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Zhang L, Chun Y, Arditi Z, Grishina G, Lo T, Wisotzkey K, Agashe C, Grishin A, Wang J, Sampson HA, Sicherer S, Berin MC, Bunyavanich S. Joint transcriptomic and cytometric study of children with peanut allergy reveals molecular and cellular cross talk in reaction thresholds. J Allergy Clin Immunol 2024; 153:1721-1728. [PMID: 38272374 PMCID: PMC11162334 DOI: 10.1016/j.jaci.2023.12.028] [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: 06/16/2023] [Revised: 11/22/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Reaction thresholds in peanut allergy are highly variable. Elucidating causal relationships between molecular and cellular processes associated with variable thresholds could point to therapeutic pathways for raising thresholds. OBJECTIVE The aim of this study was to characterize molecular and cellular systemic processes associated with reaction threshold in peanut allergy and causal relationships between them. METHODS A total of 105 children aged 4 to 14 years with suspected peanut allergy underwent double-blind, placebo-controlled food challenge to peanut. The cumulative peanut protein quantity eliciting allergic symptoms was considered the reaction threshold for each child. Peripheral blood samples collected at 0, 2, and 4 hours after challenge start were used for RNA sequencing, whole blood staining, and cytometry. Statistical and network analyses were performed to identify associations and causal mediation between the molecular and cellular profiles and peanut reaction threshold. RESULTS Within the cohort (N = 105), 81 children (77%) experienced allergic reactions after ingesting varying quantities of peanut, ranging from 43 to 9043 mg of cumulative peanut protein. Peripheral blood expression of transcripts (eg, IGF1R [false discovery rate (FDR) = 5.4e-5] and PADI4 [FDR = 5.4e-5]) and neutrophil abundance (FDR = 9.5e-4) were associated with peanut threshold. Coexpression network analyses revealed that the threshold-associated transcripts were enriched in modules for FcγR-mediated phagocytosis (FDR = 3.2e-3) and Toll-like receptor (FDR = 1.4e-3) signaling. Bayesian network, key driver, and causal mediation analyses identified key drivers (AP5B1, KLHL21, VASP, TPD52L2, and IGF2R) within these modules that are involved in bidirectional causal mediation relationships with neutrophil abundance. CONCLUSION Key driver transcripts in FcγR-mediated phagocytosis and Toll-like receptor signaling interact bidirectionally with neutrophils in peripheral blood and are associated with reaction threshold in peanut allergy.
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Affiliation(s)
- Lingdi Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zoe Arditi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tracy Lo
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kayla Wisotzkey
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Charuta Agashe
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Julie Wang
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Hugh A Sampson
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Scott Sicherer
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - M Cecilia Berin
- Division of Allergy and Immunology, Department of Medicine, Northwestern Feinberg School of Medicine, Chicago, Ill
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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Bowman WS, Schmidt RJ, Sanghar GK, Thompson Iii GR, Ji H, Zeki AA, Haczku A. "Air That Once Was Breath" Part 1: Wildfire-Smoke-Induced Mechanisms of Airway Inflammation - "Climate Change, Allergy and Immunology" Special IAAI Article Collection: Collegium Internationale Allergologicum Update 2023. Int Arch Allergy Immunol 2024; 185:600-616. [PMID: 38452750 DOI: 10.1159/000536578] [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: 12/12/2023] [Accepted: 01/23/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Wildfires are a global concern due to their wide-ranging environmental, economic, and public health impacts. Climate change contributes to an increase in the frequency and intensity of wildfires making smoke exposure a more significant and recurring health concern for individuals with airway diseases. Some of the most prominent effects of wildfire smoke exposure are asthma exacerbations and allergic airway sensitization. Likely due to the delayed recognition of its health impacts in comparison with cigarette smoke and industrial or traffic-related air pollution, research on the composition, the mechanisms of toxicity, and the cellular/molecular pathways involved is poor or non-existent. SUMMARY This review discusses potential underlying pathological mechanisms of wildfire-smoke-related allergic airway disease and asthma. We focused on major gaps in understanding the role of wildfire smoke composition in the development of airway disease and the known and potential mechanisms involving cellular and molecular players of oxidative injury at the epithelial barrier in airway inflammation. We examine how PM2.5, VOCs, O3, endotoxin, microbes, and toxic gases may affect oxidative stress and inflammation in the respiratory mucosal barrier. We discuss the role of AhR in mediating smoke's effects in alarmin release and IL-17A production and how glucocorticoid responsiveness may be impaired by IL-17A-induced signaling and epigenetic changes leading to steroid-resistant severe airway inflammation. KEY MESSAGE Effective mitigation of wildfire-smoke-related respiratory health effects would require comprehensive research efforts aimed at a better understanding of the immune regulatory effects of wildfire smoke in respiratory health and disease.
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Affiliation(s)
- Willis S Bowman
- UC Davis Lung Center, University of California, Davis, California, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Sacramento, California, USA
| | - Rebecca J Schmidt
- Department of Public Health Sciences, School of Medicine, Sacramento, California, USA
| | - Gursharan K Sanghar
- UC Davis Lung Center, University of California, Davis, California, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Sacramento, California, USA
| | - George R Thompson Iii
- UC Davis Lung Center, University of California, Davis, California, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Sacramento, California, USA
| | - Hong Ji
- UC Davis Lung Center, University of California, Davis, California, USA
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, Davis, California, USA
| | - Amir A Zeki
- UC Davis Lung Center, University of California, Davis, California, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Sacramento, California, USA
| | - Angela Haczku
- UC Davis Lung Center, University of California, Davis, California, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Sacramento, California, USA
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Ahmad S, Zhang XL, Ahmad A. Epigenetic regulation of pulmonary inflammation. Semin Cell Dev Biol 2024; 154:346-354. [PMID: 37230854 PMCID: PMC10592630 DOI: 10.1016/j.semcdb.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023]
Abstract
Pulmonary disease such as chronic obstructive pulmonary disease (COPD), asthma, pulmonary fibrosis and pulmonary hypertension are the leading cause of deaths. More importantly, lung diseases are on the rise and environmental factors induced epigenetic modifications are major players on this increased prevalence. It has been reported that dysregulation of genes involved in epigenetic regulation such as the histone deacetylase (HDACs) and histone acetyltransferase (HATs) play important role in lung health and pulmonary disease pathogenesis. Inflammation is an essential component of respiratory diseases. Injury and inflammation trigger release of extracellular vesicles that can act as epigenetic modifiers through transfer of epigenetic regulators such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), proteins and lipids, from one cell to another. The immune dysregulations caused by the cargo contents are important contributors of respiratory disease pathogenesis. N6 methylation of RNA is also emerging to be a critical mechanism of epigenetic alteration and upregulation of immune responses to environmental stressors. Epigenetic changes such as DNA methylation are stable and often long term and cause onset of chronic lung conditions. These epigenetic pathways are also being utilized for therapeutic intervention in several lung conditions.
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Affiliation(s)
- Shama Ahmad
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Xiao Lu Zhang
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aftab Ahmad
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Gupta MK, Peng H, Li Y, Xu CJ. The role of DNA methylation in personalized medicine for immune-related diseases. Pharmacol Ther 2023; 250:108508. [PMID: 37567513 DOI: 10.1016/j.pharmthera.2023.108508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Epigenetics functions as a bridge between host genetic & environmental factors, aiding in human health and diseases. Many immune-related diseases, including infectious and allergic diseases, have been linked to epigenetic mechanisms, particularly DNA methylation. In this review, we summarized an updated overview of DNA methylation and its importance in personalized medicine, and demonstrated that DNA methylation has excellent potential for disease prevention, diagnosis, and treatment in a personalized manner. The future implications and limitations of the DNA methylation study have also been well-discussed.
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Affiliation(s)
- Manoj Kumar Gupta
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), 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
| | - He Peng
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), 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
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), 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 Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), 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 Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.
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Cardenas A, Fadadu RP, Koppelman GH. Epigenome-wide association studies of allergic disease and the environment. J Allergy Clin Immunol 2023; 152:582-590. [PMID: 37295475 PMCID: PMC10564109 DOI: 10.1016/j.jaci.2023.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
The epigenome is at the intersection of the environment, genotype, and cellular response. DNA methylation of cytosine nucleotides, the most studied epigenetic modification, has been systematically evaluated in human studies by using untargeted epigenome-wide association studies (EWASs) and shown to be both sensitive to environmental exposures and associated with allergic diseases. In this narrative review, we summarize findings from key EWASs previously conducted on this topic; interpret results from recent studies; and discuss the strengths, challenges, and opportunities regarding epigenetics research on the environment-allergy relationship. The majority of these EWASs have systematically investigated select environmental exposures during the prenatal and early childhood periods and allergy-associated epigenetic changes in leukocyte-isolated DNA and more recently in nasal cells. Overall, many studies have found consistent DNA methylation associations across cohorts for certain exposures, such as smoking (eg, aryl hydrocarbon receptor repressor gene [AHRR] gene), and allergic diseases (eg, EPX gene). We recommend the integration of both environmental exposures and allergy or asthma within long-term prospective designs to strengthen causality as well as biomarker development. Future studies should collect paired target tissues to examine compartment-specific epigenetic responses, incorporate genetic influences in DNA methylation (methylation quantitative trait locus), replicate findings across diverse populations, and carefully interpret epigenetic signatures from bulk, target tissue or isolated cells.
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Affiliation(s)
- Andres Cardenas
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford University, Stanford, Calif
| | - Raj P Fadadu
- School of Medicine, University of California, San Francisco, Calif
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen, The Netherlands; Groningen Research Institute of Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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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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Arzola-Martínez L, Ptaschinski C, Lukacs NW. Trained innate immunity, epigenetics, and food allergy. FRONTIERS IN ALLERGY 2023; 4:1105588. [PMID: 37304168 PMCID: PMC10251748 DOI: 10.3389/falgy.2023.1105588] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
In recent years the increased incidence of food allergy in Western culture has been associated with environmental factors and an inappropriate immune phenotype. While the adaptive immune changes in food allergy development and progression have been well-characterized, an increase in innate cell frequency and activation status has also recently received greater attention. Early in prenatal and neonatal development of human immunity there is a reliance on epigenetic and metabolic changes that stem from environmental factors, which are critical in training the immune outcomes. In the present review, we discuss how trained immunity is regulated by epigenetic, microbial and metabolic factors, and how these factors and their impact on innate immunity have been linked to the development of food allergy. We further summarize current efforts to use probiotics as a potential therapeutic approach to reverse the epigenetic and metabolic signatures and prevent the development of severe anaphylactic food allergy, as well as the potential use of trained immunity as a diagnostic and management strategy. Finally, trained immunity is presented as one of the mechanisms of action of allergen-specific immunotherapy to promote tolerogenic responses in allergic individuals.
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Affiliation(s)
- Llilian Arzola-Martínez
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- Mary H. Weiser Food Allergy Center (MHWFAC), University of Michigan, Ann Arbor, MI, United States
| | - Catherine Ptaschinski
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- Mary H. Weiser Food Allergy Center (MHWFAC), University of Michigan, Ann Arbor, MI, United States
| | - Nicholas W. Lukacs
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- Mary H. Weiser Food Allergy Center (MHWFAC), University of Michigan, Ann Arbor, MI, United States
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8
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Howell AE, Relton C, Martin RM, Zheng J, Kurian KM. Role of DNA methylation in the relationship between glioma risk factors and glioma incidence: a two-step Mendelian randomization study. Sci Rep 2023; 13:6590. [PMID: 37085538 PMCID: PMC10121678 DOI: 10.1038/s41598-023-33621-1] [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: 06/29/2022] [Accepted: 04/15/2023] [Indexed: 04/23/2023] Open
Abstract
Genetic evidence suggests glioma risk is altered by leukocyte telomere length, allergic disease (asthma, hay fever or eczema), alcohol consumption, childhood obesity, low-density lipoprotein cholesterol (LDLc) and triglyceride levels. DNA methylation (DNAm) variation influences many of these glioma-related traits and is an established feature of glioma. Yet the causal relationship between DNAm variation with both glioma incidence and glioma risk factors is unknown. We applied a two-step Mendelian randomization (MR) approach and several sensitivity analyses (including colocalization and Steiger filtering) to assess the association of DNAm with glioma risk factors and glioma incidence. We used data from a recently published catalogue of germline genetic variants robustly associated with DNAm variation in blood (32,851 participants) and data from a genome-wide association study of glioma risk (12,488 cases and 18,169 controls, sub-divided into 6191 glioblastoma cases and 6305 non-glioblastoma cases). MR evidence indicated that DNAm at 3 CpG sites (cg01561092, cg05926943, cg01584448) in one genomic region (HEATR3) had a putative association with glioma and glioblastoma risk (False discovery rate [FDR] < 0.05). Steiger filtering provided evidence against reverse causation. Colocalization presented evidence against genetic confounding and suggested that differential DNAm at the 3 CpG sites and glioma were driven by the same genetic variant. MR provided little evidence to suggest that DNAm acts as a mediator on the causal pathway between risk factors previously examined and glioma onset. To our knowledge, this is the first study to use MR to appraise the causal link of DNAm with glioma risk factors and glioma onset. Subsequent analyses are required to improve the robustness of our results and rule out horizontal pleiotropy.
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Affiliation(s)
- Amy E Howell
- Brain Tumour Research Centre, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Kathreena M Kurian
- Brain Tumour Research Centre, Institute of Clinical Neurosciences, University of Bristol, Bristol, UK.
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Legaki E, Taka S, Papadopoulos NG. The complexity in DNA methylation analysis of allergic diseases. Curr Opin Allergy Clin Immunol 2023; 23:172-178. [PMID: 36752374 DOI: 10.1097/aci.0000000000000895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
PURPOSE OF REVIEW This review aims to report all the recent studies that are implicated in DNA methylation analysis in the field of allergy and to underline the complexity of the study methodologies and results. RECENT FINDINGS Although the growing number of DNA methylation studies have yet to point to a specific mechanism, herein we provide an overview of the majority of pathways considered to be implicated and highlight particular genes, like KNH2 , ATPAF2 and ZNF385A , for their potential as biomarkers. SUMMARY The epigenetic profile of respiratory allergic diseases, and particularly DNA methylation, has been investigated in various populations, so as to gain a better understanding of its role in pathogenesis. Through our analysis, multiple links are presented between differential DNA methylation loci and IgE sensitization, lung functionality and severity of the disease. Additionally, associations of this epigenetic change with maternal asthma, age, sex and environmental factors are described, thus uncovering specific gene families that, after further examination could be used as methylation biomarkers in cases of allergic disease.
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Affiliation(s)
- Evangelia Legaki
- Allergy and Clinical Immunology Unit, Second Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
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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: 77] [Impact Index Per Article: 77.0] [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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11
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Bhat S, Rotti H, Prasad K, Kabekkodu SP, Saadi AV, Shenoy SP, Joshi KS, Nesari TM, Shengule SA, Dedge AP, Gadgil MS, Dhumal VR, Salvi S, Satyamoorthy K. Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function. J Ayurveda Integr Med 2023; 14:100692. [PMID: 37018893 PMCID: PMC10122039 DOI: 10.1016/j.jaim.2023.100692] [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: 12/15/2021] [Revised: 10/13/2022] [Accepted: 02/01/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The Indian traditional medicinal system, Ayurveda, describes several lifestyle practices, processes and medicines as an intervention to treat asthma. Rasayana therapy is one of them and although these treatment modules show improvement in bronchial asthma, their mechanism of action, particularly the effect on DNA methylation, is largely understudied. OBJECTIVES Our study aimed at identifying the contribution of DNA methylation changes in modulating bronchial asthma phenotype upon Ayurveda intervention. MATERIALS AND METHODS In this study, genome-wide methylation profiling in peripheral blood DNA of healthy controls and bronchial asthmatics before (BT) and after (AT) Ayurveda treatment was performed using array-based profiling of reference-independent methylation status (aPRIMES) coupled to microarray technique. RESULTS We identified 4820 treatment-associated DNA methylation signatures (TADS) and 11,643 asthma-associated DNA methylation signatures (AADS), differentially methylated [FDR (≤0.1) adjusted p-values] in AT and HC groups respectively, compared to BT group. Neurotrophin TRK receptor signaling pathway was significantly enriched for differentially methylated genes in bronchial asthmatics, compared to AT and HC subjects. Additionally, we identified over 100 differentially methylated immune-related genes located in the promoter/5'-UTR regions of TADS and AADS. Various immediate-early response and immune regulatory genes with functions such as transcription factor activity (FOXD1, FOXD2, GATA6, HOXA3, HOXA5, MZF1, NFATC1, NKX2-2, NKX2-3, RUNX1, KLF11), G-protein coupled receptor activity (CXCR4, PTGER4), G-protein coupled receptor binding (UCN), DNA binding (JARID2, EBF2, SOX9), SNARE binding (CAPN10), transmembrane signaling receptor activity (GP1BB), integrin binding (ITGA6), calcium ion binding (PCDHGA12), actin binding (TRPM7, PANX1, TPM1), receptor tyrosine kinase binding (PIK3R2), receptor activity (GDNF), histone methyltransferase activity (MLL5), and catalytic activity (TSTA3) were found to show consistent methylation status between AT and HC group in microarray data. CONCLUSIONS Our study reports the DNA methylation-regulated genes in bronchial asthmatics showing improvement in symptoms after Ayurveda intervention. DNA methylation regulation in the identified genes and pathways represents the Ayurveda intervention responsive genes and may be further explored as diagnostic, prognostic, and therapeutic biomarkers for bronchial asthma in peripheral blood.
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Affiliation(s)
- Smitha Bhat
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Harish Rotti
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Keshava Prasad
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sushma P Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Kalpana S Joshi
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Tanuja M Nesari
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sushant A Shengule
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Amrish P Dedge
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Maithili S Gadgil
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Vikram R Dhumal
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sundeep Salvi
- Department of Pulmonary Medicine, Chest Research Foundation, Pune, Maharashtra, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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12
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Baloh CH, Mathias RA. Recent progress in the genetic and epigenetic underpinnings of atopy. J Allergy Clin Immunol 2023; 151:60-69. [PMID: 36608983 PMCID: PMC9987265 DOI: 10.1016/j.jaci.2022.10.027] [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: 09/14/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 01/05/2023]
Abstract
In the past 2 years, there continue to be advances in our understanding of the genetic and epigenetic underpinnings of atopy pertaining to disease risk and disease severity. The joint role of genetics and the environment has been emphasized in multiple studies. Combining genetics with family history, biomarkers, and comorbidities is further refining our ability to predict the development of individual atopic diseases as well as the advancement of the atopic march. Polygenic risk scores will be an important next step for the field moving toward clinical translation of the genetic findings thus far. A systems biology approach, as illustrated by studies of the microbiome and epigenome, will be necessary to fully understand disease development and to develop increasingly targeted therapeutics.
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Affiliation(s)
- Carolyn H Baloh
- The Immune Tolerance Network, Benaroya Research Institute at Virginia Mason, Seattle, Wash; Department of Medicine, Harvard Medical School, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Rasika A Mathias
- Department of Medicine, School of Medicine, Johns Hopkins University, Division of Allergy and Clinical Immunology, Baltimore, Md.
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13
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Kilanowski A, Merid SK, Abrishamcar S, Feil D, Thiering E, Waldenberger M, Melén E, Peters A, Standl M, Hüls A. DNA methylation and aeroallergen sensitization: The chicken or the egg? Clin Epigenetics 2022; 14:114. [PMID: 36114581 PMCID: PMC9482323 DOI: 10.1186/s13148-022-01332-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Background DNA methylation (DNAm) is considered a plausible pathway through which genetic and environmental factors may influence the development of allergies. However, causality has yet to be determined as it is unknown whether DNAm is rather a cause or consequence of allergic sensitization. Here, we investigated the direction of the observed associations between well-known environmental and genetic determinants of allergy, DNAm, and aeroallergen sensitization using a combination of high-dimensional and causal mediation analyses.
Methods Using prospectively collected data from the German LISA birth cohort from two time windows (6–10 years: N = 234; 10–15 years: N = 167), we tested whether DNAm is a cause or a consequence of aeroallergen sensitization (specific immunoglobulin E > 0.35kU/l) by conducting mediation analyses for both effect directions using maternal smoking during pregnancy, family history of allergies, and a polygenic risk score (PRS) for any allergic disease as exposure variables. We evaluated individual CpG sites (EPIC BeadChip) and allergy-related methylation risk scores (MRS) as potential mediators in the mediation analyses. We applied three high-dimensional mediation approaches (HIMA, DACT, gHMA) and validated results using causal mediation analyses. A replication of results was attempted in the Swedish BAMSE cohort.
Results Using high-dimensional methods, we identified five CpGs as mediators of prenatal exposures to sensitization with significant (adjusted p < 0.05) indirect effects in the causal mediation analysis (maternal smoking: two CpGs, family history: one, PRS: two). None of these CpGs could be replicated in BAMSE. The effect of family history on allergy-related MRS was significantly mediated by aeroallergen sensitization (proportions mediated: 33.7–49.6%), suggesting changes in DNAm occurred post-sensitization. Conclusion The results indicate that DNAm may be a cause or consequence of aeroallergen sensitization depending on genomic location. Allergy-related MRS, identified as a potential cause of sensitization, can be considered as a cross-sectional biomarker of disease. Differential DNAm in individual CpGs, identified as mediators of the development of sensitization, could be used as clinical predictors of disease development. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01332-5.
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14
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Melén E, Koppelman GH, Vicedo-Cabrera AM, Andersen ZJ, Bunyavanich S. Allergies to food and airborne allergens in children and adolescents: role of epigenetics in a changing environment. THE LANCET. CHILD & ADOLESCENT HEALTH 2022; 6:810-819. [PMID: 35985346 DOI: 10.1016/s2352-4642(22)00215-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Allergic diseases affect millions of children and adolescents worldwide. In this Review, we focus on allergies to food and airborne allergens and provide examples of prevalence trends during a time when climate change is of increasing concern. Profound environmental changes have affected natural systems in terms of biodiversity loss, air pollution, and climate. We discuss the potential links between these changes and allergic diseases in children, and the clinical implications. Several exposures of relevance for allergic disease also correlate with epigenetic changes such as DNA methylation. We propose that epigenetics could be a promising tool by which exposures and hazards related to a changing environment can be captured. Epigenetics might also provide promising biomarkers and help to elucidate the mechanisms related to allergic disease initiation and progress.
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Affiliation(s)
- Erik Melén
- Department of Clinical Science and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology and Groningen Research Institute for Asthma and COPD (GRIAC), University Medical Center Groningen, Beatrix Children's Hospital, University of Groningen, Groningen, Netherlands
| | - Ana Maria Vicedo-Cabrera
- Institute of Social and Preventive Medicine and Oeschger Center for Climate Change Research, University of Bern, Bern, Switzerland
| | | | - Supinda Bunyavanich
- Division of Allergy and Immunology, Department of Pediatrics, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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15
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Kilanowski A, Chen J, Everson T, Thiering E, Wilson R, Gladish N, Waldenberger M, Zhang H, Celedón JC, Burchard EG, Peters A, Standl M, Hüls A. Methylation risk scores for childhood aeroallergen sensitization: Results from the LISA birth cohort. Allergy 2022; 77:2803-2817. [PMID: 35437756 PMCID: PMC9437118 DOI: 10.1111/all.15315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Epigenomic (e.g., DNA methylation [DNAm]) changes have been hypothesized as intermediate step linking environmental exposures with allergic disease. Associations between individual DNAm at CpGs and allergic diseases have been reported, but their joint predictive capability is unknown. METHODS Data were obtained from 240 children of the German LISA cohort. DNAm was measured in blood clots at 6 (N = 234) and 10 years (N = 227) using the Illumina EPIC chip. Presence of aeroallergen sensitization was measured in blood at 6, 10, and 15 years. We calculated six methylation risk scores (MRS) for allergy-related phenotypes, like total and specific IgE, asthma, or any allergies, based on available publications and assessed their performances both cross-sectionally (biomarker) and prospectively (predictor of the disease). Dose-response associations between aeroallergen sensitization and MRS were evaluated. RESULTS All six allergy-related MRS were highly correlated (r > .86), and seven CpGs were included in more than one MRS. Cross-sectionally, we observed an 81% increased risk for aeroallergen sensitization at 6 years with an increased MRS by one standard deviation (best-performing MRS, 95% confidence interval = [43%; 227%]). Significant associations were also seen cross-sectionally at 10 years and prospectively, though the effect of the latter was attenuated when restricted to participants not sensitized at baseline. A clear dose-response relationship with levels of aeroallergen sensitization could be established cross-sectionally, but not prospectively. CONCLUSION We found good classification and prediction capabilities of calculated allergy-related MRS cross-sectionally, underlining the relevance of altered gene-regulation in allergic diseases and providing insights into potential DNAm biomarkers of aeroallergen sensitization.
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Affiliation(s)
- Anna Kilanowski
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA.,Institute for Medical Information Processing, Biometry, and Epidemiology; Pettenkofer School of Public Health, LMU Munich, Munich, Germany,Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Todd Everson
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA.,Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Elisabeth Thiering
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Munich, Germany
| | - Rory Wilson
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Nicole Gladish
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Research Unit Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh
| | | | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Epidemiology, Ludwig-Maximilians University, Marchioninistr. 15, 81377 Munich, Germany
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Lung Research (DZL), Gießen, Germany.,Corresponding Author Dr. Anke Huels (for methodologic requests), Rollins School of Public Health, Emory University, Department of Epidemiology, 1518 Clifton Rd NE, Atlanta, GA 30322, Phone: 404-727-4103, ; Dr. Marie Standl (for data related requests), Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epidemiology, Ingolstädter Landstraße 1, D-85764 Neuherberg, Phone: +49 89 3187-2952,
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA.,Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA.,Corresponding Author Dr. Anke Huels (for methodologic requests), Rollins School of Public Health, Emory University, Department of Epidemiology, 1518 Clifton Rd NE, Atlanta, GA 30322, Phone: 404-727-4103, ; Dr. Marie Standl (for data related requests), Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epidemiology, Ingolstädter Landstraße 1, D-85764 Neuherberg, Phone: +49 89 3187-2952,
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16
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Wahn U, Lau S, Eigenmann P, Melen E, Krauss-Etschmann S, Lex C, Matricardi P, Schaub B, Halken S, Ege M, Jackson D, Hamelmann E, Szépfalusi Z, Garcia AN, von Mutius E. Early priming of asthma and respiratory allergies: Future aspects of prevention: A statement by the European Forum for Education and Research in Allergy and Airway Disease (EUFOREA) and the EAACI-Clemens von Pirquet Foundation. Pediatr Allergy Immunol 2022; 33:e13773. [PMID: 35470937 DOI: 10.1111/pai.13773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 11/29/2022]
Abstract
In order to summarize recent research on the prevention of allergies-particularly asthma-and stimulate new activities for future initiatives, a virtual workshop sponsored by the EAACI Clemens von Pirquet foundation and EUFOREA was held in October 2021. The determinants of the "allergic march" as well as the key messages from intervention studies were reviewed by an international faculty of experts. Several unmet needs were identified, and a number of priorities for future studies were proposed.
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Affiliation(s)
- Ulrich Wahn
- Department of Respiratory Medicine, Immunology and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Lau
- Department of Respiratory Medicine, Immunology and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Philippe Eigenmann
- Pediatric Allergy Unit, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
| | - Erik Melen
- Department of Clinical Science and Education, Södershjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Krauss-Etschmann
- Leibniz Lung Center, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Institute of Experimental Medicine, Christian Alberts University, Kiel, Germany
| | - Christiane Lex
- Department for Paediatric Cardiology, Intensive Care and Neonatology, University Medicine, Göttingen, Germany
| | - Paolo Matricardi
- Department of Respiratory Medicine, Immunology and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Bianca Schaub
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's University Hospital, LMU Munich-Member of the German Center for Lung Research-DZL-LMU Munich, Munich, Germany
| | - Susanne Halken
- Hans Cristian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - Markus Ege
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's University Hospital, LMU Munich-Member of the German Center for Lung Research-DZL-LMU Munich, Munich, Germany
| | - Daniel Jackson
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Eckard Hamelmann
- Department of Pediatrics, Children's Center Bethel, University Medicine, Bielefeld, Germany
| | - Zsolt Szépfalusi
- Department of Pediatrics, Division of Pediatrics Pulmonology, Allergology and Endocrinology, Comprehensive Center Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Antonio N Garcia
- Health Research Institute, Hospital Universitario La Fe., Valencia, Spain
| | - Erika von Mutius
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's University Hospital, LMU Munich-Member of the German Center for Lung Research-DZL-LMU Munich, Munich, Germany
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17
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Asthma and Allergy: Unravelling a Tangled Relationship with a Focus on New Biomarkers and Treatment. Int J Mol Sci 2022; 23:ijms23073881. [PMID: 35409241 PMCID: PMC8999577 DOI: 10.3390/ijms23073881] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 12/19/2022] Open
Abstract
Asthma is a major driver of health care costs across ages. Despite widely disseminated asthma-treatment guidelines and a growing variety of effective therapeutic options, most patients still experience symptoms and/or refractoriness to standard of care treatments. As a result, most patients undergo a further intensification of therapy to optimize symptom control with a subsequent increased risk of side effects. Raising awareness about the relevance of evaluating aeroallergen sensitizations in asthmatic patients is a key step in better informing clinical practice while new molecular tools, such as the component resolved diagnosis, may be of help in refining the relationship between sensitization and therapeutic recommendations. In addition, patient care should benefit from reliable, easy-to-measure and clinically accessible biomarkers that are able to predict outcome and disease monitoring. To attain a personalized asthma management and to guide adequate treatment decisions, it is of paramount importance to expand clinicians' knowledge about the tangled relationship between asthma and allergy from a molecular perspective. Our review explores the relevance of allergen testing along the asthma patient's journey, with a special focus on recurrent wheezing children. Here, we also discuss the unresolved issues regarding currently available biomarkers and summarize the evidence supporting the eosinophil-derived neurotoxin as promising biomarker.
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18
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Legaki E, Arsenis C, Taka S, Papadopoulos NG. DNA methylation biomarkers in asthma and rhinitis: Are we there yet? Clin Transl Allergy 2022; 12:e12131. [PMID: 35344303 PMCID: PMC8967268 DOI: 10.1002/clt2.12131] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/01/2022] [Accepted: 02/22/2022] [Indexed: 12/16/2022] Open
Abstract
The study of epigenetics has improved our understanding of mechanisms underpinning gene‐environment interactions and is providing new insights in the pathophysiology of respiratory allergic diseases. We reviewed the literature on DNA methylation patterns across different tissues in asthma and/or rhinitis and attempted to elucidate differentially methylated loci that could be used to characterize asthma or rhinitis. Although nasal and bronchial epithelia are similar in their histological structure and cellular composition, genetic and epigenetic regulation may differ across tissues. Advanced methods have enabled comprehensive, high‐throughput methylation profiling of different tissues (bronchial or nasal epithelial cells, whole blood or isolated mononuclear cells), in subjects with respiratory conditions, aiming to elucidate gene regulation mechanisms and identify new biomarkers. Several genes and CpGs have been suggested as asthma biomarkers, though research on allergic rhinitis is still lacking. The most common differentially methylated loci presented in both blood and nasal samples are ACOT7, EPX, KCNH2, SIGLEC8, TNIK, FOXP1, ATPAF2, ZNF862, ADORA3, ARID3A, IL5RA, METRNL and ZFPM1. Overall, there is substantial variation among studies, (i.e. sample sizes, age groups and disease phenotype). Greater variability of analysis method detailed phenotypic characterization and age stratification should be taken into account in future studies.
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Affiliation(s)
- Evangelia Legaki
- Allergy and Clinical Immunology Unit Second Pediatric Clinic National and Kapodistrian University of Athens Athens Greece
| | - Christos Arsenis
- Allergy and Clinical Immunology Unit Second Pediatric Clinic National and Kapodistrian University of Athens Athens Greece
| | - Styliani Taka
- Allergy and Clinical Immunology Unit Second Pediatric Clinic National and Kapodistrian University of Athens Athens Greece
| | - Nikolaos G. Papadopoulos
- Allergy and Clinical Immunology Unit Second Pediatric Clinic National and Kapodistrian University of Athens Athens Greece
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19
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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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20
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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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21
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Cosín-Tomás M, Bustamante M, Sunyer J. Epigenetic association studies at birth and the origin of lung function development. Eur Respir J 2021; 57:57/4/2100109. [PMID: 33858853 DOI: 10.1183/13993003.00109-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Marta Cosín-Tomás
- ISGlobal, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Centro de investigación biomédica en red en epidemiología y salud pública (ciberesp), Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Centro de investigación biomédica en red en epidemiología y salud pública (ciberesp), Madrid, Spain
| | - Jordi Sunyer
- ISGlobal, Barcelona, Spain .,Universitat Pompeu Fabra, Barcelona, Spain.,Centro de investigación biomédica en red en epidemiología y salud pública (ciberesp), Madrid, Spain.,IMIM Parc Salut Mar, Barcelona, Spain
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