental studies is critical for successful molecular dynamic simulations.
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Affiliation(s)
- Nathanael K Proctor
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - Tugba Ertan-Bolelli
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, United States.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, TR 06560, Turkey
| | - Kayhan Bolelli
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, United States.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, Ankara, TR 06560, Turkey.,LumiLabs LLC, Ulus, Ankara, TR 06050, Turkey
| | - Ethan W Taylor
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - Norman H L Chiu
- Department of Chemistry & Biochemistry, University of North Carolina Greensboro, Greensboro, NC 27402, United States
| | - J Phillip Bowen
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA 30341, United States
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34
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Watanabe H, Miyake K, Matsuoka T, Kojima R, Sakurai D, Masuyama K, Yamagata Z. LPCAT2 Methylation, a Novel Biomarker for the Severity of Cedar Pollen Allergic Rhinitis in Japan. Am J Rhinol Allergy 2020; 35:631-639. [PMID: 33356413 DOI: 10.1177/1945892420983646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Recently, the role of the epigenome in allergies has been receiving increasing attention. Although several genes that are methylated in relation to serum immunoglobulin E (IgE) concentration have been reported by epigenome-wide association studies, little is known about the DNA methylation sites associated with the symptoms and severity of cedar pollinosis (CP). OBJECTIVE Our aim was to analyze the association between DNA methylation and the symptoms and severity of CP in peripheral blood mononuclear cells (PBMCs) and nasal mucosa scraping cells (NMSCs). METHODS We recruited 70 participants during the cedar pollen dispersal season. IgE levels were measured by a fluorescence enzyme immunoassay. We analyzed DNA methylation of acyl-CoA thioesterase 7 (ACOT7), mucin 4 (MUC4), schlafen 12 (SLFN12), lysophosphatidylcholine acyltransferase 2 (LPCAT2), and interleukin-4 (IL4) in PBMCs and NMSCs using bisulfite next-generation sequencing; the correlation of DNA methylation with non-specific IgE and cedar pollen-specific IgE levels in peripheral blood samples was also investigated. Symptom severity and DNA methylation were investigated in 15 untreated CP patients. RESULTS Non-specific IgE levels showed a significant negative correlation with average IL4 methylation in PBMCs (r = -0.46, P < 0.0001) but not with methylation of ACOT7, MUC4, SLFN12, and LPCAT2. Cedar pollen-specific IgE levels showed a significant negative correlation with average IL4 and MUC4 methylation in PBMCs (r = -0.31, P = 0.01 and r = -0.241, P = 0.046, respectively) but not with methylation of ACOT7, SLFN12, and LPCAT2. The methylation of some genes in NMSCs was not significantly correlated with IgE levels. The mean methylation of LPCAT2 in NMSCs showed a decreasing trend with increasing severity of CP (P = 0.027). CONCLUSION LPCAT2 methylation in NMSCs may reflect the severity of CP and could be used as a novel biomarker to identify suitable treatment options for CP.
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Affiliation(s)
- Hiroyuki Watanabe
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan.,Department of Health Sciences, Graduate School of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Kunio Miyake
- Department of Health Sciences, Graduate School of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Tomokazu Matsuoka
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Reiji Kojima
- Department of Health Sciences, Graduate School of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Daiju Sakurai
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Keisuke Masuyama
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan.,Department of Otorhinolaryngology, Suwa Central Hospital, Chino, Japan
| | - Zentaro Yamagata
- Department of Health Sciences, Graduate School of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
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35
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Feng YCA, Guo Y, Pain L, Lathrop GM, Laprise C, Moffatt MF, Cookson WO, Liang L. Estimating cell-type-specific DNA methylation effects in heterogeneous cellular populations. Epigenomics 2020; 13:87-97. [PMID: 33350870 DOI: 10.2217/epi-2020-0147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: To develop a method for estimating cell-specific effects in epigenomic association studies in the presence of cell type heterogeneity. Materials & methods: We utilized Monte Carlo Expectation-Maximization algorithm with Metropolis-Hastings sampler to reconstruct the 'missing' cell-specific methylations and to estimate their associations with phenotypes free of confounding by cell type proportions. Results: Simulations showed reliable performance of the method under various settings including when the cell type is rare. Application to a real dataset recapitulated the directly measured cell-specific methylation pattern in whole blood. Conclusion: This work provides a framework to identify important cell groups and account for cell type composition useful for studying the role of epigenetic changes in human traits and diseases.
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Affiliation(s)
- Yen-Chen A Feng
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.,Broad Institute of Harvard & MIT, Cambridge, MA, 02142, USA
| | - Yichen Guo
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Lucile Pain
- Basic Sciences Department, Université du Québec à Chicoutimi, Québec, G7H 2B1, Canada
| | - G Mark Lathrop
- Department of Human Genetics, McGill University & Génome Québec Innovation Centre, Montréal, H3A 1B1, Canada
| | - Catherine Laprise
- Centre de recherche en santé durable (CIHR), Université du Québec à Chicoutimi, Québec, G7H 2B1, Canada.,Centre intégré universitaire de santé et de service sociaux du Saguenay-Lac-St-Jean (CIUSSS), Québec, G7H 7K9, Canada
| | - Miriam F Moffatt
- National Heart & Lung Institute, Imperial College, London, SW3 6LY, UK
| | | | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
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36
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Xu CJ, Gruzieva O, Qi C, Esplugues A, Gehring U, Bergström A, Mason D, Chatzi L, Porta D, Lodrup Carlsen KC, Baïz N, Madore AM, Alenius H, van Rijkom B, Jankipersadsing SA, van der Vlies P, Kull I, van Hage M, Bustamante M, Lertxundi A, Torrent M, Santorelli G, Fantini MP, Hovland V, Pesce G, Fyhrquist N, Laatikainen T, Nawijn MC, Li Y, Wijmenga C, Netea MG, Bousquet J, Anto JM, Laprise C, Haahtela T, Annesi-Maesano I, Carlsen KH, Gori D, Kogevinas M, Wright J, Söderhäll C, Vonk JM, Sunyer J, Melén E, Koppelman GH. Shared DNA methylation signatures in childhood allergy: The MeDALL study. J Allergy Clin Immunol 2020; 147:1031-1040. [PMID: 33338541 DOI: 10.1016/j.jaci.2020.11.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/14/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Differential DNA methylation associated with allergy might provide novel insights into the shared or unique etiology of asthma, rhinitis, and eczema. OBJECTIVE We sought to identify DNA methylation profiles associated with childhood allergy. METHODS Within the European Mechanisms of the Development of Allergy (MeDALL) consortium, we performed an epigenome-wide association study of whole blood DNA methylation by using a cross-sectional design. Allergy was defined as having symptoms from at least 1 allergic disease (asthma, rhinitis, or eczema) and positive serum-specific IgE to common aeroallergens. The discovery study included 219 case patients and 417 controls at age 4 years and 228 case patients and 593 controls at age 8 years from 3 birth cohorts, with replication analyses in 325 case patients and 1111 controls. We performed additional analyses on 21 replicated sites in 785 case patients and 2124 controls by allergic symptoms only from 8 cohorts, 3 of which were not previously included in analyses. RESULTS We identified 80 differentially methylated CpG sites that showed a 1% to 3% methylation difference in the discovery phase, of which 21 (including 5 novel CpG sites) passed genome-wide significance after meta-analysis. All 21 CpG sites were also significantly differentially methylated with allergic symptoms and shared between asthma, rhinitis, and eczema. The 21 CpG sites mapped to relevant genes, including ACOT7, LMAN3, and CLDN23. All 21 CpG sties were differently methylated in asthma in isolated eosinophils, and 10 were replicated in respiratory epithelium. CONCLUSION Reduced whole blood DNA methylation at 21 CpG sites was significantly associated with childhood allergy. The findings provide novel insights into the shared molecular mechanisms underlying asthma, rhinitis, and eczema.
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Affiliation(s)
- Cheng-Jian Xu
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Centre for Individualized Infection Medicine, CiiM, a joint venture between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Cancan Qi
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ana Esplugues
- Nursing Department, Faculty of Nursing and Chiropody, Universitat de València, València, Spain; FISABIO-Universitat Jaume I-Universitat de València Joint Research Unit of Epidemiology and Environmental Health, València, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Dan Mason
- Bradford Institute for Health Research, Bradford, United Kingdom
| | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles
| | - Daniela Porta
- Department of Epidemiology, Lazio Regional Health Service, Rome, Italy
| | - Karin C Lodrup Carlsen
- Division of Paediatric and Adolescent Medicine, The Faculty of Medicine, University of Oslo, Oslo, Norway; Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Nour Baïz
- Sorbonne University and INSERM, Epidemiology of Allergic and Respiratory Diseases (EPAR) Department, IPLESP, Medical School Saint Antoine, Paris, France
| | - Anne-Marie Madore
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec City, Canada
| | - Harri Alenius
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bianca van Rijkom
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Soesma A Jankipersadsing
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Pieter van der Vlies
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; HZPC Research BV, Metslawier, The Netherlands
| | - Inger Kull
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Marianne van Hage
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Mariona Bustamante
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Institute of Global Health, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - Aitana Lertxundi
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Preventive Medicine and Public Health Department, University of Basque Country (UPV/EHU), Leioa, Bizkaia, Spain; Health Research institute Biodonostia, Donostia-San Sebastian, Gipuzkoa, Spain
| | - Matias Torrent
- Health Research Institute of the Balearic Islands, Spain; ib-salut, Area de Salut de Menorca, Spain
| | | | - Maria Pia Fantini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Vegard Hovland
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Giancarlo Pesce
- Sorbonne University and INSERM, Epidemiology of Allergic and Respiratory Diseases (EPAR) Department, IPLESP, Medical School Saint Antoine, Paris, France
| | | | - Nanna Fyhrquist
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Human Microbiome Program, Medicum, University of Helsinki, Helsinki, Finland
| | - Tiina Laatikainen
- Finnish Institute for Health and Welfare, Helsinki, Finland; Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Martijn C Nawijn
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, Experimental Pulmonology and Inflammation Research, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yang Li
- Centre for Individualized Infection Medicine, CiiM, a joint venture between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands; Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Jean Bousquet
- University Hospital, Montpellier, France; Department of Dermatology, Charité, Berlin, Germany
| | - Josep M Anto
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Institute of Global Health, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Québec City, Canada; Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec City, Canada; Centre de santé et de services sociaux du Saguenay-Lac-Saint-Jean, Saguenay, Québec, Canada
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Isabella Annesi-Maesano
- Sorbonne University and INSERM, Epidemiology of Allergic and Respiratory Diseases (EPAR) Department, IPLESP, Medical School Saint Antoine, Paris, France
| | - Kai-Håkon Carlsen
- Division of Paediatric and Adolescent Medicine, The Faculty of Medicine, University of Oslo, Oslo, Norway; Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Davide Gori
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | | | - John Wright
- Bradford Institute for Health Research, Bradford, United Kingdom
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Judith M Vonk
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jordi Sunyer
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Institute of Global Health, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Erik Melén
- Department of Clinical Sciences and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden; Sachs' Children's Hospital, Stockholm, Sweden
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Zheng P, Huang C, Leng D, Sun B, Zhang XD. Transcriptome analysis of peripheral whole blood identifies crucial lncRNAs implicated in childhood asthma. BMC Med Genomics 2020; 13:136. [PMID: 32948203 PMCID: PMC7501638 DOI: 10.1186/s12920-020-00785-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
Background Asthma is a chronic disorder of both adults and children affecting more than 300 million people heath worldwide. Diagnose and treatment for asthma, particularly in childhood asthma have always remained a great challenge because of its complex pathogenesis and multiple triggers, such as allergen, viral infection, tobacco smoke, dust, etc. It is thereby great significant to deeply investigate the transcriptome changes in asthmatic children before and after desensitization treatment, in order that we could identify potential and key mRNAs and lncRNAs which might be considered as useful RNA molecules for observing and supervising desensitization therapy for asthma, which might guide the diagnose and therapy in childhood asthma. Methods In the present study, we performed a systematic transcriptome analysis based on the deep RNA sequencing of ten asthmatic children before and after desensitization treatment, including identification of lncRNAs using a stringent filtering pipeline, differential expression analysis and network analysis, etc. Results First, a large number of lncRNAs were identified and characterized. Then differential expression analysis revealed 39 mRNAs and 15 lncRNAs significantly differentially expressed which involved in two biological processes and pathways. A co-expressed network analysis figured out a desensitization-treatment-related module which contains 27 mRNAs and 21 lncRNAs using WGCNA R package. Module analysis disclosed 17 genes associated to asthma at distinct level. Subsequent network analysis based on PCC figured out several key lncRNAs probably interacted to those key asthma-related genes, i.e., LINC02145, GUSBP2. Our functional investigation indicated that their functions might involve in immune, inflammatory response and apoptosis process. Conclusions Our study successfully discovered many key noncoding RNA molecules related to pathogenesis of asthma and relevant treatment, which may provide some clues for asthmatic diagnose and therapy in future.
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Affiliation(s)
- Peiyan Zheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chen Huang
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Dongliang Leng
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Baoqing Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Xiaohua Douglas Zhang
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau, China. .,Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510, USA.
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38
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Hoang TT, Sikdar S, Xu CJ, Lee MK, Cardwell J, Forno E, Imboden M, Jeong A, Madore AM, Qi C, Wang T, Bennett BD, Ward JM, Parks CG, Beane-Freeman LE, King D, Motsinger-Reif A, Umbach DM, Wyss AB, Schwartz DA, Celedón JC, Laprise C, Ober C, Probst-Hensch N, Yang IV, Koppelman GH, London SJ. Epigenome-wide association study of DNA methylation and adult asthma in the Agricultural Lung Health Study. Eur Respir J 2020; 56:13993003.00217-2020. [PMID: 32381493 PMCID: PMC7469973 DOI: 10.1183/13993003.00217-2020] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022]
Abstract
Epigenome-wide studies of methylation in children support a role for epigenetic mechanisms in asthma; however, studies in adults are rare and few have examined non-atopic asthma. We conducted the largest epigenome-wide association study (EWAS) of blood DNA methylation in adults in relation to non-atopic and atopic asthma. We measured DNA methylation in blood using the Illumina MethylationEPIC array among 2286 participants in a case-control study of current adult asthma nested within a United States agricultural cohort. Atopy was defined by serum specific immunoglobulin E (IgE). Participants were categorised as atopy without asthma (n=185), non-atopic asthma (n=673), atopic asthma (n=271), or a reference group of neither atopy nor asthma (n=1157). Analyses were conducted using logistic regression. No associations were observed with atopy without asthma. Numerous cytosine–phosphate–guanine (CpG) sites were differentially methylated in non-atopic asthma (eight at family-wise error rate (FWER) p<9×10−8, 524 at false discovery rate (FDR) less than 0.05) and implicated 382 novel genes. More CpG sites were identified in atopic asthma (181 at FWER, 1086 at FDR) and implicated 569 novel genes. 104 FDR CpG sites overlapped. 35% of CpG sites in non-atopic asthma and 91% in atopic asthma replicated in studies of whole blood, eosinophils, airway epithelium, or nasal epithelium. Implicated genes were enriched in pathways related to the nervous system or inflammation. We identified numerous, distinct differentially methylated CpG sites in non-atopic and atopic asthma. Many CpG sites from blood replicated in asthma-relevant tissues. These circulating biomarkers reflect risk and sequelae of disease, as well as implicate novel genes associated with non-atopic and atopic asthma. Distinct methylation signals are found in non-atopic and atopic asthma. Most are related to gene expression and are replicated in asthma-relevant tissues, confirming the value of blood DNA methylation for identifying novel genes linked in asthma pathogenesis.https://bit.ly/2VnbJg3
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Affiliation(s)
- Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA.,Joint first authors
| | - Sinjini Sikdar
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA.,Dept of Mathematics and Statistics, Old Dominion University, Norfolk, VA, USA.,Joint first authors
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Centre for Experimental and Clinical Infection Research (TWINCORE), Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Joint first authors
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Jonathan Cardwell
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Erick Forno
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.,Dept of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Medea Imboden
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Dept of Public Health, University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Dept of Public Health, University of Basel, Basel, Switzerland
| | - Anne-Marie Madore
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Cancan Qi
- Dept of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital and GRIAC Research Institute, Groningen, The Netherlands
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Brian D Bennett
- Integrative Bioinformatics Support Group, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - James M Ward
- Integrative Bioinformatics Support Group, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Christine G Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Laura E Beane-Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Debra King
- Clinical Pathology Group, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - David A Schwartz
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Juan C Celedón
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.,Dept of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Centre Intersectoriel en Santé Durable, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Dept of Pediatrics, Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Saguenay, QC, Canada
| | - Carole Ober
- Dept of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Nicole Probst-Hensch
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Dept of Public Health, University of Basel, Basel, Switzerland
| | - Ivana V Yang
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gerard H Koppelman
- Dept of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital and GRIAC Research Institute, Groningen, The Netherlands
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
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Gutierrez MJ, Nino G, Hong X, Wang X. Epigenomics and Early Life Human Humoral Immunity: Novel Paradigms and Research Opportunities. Front Immunol 2020; 11:1766. [PMID: 32983086 PMCID: PMC7492271 DOI: 10.3389/fimmu.2020.01766] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/01/2020] [Indexed: 12/24/2022] Open
Abstract
The molecular machinery controlling immune development has been extensively investigated. Studies in animal models and adult individuals have revealed fundamental mechanisms of disease and have been essential to understanding how humans sense and respond to cellular stress, tissue damage, pathogens and their environment. Nonetheless, our understanding of how immune responses originate during human development is just starting to emerge. In particular, studies to unveil how environmental and other non-heritable factors shape the immune system at the beginning of life offer great promise to yield important knowledge about determinants of normal inter-individual immune variation and to prevent and treat many human diseases. In this review, we summarize our current understanding of some of the mechanisms determining early life antibody production as a model of an immune process with sequential molecular checkpoints susceptible to influence by non-heritable factors. We discuss the potential of epigenomics as a valuable approach that may reveal not only relevant gene-environment interactions but important clues about immune developmental processes and homeostasis in early life. We then highlight the novel paradigm of human immunology as a complex field that nowadays requires a longitudinal systems-biology approach to understand normal variation and developmental changes during the first few years of life.
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Affiliation(s)
- Maria J Gutierrez
- Division of Pediatric Allergy, Immunology and Rheumatology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Gustavo Nino
- Division of Pediatric Pulmonary and Sleep Medicine, Children's National Medical Center, George Washington University, Washington, DC, United States.,Center for Genetic Medicine, Children's National Medical Center, Washington, DC, United States
| | - Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on Early Life Origins of Disease, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center on Early Life Origins of Disease, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Division of General Pediatrics and Adolescent Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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40
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Guo TL, Lefever DE, Nagy T, Meng AH. In utero exposure to genistein decreased intranasal house dust mite-induced respiratory allergy in middle-aged male B6C3F1 offspring. Toxicol Lett 2020; 333:222-231. [PMID: 32798538 DOI: 10.1016/j.toxlet.2020.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/22/2020] [Accepted: 07/09/2020] [Indexed: 10/23/2022]
Abstract
Despite many hypothesized benefits of dietary isoflavone genistein (GEN) deriving from soy-based products, questions surrounding GEN's developmental effects are increasing. To understand if in utero GEN exposure modulated postnatal respiratory allergies in the middle age, we conducted a time course study in the B6C3F1 offspring (PND 240-330) using a common household allergen (house dust mites: HDM; 10 μg/mouse for PND 240 and 290, and 50 μg/mouse for PND 330, a middle age in mice) following intranasal instillation, a physiological route of allergen exposure. GEN was administered to dams by gavage from gestational day 14 to parturition at a physiologically relevant dose (20 mg/kg body weight). Female and male offspring were sensitized with HDM allergens beginning about one month prior to sacrifice followed by challenges with three weekly dosings of HDM extracts, and they were euthanized at day 3 following the final HDM exposure. In utero exposure to GEN decreased HDM allergen-induced respiratory allergy in male B6C3F1 offspring at PND 330 as reflected by decreases in airway hyperresponsiveness (e.g., Penh value), HDM-specific IgG1 (a Th2 type Ab) and the activity of eosinophil peroxidase in the lung (an indication of eosinophil recruitment to the lungs). However, in utero exposure to GEN had minimal effects on HDM allergen-induced respiratory allergy in the middle-aged female offspring. Changes in serum total IgE, HDM-specific IgE, and lung histopathology scores in both male and female offspring were not biologically significant. Overall, in utero GEN exposure exerted a protective effect on respiratory allergy in the middle-aged male, but not female, B6C3F1 offspring following later-life HDM exposures.
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Affiliation(s)
- Tai L Guo
- Department of Veterinary Biosciences and Diagnostic Imaging, United States.
| | - Daniel E Lefever
- Department of Veterinary Biosciences and Diagnostic Imaging, United States
| | - Tamas Nagy
- Department of Veterinary Pathology, University of Georgia, Athens, GA 30602-7382, United States
| | - Andrew H Meng
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298-0613, United States
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41
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Koh IU, Choi NH, Lee K, Yu HY, Yun JH, Kong JH, Kim HJ, Lee S, Kim SC, Kim BJ, Moon S. Obesity susceptible novel DNA methylation marker on regulatory region of inflammation gene: results from the Korea Epigenome Study (KES). BMJ Open Diabetes Res Care 2020; 8:8/1/e001338. [PMID: 32788176 PMCID: PMC7422660 DOI: 10.1136/bmjdrc-2020-001338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/03/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Obesity is growing global health concern and highly associated with increased risk of metabolic diseases including type 2 diabetes. We aimed to discover new differential DNA methylation patterns predisposing obesity and prioritize surrogate epigenetic markers in Koreans. RESEARCH DESIGN AND METHODS We performed multistage epigenome-wide analyses to identify differentially expressed CpGs in obesity using the Illumina HumanMethylationEPIC array (EPIC). Forty-eight CpGs showed significant differences across three phases: 902 whole blood DNAs from two cohorts (phase 1: n=450, phase 2: n=377) and a hospital-based sample (phase 3: n=75). Samples from phase III participants were used to examine whether the 48 CpGs are significant in the fat tissue and influenced gene expression. Furthermore, we investigated the epigenetic effect of CpG loci in childhood obesity (n=94). RESULTS Seven of the 48 CpGs exhibited similar changes in the fat tissue along with gene expression changes. In particular, hypomethylated CpG (cg13424229) on the GATA1 transcription factor cluster of CPA3 promoter was related to its increased gene expression and showed consistent effect in childhood obesity. Interestingly, subsequent analysis using RNA sequencing data from 21 preadipocytes and 26 adipocytes suggested CPA3 as a potential obesity-related gene. Moreover, expression patterns from RNA sequencing and public Gene Expression Omnibus showed the correlation between CPA3 and type 2 diabetes (T2D) and asthma. CONCLUSIONS Our finding prioritizes influential genes in obesity and provides new evidence for the role of CPA3 linking obesity, T2D, and asthma.
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Affiliation(s)
- In-Uk Koh
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, South Korea
| | - Nak-Hyeon Choi
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, South Korea
| | - Kibaick Lee
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, South Korea
| | - Ho-Yeong Yu
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, South Korea
| | - Jun Ho Yun
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, South Korea
| | - Jin-Hwa Kong
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, South Korea
| | - Hyo Jin Kim
- Division of Endocrine and Metabolic Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, South Korea
| | - Song Lee
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Asan Medical Center, Songpa-gu, Seoul, South Korea
| | - Song Cheol Kim
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, Asan Medical Center, AMIST, University of Ulsan College of Medicine, Asan Medical Center, Songpa-gu, Seoul, South Korea
| | - Bong-Jo Kim
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, South Korea
| | - Sanghoon Moon
- Division of Genome Research, Center for Genome Science, Korea National Institute of Health, Cheongju-si, Chungcheongbuk-do, South Korea
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Li N, Gao S, Tong J, Yu Y, Zhang Q, Xu C. Probiotics as a functional food ingredient in allergic diseases: regulation of CD4+ T helper cell differentiation. Crit Rev Microbiol 2020; 46:463-474. [PMID: 32720543 DOI: 10.1080/1040841x.2020.1796578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Allergic diseases are increasing worldwide, associating with increased health costs and decreased quality of life. Allergy is immune-related diseases caused by an allergic immune response to innocuous substance in the environment. At present, research has focussed on the study of the relevance to the microbiome and the phenotypes of allergy, including the relationships among the gastrointestinal microbiome, immune function, and allergic sensitisation. Probiotics as functional food ingredient are thought to secrete functional metabolites that have antibacterial effects on ameliorating intestinal health and CD4+ T helper cells-mediated immunity. This review will summarise the role of probiotics in the immune regulation and flora balance, highlighting recent advances in our understanding of the imbalance of Th subsets and cytokine leading to the immunopathology of allergic reactions. Finally, we discussed the unresolved problems and future research directions in order to promote the clinical application of probiotics immunotherapy.
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Affiliation(s)
- Na Li
- Pediatric Department, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Tropical Medicine, Hainan Medical University, HaiKou, China
| | - Shenshen Gao
- Pediatric Department, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Tong
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Yi Yu
- Pediatric Department, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qingqing Zhang
- Pediatric Department, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chundi Xu
- Pediatric Department, School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, China
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Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Genome Med 2020; 12:60. [PMID: 32641083 PMCID: PMC7346642 DOI: 10.1186/s13073-020-00754-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets. METHODS In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). RESULTS We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn's disease. CONCLUSIONS Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease.
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Affiliation(s)
- Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Daniel Trejo-Banos
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Athanasios Kousathanas
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah E Harris
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Marion Patxot
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Sven Erik Ojavee
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - David C Liewald
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Craig W Ritchie
- Edinburgh Dementia Prevention, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Elliot M Tucker-Drob
- Department of Psychology, The University of Texas at Austin, Austin, TX, 78712, USA
- Population Research Center, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Ian J Deary
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Matthew R Robinson
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
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Long A, Bunning B, Sampath V, DeKruyff RH, Nadeau KC. Epigenetics and the Environment in Airway Disease: Asthma and Allergic Rhinitis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1253:153-181. [PMID: 32445095 DOI: 10.1007/978-981-15-3449-2_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Asthma and rhinitis are complex, heterogeneous diseases characterized by chronic inflammation of the upper and lower airways. While genome-wide association studies (GWAS) have identified a number of susceptible loci and candidate genes associated with the pathogenesis of asthma and allergic rhinitis (AR), the risk-associated alleles account for only a very small percent of the genetic risk. In allergic airway and other complex diseases, it is thought that epigenetic modifications, including DNA methylation, histone modifications, and non-coding microRNAs, caused by complex interactions between the underlying genome and the environment may account for some of this "missing heritability" and may explain the high degree of plasticity in immune responses. In this chapter, we will focus on the current knowledge of classical epigenetic modifications, DNA methylation and histone modifications, and their potential role in asthma and AR. In particular, we will review epigenetic variations associated with maternal airway disease, demographics, environment, and non-specific associations. The role of specific genetic haplotypes in environmentally induced epigenetic changes are also discussed. A major limitation of many of the current studies of asthma epigenetics is that they evaluate epigenetic modifications in both allergic and non-allergic asthma, making it difficult to distinguish those epigenetic modifications that mediate allergic asthma from those that mediate non-allergic asthma. Additionally, most DNA methylation studies in asthma use peripheral or cord blood due to poor accessibility of airway cells or tissue. Unlike DNA sequences, epigenetic alterations are quite cell- and tissue-specific, and epigenetic changes found in airway tissue or cells may be discordant from that of circulating blood. These two confounding factors should be considered when reviewing epigenetic studies in allergic airway disease.
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Affiliation(s)
- Andrew Long
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.,Department of Pharmacy, Lucile Packard Children's Hospital, Stanford, CA, 94304, USA
| | - Bryan Bunning
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Vanitha Sampath
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Rosemarie H DeKruyff
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Kari C Nadeau
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.
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Genome‑wide analysis of DNA methylation and gene expression changes in an ovalbumin‑induced asthma mouse model. Mol Med Rep 2020; 22:1709-1716. [PMID: 32705270 PMCID: PMC7411290 DOI: 10.3892/mmr.2020.11245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 02/04/2020] [Indexed: 12/12/2022] Open
Abstract
The aim of the present study was to establish an integrated network of DNA methylation and RNA expression in an ovalbumin (OVA)-induced asthma model, and to investigate the epigenetically-regulated genes involved in asthma development. Genome-wide CpG-DNA methylation profiling was conducted through the use of a methylated DNA immunoprecipitation microarray and RNA sequencing was performed using three lung samples from mice with OVA-induced asthma. A total of 35,401 differentially methylated regions (DMRs) were identified between mice with OVA-induced asthma and control mice. Of these, 3,060 were located in promoter regions and 370 of the genes containing these DMRs demonstrated an inverse correlation between methylation and gene expression. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified that 368 genes were upregulated or downregulated in OVA-induced asthma samples, including genes involved in ‘chemokine signalling pathway’, ‘focal adhesion’, ‘leukocyte transendothelial migration’ and ‘vascular smooth muscle contraction signaling’ pathways. Integrated network analysis identified four hub genes, consisting of three upregulated genes [forkhead box O1 (FOXO1), SP1 transcription factor (SP1) and amyloid β precursor protein (APP)], and one downregulated gene [RUNX family transcription factor 1 (RUNX1)], all of which demonstrated an association between DNA methylation and gene expression. These genes were highly interconnected nodes in the Ingenuity Pathway Analysis module and were functionally significant. A total of four interconnected hub genes, FOXO1, RUNX1, SP1 and APP, were identified from the integrated DNA methylation and gene expression networks involved in asthma development. These results suggested that modulating these four genes could effectively control the development of asthma.
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Leveraging -omics for asthma endotyping. J Allergy Clin Immunol 2020; 144:13-23. [PMID: 31277743 DOI: 10.1016/j.jaci.2019.05.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/13/2022]
Abstract
Asthma is a highly heterogeneous disease, often manifesting with wheeze, dyspnea, chest tightness, and cough as prominent symptoms. The eliciting factors, natural history, underlying molecular biology, and clinical management of asthma vary highly among affected subjects. Because of this variation, many efforts have gone into subtyping asthma. Endotypes are subtypes of disease based on distinct pathophysiologic mechanisms. Endotypes can be clinically useful because they organize our mechanistic understanding of heterogeneous diseases and can direct treatment toward modalities that are likely to be the most effective. Asthma endotyping can be shaped by clinical features, laboratory parameters, and/or -omics approaches. We discuss the application of -omics approaches, including transcriptomics, epigenomics, microbiomics, metabolomics, and proteomics, to asthma endotyping. -Omics approaches have provided supporting evidence for many existing endotyping paradigms and also suggested novel ways to conceptualize asthma endotypes. Although endotypes based on single -omics approaches are relatively common, their integrated multi-omics application to asthma endotyping has been more limited thus far. We discuss paths forward to integrate multi-omics with clinical features and laboratory parameters to achieve the goal of precise asthma endotypes.
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Resolving Clinical Phenotypes into Endotypes in Allergy: Molecular and Omics Approaches. Clin Rev Allergy Immunol 2020; 60:200-219. [PMID: 32378146 DOI: 10.1007/s12016-020-08787-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allergic diseases are highly complex with respect to pathogenesis, inflammation, and response to treatment. Current efforts for allergic disease diagnosis have focused on clinical evidence as a binary outcome. Although outcome status based on clinical phenotypes (observable characteristics) is convenient and inexpensive to measure in large studies, it does not adequately provide insight into the complex molecular determinants of allergic disease. Individuals with similar clinical diagnoses do not necessarily have similar disease etiologies, natural histories, or responses to treatment. This heterogeneity contributes to the ineffective response to treatment leading to an annual estimated cost of $350 billion in the USA alone. There has been a recent focus to deconvolute the clinical heterogeneity of allergic diseases into specific endotypes using molecular and omics approaches. Endotypes are a means to classify patients based on the underlying pathophysiological mechanisms involving distinct functions or treatment response. The advent of high-throughput molecular omics, immunophenotyping, and bioinformatics methods including machine learning algorithms is facilitating the development of endotype-based diagnosis. As we move to the next decade, we should truly start treating clinical endotypes not clinical phenotype. This review highlights current efforts taking place to improve allergic disease endotyping via molecular omics profiling, immunophenotyping, and machine learning approaches in the context of precision diagnostics in allergic diseases. Graphical Abstract.
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Zakzuk J, Acevedo N, Harb H, Eick L, Renz H, Potaczek DP, Caraballo L. IgE Levels to Ascaris and House Dust Mite Allergens Are Associated With Increased Histone Acetylation at Key Type-2 Immune Genes. Front Immunol 2020; 11:756. [PMID: 32425942 PMCID: PMC7204827 DOI: 10.3389/fimmu.2020.00756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/03/2020] [Indexed: 12/18/2022] Open
Abstract
Background Epigenetic changes in response to allergen exposure are still not well understood. The aim of this study was to evaluate histone acetylation levels in peripheral blood leukocytes from humans naturally infected by intestinal parasites and perennially exposed to house dust mites (HDM). Methods Peripheral blood mononuclear cells (PBMCs) were isolated by gradient centrifugation from 20 infected and 21 non-infected individuals living in a rural/village in Colombia. Histone 3 acetylation (H3Ac) and histone 4 acetylation (H4Ac) levels were measured in six immune genes previously associated with helminth immunity by chromatin immunoprecipitation (ChIP)-quantitative PCR. Then we analyzed the association between histone acetylation levels with total parasite egg burden and IgE levels. Results We found an inverse correlation between H4Ac levels in the IL13 gene and egg worm burden that remained significant after adjustment by age [−0.20 (−0.32 to −0.09), p < 0.0001]. Moreover, we found significant associations between H4Ac levels in IL4 [0.32 (0.05–0.60), p = 0.02] and CHI3L1 [0.29 (0.08–0.51), p = 0.008] with the IgE levels to Ascaris lumbricoides. In addition, the levels of specific IgE antibodies to HDM were associated with H4Ac levels in the gene TNFSF13B encoding the B cell activating factor (BAFF) [0.51 (0.26–0.76), p < 0.001]. All values are presented as beta (95% CI). Conclusion Histone acetylation levels at key type-2 immune genes in humans were modified by nematode infection and HDM allergens and are associated with the intensity of the IgE response.
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Affiliation(s)
- Josefina Zakzuk
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | - Nathalie Acevedo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | - Hani Harb
- Institute of Laboratory Medicine, Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Lisa Eick
- Institute of Laboratory Medicine, Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine, Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany
| | - Daniel P Potaczek
- Institute of Laboratory Medicine, Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), Philipps-University Marburg, Marburg, Germany.,John Paul II Hospital, Krakow, Poland
| | - Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
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Multilevel omics for the discovery of biomarkers and therapeutic targets for stroke. Nat Rev Neurol 2020; 16:247-264. [PMID: 32322099 DOI: 10.1038/s41582-020-0350-6] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2020] [Indexed: 02/07/2023]
Abstract
Despite many years of research, no biomarkers for stroke are available to use in clinical practice. Progress in high-throughput technologies has provided new opportunities to understand the pathophysiology of this complex disease, and these studies have generated large amounts of data and information at different molecular levels. The integration of these multi-omics data means that thousands of proteins (proteomics), genes (genomics), RNAs (transcriptomics) and metabolites (metabolomics) can be studied simultaneously, revealing interaction networks between the molecular levels. Integrated analysis of multi-omics data will provide useful insight into stroke pathogenesis, identification of therapeutic targets and biomarker discovery. In this Review, we detail current knowledge on the pathology of stroke and the current status of biomarker research in stroke. We summarize how proteomics, metabolomics, transcriptomics and genomics are all contributing to the identification of new candidate biomarkers that could be developed and used in clinical stroke management.
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50
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Yamada K, Huang ZQ, Raska M, Reily C, Anderson JC, Suzuki H, Kiryluk K, Gharavi AG, Julian BA, Willey CD, Novak J. Leukemia Inhibitory Factor Signaling Enhances Production of Galactose-Deficient IgA1 in IgA Nephropathy. KIDNEY DISEASES 2020; 6:168-180. [PMID: 32523959 DOI: 10.1159/000505748] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022]
Abstract
Objectives IgA nephropathy (IgAN) is thought to involve an autoimmune process wherein galactose-deficient IgA1 (Gd-IgA1), recognized as autoantigen by autoantibodies, forms pathogenic immune complexes. Mounting evidence has implicated abnormal activation of some protein-tyrosine kinases (PTKs) in IgAN. Furthermore, genome-wide association studies (GWAS) of IgAN provided insight into disease pathobiology and genetics. A GWAS locus on chromosome 22q12 contains genes encoding leukemia inhibitory factor (LIF) and oncostatin M, interleukin (IL)-6-related cytokines implicated in mucosal immunity and inflammation. We have previously shown that IL-6 mediates overproduction of Gd-IgA1 through aberrant STAT3 activation. Here, we show that LIF enhanced production of Gd-IgA1 in IgA1-secreting cells of patients with IgAN and provide initial analyses of LIF signaling. Methods We characterized LIF signaling that is involved in the overproduction of Gd-IgA1, using IgA1-secreting cell lines derived from peripheral blood of patients with IgAN and healthy controls (HC). We used global PTK activity profiling, immunoblotting, lectin ELISA, and siRNA knock-down. Results LIF stimulation did not significantly affect production of total IgA1 in IgA1-secreting cells from patients with IgAN or HC. However, LIF increased production of Gd-IgA1, but only in the cells from patients with IgAN. LIF stimulation enhanced phosphorylation of STAT1 in IgA1-secreting cells from patients with IgAN to a higher degree than in the cells from HC. siRNA knock-down of STAT1 blocked LIF-mediated overproduction of Gd-IgA1. Unexpectedly, this abnormal phosphorylation of STAT1 in IgA1-secreting cells from patients with IgAN was not mediated by JAK, but rather involved activation of Src-family PTKs (SFKs). Conclusion Abnormal LIF/STAT1 signaling represents another pathway potentially leading to overproduction of Gd-IgA1 in IgAN, providing possible explanation for the phenotype associated with chromosome 22q12 GWAS locus. Abnormal LIF/STAT1 signaling and the associated SFKs may represent potential diagnostic and/or therapeutic targets in IgAN.
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Affiliation(s)
- Koshi Yamada
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Zhi Qiang Huang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Milan Raska
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Immunology, Palacky University Olomouc, Olomouc, Czechia
| | - Colin Reily
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Joshua C Anderson
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hitoshi Suzuki
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Nephrology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Krzysztof Kiryluk
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Ali G Gharavi
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Bruce A Julian
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christopher D Willey
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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