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Marriott H, Duchesne M, Moitra S, Okoye I, Gerla L, Mayers I, Moolji J, Adatia A, Lacy P. Upper Airway Alarmin Cytokine Expression in Asthma of Different Severities. J Clin Med 2024; 13:3721. [PMID: 38999286 PMCID: PMC11242732 DOI: 10.3390/jcm13133721] [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: 06/04/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Background: The secretion of alarmin cytokines by epithelial cells, including thymic stromal lymphopoietin (TSLP), interleukin (IL)-25, and IL-33, initiates inflammatory cascades in asthma. However, alarmin cytokine expression in the upper airways in asthma remains largely unknown. Methods: We recruited 40 participants with asthma into four groups as per the Global Initiative for Asthma (GINA) steps (10 in each group of GINA 1/2, 3, 4, and 5). Cells were derived from nasal, buccal, and throat brushings. Intracellular cytokine expression (TSLP, IL-25, and IL-33) was assessed by flow cytometry in cytokeratin 8+ (Ck8+) epithelial cells immediately following collection. Results: TSLP was significantly increased (p < 0.001) in GINA 5 patients across nasal, buccal, and throat Ck8+ epithelial cells, while IL-25 was elevated in nasal and throat samples (p < 0.003), and IL-33 levels were variable, compared with GINA 1-4 patients. Individual GINA subgroup comparison showed that TSLP levels in nasal samples from GINA 5 patients were significantly (p = 0.03) elevated but did not differ between patients with and without nasal comorbidities. IL-25 and IL-33 (obtained from nasal, buccal, and throat samples) were not significantly different in individual groups. Conclusions: Our study demonstrates for the first time that Ck8+ nasal epithelial cells from GINA 5 asthma patients express elevated levels of TSLP.
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Affiliation(s)
- Hazel Marriott
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Marc Duchesne
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Subhabrata Moitra
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Isobel Okoye
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Luke Gerla
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Irvin Mayers
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Jalal Moolji
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Adil Adatia
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Paige Lacy
- Division of Pulmonary Medicine, Department of Medicine, University of Alberta, Edmonton, AB T6G 2R3, Canada
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2
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Calcaterra V, Farolfi A, D'Auria E, De Silvestri A, Baldassarre P, Ferrara F, Tiranini L, Ghezzi M, Garancini N, Bernardo L, Nappi RE, Zuccotti G. Perimenstrual Asthma and Premenstrual Disorders in Adolescents with Asthma. J Pediatr Adolesc Gynecol 2024; 37:132-136. [PMID: 37977436 DOI: 10.1016/j.jpag.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Asthma is a common chronic disease in pediatric patients, and perimenstrual asthma (PMA), refers to the worsening of asthma symptoms during the perimenstrual period, mainly reported in adult women. However, there is limited information regarding the exacerbation of symptoms in the presence of premenstrual disorders (PMDs) in adolescents. The aim of this pilot observational study was to investigate the frequency and potential association of PMA and PMDs in a clinical sample of adolescents with asthma. PATIENTS AND METHODS The study included 50 adolescents (aged 12-18 years, mean 16.08 ± 2.35) with asthma and at least 2 years of gynecological age. The participants completed the Asthma Control Test (ACT) to assess asthma control (considered pathological if ACT score < 20) and the modified Premenstrual Symptoms Screening Tool for Adolescents (PSST-A) to evaluate PMDs. RESULTS A total of 75.5% of adolescents reported PMA. The prevalence of premenstrual symptoms did not significantly differ between the PMA and no-PMA group. Among the study sample, 38.7% experienced symptoms indicative of moderate/severe premenstrual syndrome, and 8.1% exhibited symptoms of premenstrual dysphoric disorder. Compared with the no-PMA group, patients with PMA showed a significant impairment in daily and home activities (P = .03 and P = .02, respectively) and exhibited a difference in the frequency of asthma symptoms (P < .001) and medication use (P ≤ .01). CONCLUSION Perimenstrual worsening of asthma symptoms may be common in adolescents with a severe form of asthma. Prospective data collection through menstrual diaries is necessary to further explore the association between PMA and PMDs. Identifying early risk factors for PMA could facilitate the development of preventive strategies and early interventions for adolescents with asthma.
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Affiliation(s)
- Valeria Calcaterra
- Pediatric and Adolescent Unit, Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy; Department of Pediatrics, Buzzi Children's Hospital, Milano, Italy
| | - Andrea Farolfi
- Department of Pediatrics, Buzzi Children's Hospital, Milano, Italy
| | - Enza D'Auria
- Department of Pediatrics, Buzzi Children's Hospital, Milano, Italy.
| | - Annalisa De Silvestri
- Scientific Direction, Clinical Epidemiology and Biometric Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | - Francesca Ferrara
- Department of Childhood and Adolescent Medicine and Gender Medicine, The Fatebenefratelli-Melloni Hospital, Milan, Italy
| | - Lara Tiranini
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, School of Medicine, University of Pavia, Italy
| | - Michele Ghezzi
- Department of Pediatrics, Buzzi Children's Hospital, Milano, Italy
| | - Nicolò Garancini
- Department of Pediatrics, Buzzi Children's Hospital, Milano, Italy
| | - Luca Bernardo
- Department of Childhood and Adolescent Medicine and Gender Medicine, The Fatebenefratelli-Melloni Hospital, Milan, Italy
| | - Rossella E Nappi
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, School of Medicine, University of Pavia, Italy; Research Center for Reproductive Medicine, Gynecological Endocrinology and Menopause, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gianvincenzo Zuccotti
- Department of Pediatrics, Buzzi Children's Hospital, Milano, Italy; Department of Biomedical and Clinical Science, University of Milano, Milano, Italy
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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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4
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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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5
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Koumpagioti D, Moriki D, Boutopoulou B, Matziou V, Loukou I, Priftis KN, Douros K. The Association between CFTR Gene Mutation Heterozygosity and Asthma Development: A Systematic Review. J Clin Med 2023; 12:jcm12062403. [PMID: 36983403 PMCID: PMC10054146 DOI: 10.3390/jcm12062403] [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: 02/18/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Asthma is caused by complex interactions between environmental and genetic factors. Various genes have been implicated as potential risk factors in the development of asthma; among them is cystic fibrosis transmembrane conductance regulator (CFTR) gene. The aim of this systematic review was to investigate the association of CFTR mutation heterozygosity with the development of asthma, by updating the existing data with recent studies' findings. Therefore, a systematic review of the literature was conducted on Pubmed, ESBCO (Cinahl) and Scopus Databases up to December 2022. After the eligibility assessment, 17 studies were included in this review. Nine of them supported a lack of relationship between CFTR mutation heterozygosity and asthma susceptibility, and eight reported a positive association. Consequently, more extensive research is needed through high-quality studies to provide valid evidence and highlight the clinical benefits of identifying CFTR mutations in asthma patients, their impact on asthma severity, or treatment perspectives.
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Affiliation(s)
- Despoina Koumpagioti
- Department of Nursing, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dafni Moriki
- Third Department of Pediatrics, School of Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Barbara Boutopoulou
- Department of Nursing, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Vasiliki Matziou
- Department of Nursing, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Ioanna Loukou
- Department of Cystic Fibrosis, Aghia Sophia Children's Hospital, 11527 Athens, Greece
| | - Kostas N Priftis
- Third Department of Pediatrics, School of Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Konstantinos Douros
- Third Department of Pediatrics, School of Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, 12462 Athens, Greece
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6
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Ekpruke CD, Silveyra P. Sex Differences in Airway Remodeling and Inflammation: Clinical and Biological Factors. FRONTIERS IN ALLERGY 2022; 3:875295. [PMID: 35769576 PMCID: PMC9234861 DOI: 10.3389/falgy.2022.875295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Asthma is characterized by an increase in the contraction and inflammation of airway muscles, resulting in airflow obstruction. The prevalence of asthma is lower in females than in males until the start of puberty, and higher in adult women than men. This sex disparity and switch at the onset of puberty has been an object of debate among many researchers. Hence, in this review, we have summarized these observations to pinpoint areas needing more research work and to provide better sex-specific diagnosis and management of asthma. While some researchers have attributed it to the anatomical and physiological differences in the male and female respiratory systems, the influences of hormonal interplay after puberty have also been stressed. Other hormones such as leptin have been linked to the sex differences in asthma in both obese and non-obese patients. Recently, many scientists have also demonstrated the influence of the sex-specific genomic framework as a key player, and others have linked it to environmental, social lifestyle, and occupational exposures. The majority of studies concluded that adult men are less susceptible to developing asthma than women and that women display more severe forms of the disease. Therefore, the understanding of the roles played by sex- and gender-specific factors, and the biological mechanisms involved will help develop novel and more accurate diagnostic and therapeutic plans for sex-specific asthma management.
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Affiliation(s)
- Carolyn Damilola Ekpruke
- Department of Environmental and Occupational Health, Indiana University Bloomington School of Public Health, Bloomington, IN, United States
| | - Patricia Silveyra
- Department of Environmental and Occupational Health, Indiana University Bloomington School of Public Health, Bloomington, IN, United States
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
- *Correspondence: Patricia Silveyra
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7
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Sheikhpour M, Maleki M, Ebrahimi Vargoorani M, Amiri V. A review of epigenetic changes in asthma: methylation and acetylation. Clin Epigenetics 2021; 13:65. [PMID: 33781317 PMCID: PMC8008616 DOI: 10.1186/s13148-021-01049-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/04/2021] [Indexed: 12/30/2022] Open
Abstract
Several studies show that childhood and adulthood asthma and its symptoms can be modulated through epigenetic modifications. Epigenetic changes are inheritable modifications that can modify the gene expression without changing the DNA sequence. The most common epigenetic alternations consist of DNA methylation and histone modifications. How these changes lead to asthmatic phenotype or promote the asthma features, in particular by immune pathways regulation, is an understudied topic. Since external effects, like exposure to tobacco smoke, air pollution, and drugs, influence both asthma development and the epigenome, elucidating the role of epigenetic changes in asthma is of great importance. This review presents available evidence on the epigenetic process that drives asthma genes and pathways, with a particular focus on DNA methylation, histone methylation, and acetylation. We gathered and assessed studies conducted in this field over the past two decades. Our study examined asthma in different aspects and also shed light on the limitations and the important factors involved in the outcomes of the studies. To date, most of the studies in this area have been carried out on DNA methylation. Therefore, the need for diagnostic and therapeutic applications through this molecular process calls for more research on the histone modifications in this disease.
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Affiliation(s)
- Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Mobina Maleki
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Ebrahimi Vargoorani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, College of Basic Sciences, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Vahid Amiri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
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8
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Selber-Hnatiw S, Sultana T, Tse W, Abdollahi N, Abdullah S, Al Rahbani J, Alazar D, Alrumhein NJ, Aprikian S, Arshad R, Azuelos JD, Bernadotte D, Beswick N, Chazbey H, Church K, Ciubotaru E, D'Amato L, Del Corpo T, Deng J, Di Giulio BL, Diveeva D, Elahie E, Frank JGM, Furze E, Garner R, Gibbs V, Goldberg-Hall R, Goldman CJ, Goltsios FF, Gorjipour K, Grant T, Greco B, Guliyev N, Habrich A, Hyland H, Ibrahim N, Iozzo T, Jawaheer-Fenaoui A, Jaworski JJ, Jhajj MK, Jones J, Joyette R, Kaudeer S, Kelley S, Kiani S, Koayes M, Kpata AJAAL, Maingot S, Martin S, Mathers K, McCullogh S, McNamara K, Mendonca J, Mohammad K, Momtaz SA, Navaratnarajah T, Nguyen-Duong K, Omran M, Ortiz A, Patel A, Paul-Cole K, Plaisir PA, Porras Marroquin JA, Prevost A, Quach A, Rafal AJ, Ramsarun R, Rhnima S, Rili L, Safir N, Samson E, Sandiford RR, Secondi S, Shahid S, Shahroozi M, Sidibé F, Smith M, Sreng Flores AM, Suarez Ybarra A, Sénéchal R, Taifour T, Tang L, Trapid A, Tremblay Potvin M, Wainberg J, Wang DN, Weissenberg M, White A, Wilkinson G, Williams B, Wilson JR, Zoppi J, Zouboulakis K, Gamberi C. Metabolic networks of the human gut microbiota. MICROBIOLOGY-SGM 2020; 166:96-119. [PMID: 31799915 DOI: 10.1099/mic.0.000853] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human gut microbiota controls factors that relate to human metabolism with a reach far greater than originally expected. Microbial communities and human (or animal) hosts entertain reciprocal exchanges between various inputs that are largely controlled by the host via its genetic make-up, nutrition and lifestyle. The composition of these microbial communities is fundamental to supply metabolic capabilities beyond those encoded in the host genome, and contributes to hormone and cellular signalling that support the dynamic adaptation to changes in food availability, environment and organismal development. Poor functional exchange between the microbial communities and their human host is associated with dysbiosis, metabolic dysfunction and disease. This review examines the biology of the dynamic relationship between the reciprocal metabolic state of the microbiota-host entity in balance with its environment (i.e. in healthy states), the enzymatic and metabolic changes associated with its imbalance in three well-studied diseases states such as obesity, diabetes and atherosclerosis, and the effects of bariatric surgery and exercise.
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Affiliation(s)
- Susannah Selber-Hnatiw
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Tarin Sultana
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - W Tse
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Niki Abdollahi
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Sheyar Abdullah
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Jalal Al Rahbani
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Diala Alazar
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Nekoula Jean Alrumhein
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Saro Aprikian
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Rimsha Arshad
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Jean-Daniel Azuelos
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Daphney Bernadotte
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Natalie Beswick
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Hana Chazbey
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Kelsey Church
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Emaly Ciubotaru
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Lora D'Amato
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Tavia Del Corpo
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Jasmine Deng
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Briana Laura Di Giulio
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Diana Diveeva
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Elias Elahie
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - James Gordon Marcel Frank
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Emma Furze
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Rebecca Garner
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Vanessa Gibbs
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Rachel Goldberg-Hall
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Chaim Jacob Goldman
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Fani-Fay Goltsios
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Kevin Gorjipour
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Taylor Grant
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Brittany Greco
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Nadir Guliyev
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Andrew Habrich
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Hillary Hyland
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Nabila Ibrahim
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Tania Iozzo
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Anastasia Jawaheer-Fenaoui
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Julia Jane Jaworski
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Maneet Kaur Jhajj
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Jermaine Jones
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Rodney Joyette
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Samad Kaudeer
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Shawn Kelley
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Shayesteh Kiani
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Marylin Koayes
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | | | - Shannon Maingot
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Sara Martin
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Kelly Mathers
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Sean McCullogh
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Kelly McNamara
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - James Mendonca
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Karamat Mohammad
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Sharara Arezo Momtaz
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Thiban Navaratnarajah
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Kathy Nguyen-Duong
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Mustafa Omran
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Angela Ortiz
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Anjali Patel
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Kahlila Paul-Cole
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Paul-Arthur Plaisir
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | | | - Ashlee Prevost
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Angela Quach
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Aries John Rafal
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Rewaparsad Ramsarun
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Sami Rhnima
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Lydia Rili
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Naomi Safir
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Eugenie Samson
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Rebecca Rose Sandiford
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Stefano Secondi
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Stephanie Shahid
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Mojdeh Shahroozi
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Fily Sidibé
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Megan Smith
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Alina Maria Sreng Flores
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Anabel Suarez Ybarra
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Rebecca Sénéchal
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Tarek Taifour
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Lawrence Tang
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Adam Trapid
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Maxim Tremblay Potvin
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Justin Wainberg
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Dani Ni Wang
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Mischa Weissenberg
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Allison White
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Gabrielle Wilkinson
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Brittany Williams
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Joshua Roth Wilson
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Johanna Zoppi
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Katerina Zouboulakis
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
| | - Chiara Gamberi
- Biology Department, Concordia University, 7141 Sherbrooke St W, SP-375-09 Montreal, Quebec, H4B 1R6, Canada
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9
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Patel R, Solatikia F, Zhang H, Wolde A, Kadalayil L, Karmaus W, Ewart S, Arathimos R, Relton C, Ring S, Henderson AJ, Arshad SH, Holloway JW. Sex-specific associations of asthma acquisition with changes in DNA methylation during adolescence. Clin Exp Allergy 2020; 51:318-328. [PMID: 33150670 DOI: 10.1111/cea.13776] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/24/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Underlying biological mechanisms involved in sex differences in asthma status changes from pre- to post-adolescence are unclear. DNA methylation (DNAm) has been shown to be associated with the risk of asthma. OBJECTIVE We hypothesized that asthma acquisition from pre- to post-adolescence was associated with changes in DNAm during this period at asthma-associated cytosine-phosphate-guanine (CpG) sites and such an association was sex-specific. METHODS Subjects from the Isle of Wight birth cohort (IOWBC) with DNAm in blood at ages 10 and 18 years (n = 124 females, 151 males) were studied. Using a training-testing approach, epigenome-wide CpGs associated with asthma were identified. Logistic regression was used to examine sex-specific associations of DNAm changes with asthma acquisition between ages 10 and 18 at asthma-associated CpGs. The ALSPAC birth cohort was used for independent replication. To assess functional relevance of identified CpGs, association of DNAm with gene expression in blood was assessed. RESULTS We identified 535 CpGs potentially associated with asthma. Significant interaction effects of DNAm changes and sex on asthma acquisition in adolescence were found at 13 of the 535 CpGs in IOWBC (P-values <1.0 × 10-3 ). In the replication cohort, consistent interaction effects were observed at 10 of the 13 CpGs. At 7 of these 10 CpGs, opposite DNAm changes across adolescence were observed between sexes in both cohorts. In both cohorts, cg20891917, located on IFRD1 linked to asthma, shows strong sex-specific effects on asthma transition (P-values <.01 in both cohorts). CONCLUSION AND CLINICAL RELEVANCE Gender reversal in asthma acquisition is associated with opposite changes in DNAm (males vs females) from pre- to post-adolescence at asthma-associated CpGs. These CpGs are potential biomarkers of sex-specific asthma acquisition in adolescence.
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Affiliation(s)
- Rutu Patel
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Farnaz Solatikia
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA.,Department of Mathematical Sciences, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Alemayehu Wolde
- Department of Mathematical Sciences, University of Memphis, Memphis, TN, USA
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Ryan Arathimos
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK.,Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | | | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,David Hide Asthma and Allergy Research Centre, Isle of Wight, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
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10
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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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11
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Novel Comprehensive Bioinformatics Approaches to Determine the Molecular Genetic Susceptibility Profile of Moderate and Severe Asthma. Int J Mol Sci 2020; 21:ijms21114022. [PMID: 32512817 PMCID: PMC7312607 DOI: 10.3390/ijms21114022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/19/2020] [Accepted: 05/26/2020] [Indexed: 12/25/2022] Open
Abstract
Background: Asthma is a chronic inflammatory condition linked to hyperresponsiveness in the airways. There is currently no cure available for asthma, and therapy choices are limited. Asthma is the result of the interplay between genes and the environment. The exact molecular genetic mechanism of asthma remains elusive. Aims: The aim of this study is to provide a comprehensive, detailed molecular etiology profile for the molecular factors that regulate the severity of asthma and pathogenicity using integrative bioinformatics tools. Methods: The GSE43696 omnibus gene expression dataset, which contains 50 moderate cases, 38 severe cases, and 20 healthy controls, was used to investigate differentially expressed genes (DEGs), susceptible chromosomal loci, gene networks, pathways, gene ontologies, and protein–protein interactions (PPIs) using an intensive bioinformatics pipeline. Results: The PPI network analysis yielded DEGs that contribute to interactions that differ from moderate-to-severe asthma. The combined interaction scores resulted in higher interactions for the genes STAT3, AGO2, COL1A1, CLCN6, and KSR for moderate asthma and JAK2, INSR, ERBB2, NR3C1, and PTK6 for severe asthma. Enrichment analysis (EA) demonstrated differential enrichment between moderate and severe asthma phenotypes; the ion transport regulation pathway was significantly enhanced in severe asthma phenotypes compared to that in moderate asthma phenotypes and involved PER2, GCR, IRS-2, KCNK7, KCNK6, NOX1, and SCN7A. The most enriched common pathway in both moderate and severe asthma is the development of the glucocorticoid receptor (GR) signaling pathway followed by glucocorticoid-mediated inhibition of proinflammatory and proconstrictory signaling in the airway of smooth muscle cell pathways. Gene sets were shared between severe and moderate asthma at 16 chromosome locations, including 17p13.1, 16p11.2, 17q21.31, 1p36, and 19q13.2, while 60 and 48 chromosomal locations were unique for both moderate and severe asthma, respectively. Phylogenetic analysis for DEGs showed that several genes have been intersected in phases of asthma in the same cluster of genes. This could indicate that several asthma-associated genes have a common ancestor and could be linked to the same biological function or gene family, implying the importance of these genes in the pathogenesis of asthma. Conclusion: New genetic risk factors for the development of moderate-to-severe asthma were identified in this study, and these could provide a better understanding of the molecular pathology of asthma and might provide a platform for the treatment of asthma.
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12
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Bae DJ, Jun JA, Chang HS, Park JS, Park CS. Epigenetic Changes in Asthma: Role of DNA CpG Methylation. Tuberc Respir Dis (Seoul) 2020; 83:1-13. [PMID: 31905427 PMCID: PMC6953489 DOI: 10.4046/trd.2018.0088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/19/2019] [Accepted: 08/30/2019] [Indexed: 12/21/2022] Open
Abstract
For the past three decades, more than a thousand of genetic studies have been performed to find out the genetic variants responsible for the risk of asthma. Until now, all of the discovered single nucleotide polymorphisms have explained genetic effects less than initially expected. Thus, clarification of environmental factors has been brought up to overcome the 'missing' heritability. The most exciting solution is epigenesis because it intervenes at the junction between the genome and the environment. Epigenesis is an alteration of genetic expression without changes of DNA sequence caused by environmental factors such as nutrients, allergens, cigarette smoke, air pollutants, use of drugs and infectious agents during pre- and post-natal periods and even in adulthood. Three major forms of epigenesis are composed of DNA methylation, histone modifications, and specific microRNA. Recently, several studies have been published on epigenesis in asthma and allergy as a powerful tool for research of genetic heritability in asthma albeit epigenetic changes are at the starting point to obtain the data on specific phenotypes of asthma. In this presentation, we mainly review the potential role of DNA CpG methylation in the risk of asthma and its sub-phenotypes including nonsteroidal anti-inflammatory exacerbated respiratory diseases.
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Affiliation(s)
- Da Jeong Bae
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Ji Ae Jun
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Hun Soo Chang
- Department of Environmental Health Sciences, Soonchunhyang University, Asan, Korea
| | - Jong Sook Park
- Division of Allergy and Respiratory Medicine, Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Choon Sik Park
- Division of Allergy and Respiratory Medicine, Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Korea.
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13
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Understanding Root Causes of Asthma. Perinatal Environmental Exposures and Epigenetic Regulation. Ann Am Thorac Soc 2019; 15:S103-S108. [PMID: 29676631 DOI: 10.1513/annalsats.201706-514mg] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A common explanation for the origins and rising prevalence of asthma is that they involve complex interactions between hereditary predispositions and environmental exposures that are incompletely understood. Yet, emerging evidence substantiates the paradigm that environmental exposures prenatally and during very early childhood induce epigenetic alterations that affect the expression of asthma genes and, thereby, asthma itself. Here, we review much of the key evidence supporting this paradigm. First, we describe evidence that the prenatal and early postnatal periods are key time windows of susceptibility to environmental exposures that may trigger asthma. Second, we explain how environmental epigenetic regulation may explain the immunopathology underlying asthma. Third, we outline specific evidence that environmental exposures induce epigenetic regulation, both from animal models and robust human epidemiological research. Finally, we review some emerging topics, including the importance of coexposures, population divergence, and how epigenetic regulation may change over time. Despite all the inherent complexity, great progress has been made toward understanding what we still consider reversible asthma risk factors. These, in time, may impact patient care.
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14
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Qi C, Xu CJ, Koppelman GH. The role of epigenetics in the development of childhood asthma. Expert Rev Clin Immunol 2019; 15:1287-1302. [PMID: 31674254 DOI: 10.1080/1744666x.2020.1686977] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: The development of childhood asthma is caused by a combination of genetic factors and environmental exposures. Epigenetics describes mechanisms of (heritable) regulation of gene expression that occur without changes in DNA sequence. Epigenetics is strongly related to aging, is cell-type specific, and includes DNA methylation, noncoding RNAs, and histone modifications.Areas covered: This review summarizes recent epigenetic studies of childhood asthma in humans, which mostly involve studies of DNA methylation published in the recent five years. Environmental exposures, in particular cigarette smoking, have significant impact on epigenetic changes, but few of these epigenetic signals are also associated with asthma. Several asthma-associated genetic variants relate to DNA methylation. Epigenetic signals can be better understood by studying their correlation with gene expression, which revealed higher presence and activation of blood eosinophils in asthma. Strong associations of nasal methylation signatures and atopic asthma were identified, which were replicable across different populations.Expert commentary: Epigenetic markers have been strongly associated with asthma, and might serve as biomarker of asthma. The causal and longitudinal relationships between epigenetics and disease, and between environmental exposures and epigenetic changes need to be further investigated. Efforts should be made to understand cell-type-specific epigenetic mechanisms in asthma.
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Affiliation(s)
- Cancan Qi
- Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cheng-Jian Xu
- Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Gastroenterology, Hepatology and Endocrinology, CiiM, Centre for individualised infection medicine, A joint venture between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gerard H Koppelman
- Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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15
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Abstract
Twin registries have developed as a valuable resource for the study of many aspects of disease and society over the years in many different countries. A number of these registries include large numbers of twins with data collected at varying information levels for twin cohorts over the past several decades. More recent expansion of twin datasets has allowed for the collection of genetic data, together with many other levels of 'omic' information along with multiple demographic, physiological, health outcomes and other measures typically used in epidemiologic research. Other twin data sources outside these registries reflect research interests in particular aspects of disease or specific phenotypic assessment. Twin registries have the potential to play a key role in many aspects of the artificial intelligence/machine learning-driven projects of the future and will continue to keep adapting to the changing research landscape.
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16
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Mohandas N, Loke YJ, Hopkins S, Mackenzie L, Bennett C, Berkovic SF, Vadlamudi L, Craig JM. Evidence for type-specific DNA methylation patterns in epilepsy: a discordant monozygotic twin approach. Epigenomics 2019; 11:951-968. [DOI: 10.2217/epi-2018-0136] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Aim: Epilepsy is a common neurological disorder characterized by recurrent seizures. We performed epigenetic analyses between and within 15 monozygotic (MZ) twin pairs discordant for focal or generalized epilepsy. Methods: DNA methylation analysis was performed using Illumina Infinium MethylationEPIC arrays, in blood and buccal samples. Results: Differentially methylated regions between epilepsy types associated with PM20D1 and GFPT2 genes in both tissues. Within MZ discordant twin pairs, differentially methylated regions associated with OTX1 and ARID5B genes for generalized epilepsy and TTC39C and DLX5 genes for focal epilepsy. Conclusion: This is the first epigenome-wide association study, utilizing the discordant MZ co-twin model, to deepen our understanding of the neurobiology of epilepsy.
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Affiliation(s)
- Namitha Mohandas
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, Australia
| | - Yuk Jing Loke
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
| | - Stephanie Hopkins
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- School of Medicine & Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Lisa Mackenzie
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
| | - Carmen Bennett
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, University of Melbourne, Austin Health, Victoria, Australia
| | - Lata Vadlamudi
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Queensland, Australia
- Royal Brisbane & Women's Hospital, Queensland, Australia
| | - Jeffrey M Craig
- Environmental & Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Flemington Road, Parkville, Victoria, Australia
- Centre for Molecular & Medical Research, School of Medicine, Deakin University, Geelong, Victoria 3220, Australia
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17
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Mansell G, Gorrie-Stone TJ, Bao Y, Kumari M, Schalkwyk LS, Mill J, Hannon E. Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genomics 2019; 20:366. [PMID: 31088362 PMCID: PMC6518823 DOI: 10.1186/s12864-019-5761-7] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/02/2019] [Indexed: 12/12/2022] Open
Abstract
Background There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the challenges of epigenetic epidemiology regarding study design and interpretation have been discussed in detail, however there are analytical concerns that are outstanding and require further exploration. In this study we seek to address three analytical issues. First, we quantify the multiple testing burden and propose a standard statistical significance threshold for identifying DNA methylation sites that are associated with an outcome. Second, we establish whether linear regression, the chosen statistical tool for the majority of studies, is appropriate and whether it is biased by the underlying distribution of DNA methylation data. Finally, we assess the sample size required for adequately powered DNA methylation association studies. Results We quantified DNA methylation in the Understanding Society cohort (n = 1175), a large population based study, using the Illumina EPIC array to assess the statistical properties of DNA methylation association analyses. By simulating null DNA methylation studies, we generated the distribution of p-values expected by chance and calculated the 5% family-wise error for EPIC array studies to be 9 × 10− 8. Next, we tested whether the assumptions of linear regression are violated by DNA methylation data and found that the majority of sites do not satisfy the assumption of normal residuals. Nevertheless, we found no evidence that this bias influences analyses by increasing the likelihood of affected sites to be false positives. Finally, we performed power calculations for EPIC based DNA methylation studies, demonstrating that existing studies with data on ~ 1000 samples are adequately powered to detect small differences at the majority of sites. Conclusion We propose that a significance threshold of P < 9 × 10− 8 adequately controls the false positive rate for EPIC array DNA methylation studies. Moreover, our results indicate that linear regression is a valid statistical methodology for DNA methylation studies, despite the fact that the data do not always satisfy the assumptions of this test. These findings have implications for epidemiological-based studies of DNA methylation and provide a framework for the interpretation of findings from current and future studies. Electronic supplementary material The online version of this article (10.1186/s12864-019-5761-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Georgina Mansell
- University of Exeter Medical School, University of Exeter, RD&E Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Tyler J Gorrie-Stone
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester, Essex, CO3 3LG, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, Essex, CO3 3LG, UK
| | - Leonard S Schalkwyk
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, RD&E Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, RD&E Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK.
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18
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Edris A, den Dekker HT, Melén E, Lahousse L. Epigenome-wide association studies in asthma: A systematic review. Clin Exp Allergy 2019; 49:953-968. [PMID: 31009112 DOI: 10.1111/cea.13403] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/29/2019] [Accepted: 04/10/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Asthma is a common chronic respiratory airway disease influenced by environmental factors and possibly their interaction with the human genome causing epigenetic changes. Epigenome-wide association studies (EWAS) have mainly investigated DNA methylation and its association with disease or traits, exposure factors or gene expression. This systematic review aimed to identify all EWAS assessing differentially methylated sites associated with asthma in humans. DESIGN Structured systematic literature search following PRISMA guidelines, Newcastle-Ottawa Scale (NOS) for cohort studies was used for bias assessment. DATA SOURCES We searched PubMed and Embase databases from 2005 to 2019. ELIGIBILITY CRITERIA Epigenome-wide association studies testing association between differential methylation and asthma in humans. RESULTS Overall, we identified 16 EWAS studies complying with our search criteria. Twelve studies were conducted on children, and 10 were conducted on sample sizes <150 subjects. Four hundred and nineteen CpGs were reported in children studies after correction for multiple testing. In the adult studies, thousands of differentially methylated sites were identified. Differential methylation in inflammatory-related genes correlated with higher levels of gene expressions of inflammatory modulators in asthma. Differentially methylated genes associated with asthma included SMAD3, SERPINC1, PROK1, IL13, RUNX3 and TIGIT. Forty-one CpGs were replicated at least once in blood samples, and 28 CpGs were replicated in nasal samples. CONCLUSION Although many differentially methylated CpGs in genes known to be involved in asthma have been identified in EWAS to date, we conclude that further studies of larger sample sizes and analyses of differential methylation between different phenotypes are needed in order to comprehensively evaluate the role of epigenetic factors in the pathophysiology and heterogeneity of asthma, and the potential clinical utility to predict or classify patients with asthma.
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Affiliation(s)
- Ahmed Edris
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Herman T den Dekker
- The Generation R Study Group, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands.,Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children's Hospital, Södersjukhuset, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Lies Lahousse
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
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19
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Popovic M, Fiano V, Fasanelli F, Trevisan M, Grasso C, Assumma MB, Gillio-Tos A, Polidoro S, De Marco L, Rusconi F, Merletti F, Zugna D, Richiardi L. Differentially methylated DNA regions in early childhood wheezing: An epigenome-wide study using saliva. Pediatr Allergy Immunol 2019; 30:305-314. [PMID: 30681197 DOI: 10.1111/pai.13023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 01/13/2019] [Accepted: 01/14/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Epigenetics may play a role in wheezing and asthma development. We aimed to examine infant saliva DNA methylation in association with early childhood wheezing. METHODS A case-control study was nested within the NINFEA birth cohort with 68 cases matched to 68 controls by sex, age (between 6 and 18 months, median: 10.3 months) and season at saliva sampling. Using a bumphunting region-based approach, we examined associations between saliva methylome measured using Illumina Infinium HumanMethylation450k array and wheezing between 6 and 18 months of age. We tested our main findings in independent publicly available data sets of childhood respiratory allergy and atopic asthma, with DNA methylation measured in different tissues and at different ages. RESULTS We identified one wheezing-associated differentially methylated region (DMR) spanning ten sequential CpG sites in the promoter-regulatory region of PM20D1 gene (family-wise error rate < 0.05). The observed associations were enhanced in children born to atopic mothers. In the publicly available data sets, hypermethylation in the same region of PM20D1 was consistently found at different ages and in all analysed tissues (cord blood, blood, saliva and nasal epithelia) of children with respiratory allergy/atopic asthma compared with controls. CONCLUSION This study suggests that PM20D1 hypermethylation is associated with early childhood wheezing. Directionally consistent epigenetic alteration observed in cord blood and other tissues at older ages in children with respiratory allergy and atopic asthma provides suggestive evidence that a long-term epigenetic modification, likely operating from birth, may be involved in childhood atopic phenotypes.
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Affiliation(s)
- Maja Popovic
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Francesca Fasanelli
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Morena Trevisan
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Chiara Grasso
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | | | - Anna Gillio-Tos
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | | | - Laura De Marco
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Franca Rusconi
- Unit of Epidemiology, "Anna Meyer" Children's University Hospital, Florence, Italy
| | - Franco Merletti
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Daniela Zugna
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy.,Centro di Ricerca in Medicina Sperimentale (CeRMS) and CPO Piemonte, Turin, Italy
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20
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Wahabi I, Hadj Fredj S, Nefzi M, Dabboubi R, Siala H, Khalsi F, Bousetta K, Messaoud T. Association of M470V polymorphism of CFTR gene with variability of clinical expression of asthma: Case-report study. Allergol Immunopathol (Madr) 2019; 47:159-165. [PMID: 30268379 DOI: 10.1016/j.aller.2018.06.007] [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: 03/05/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
Abstract
INTRODUCTION AND OBJECTIVES Asthma is a complex genetic disorder. Several genes have been found associated with asthma. The cystic fibrosis transmembrane conductance regulator (CFTR) gene is one of them. The aim of this study was to perform a comparative analysis of the genotype and allele frequency distributions of the biallelic marker M470V within the CFTR gene on mutant and wide chromosomes. PATIENTS AND METHODS The molecular approach consists in the genotyping of the M470V marker by the PCR-RFLP technique in 105 asthmatic patients, aged between four months and 17 years, and 105 healthy subjects. RESULTS We found a significant difference in the genotype frequencies between the two studied groups (χ2=9.855, P=0.007). The V/V genotype was over represented in the asthmatic group as compared to the controls (32.38% vs. 16.19%). Whereas, the M/V genotype is more frequent in healthy subjects (40.95% vs. 28.71%). We also noted a significant difference in allelic distribution of M470V with associated diseases (χ2=9.610, P=0.022). CONCLUSIONS The present study is the first report on the distribution of the M470V polymorphism in asthmatic Tunisian patients. We noticed that the M470V variant could modulate the clinical phenotype of asthmatic patients. This preliminary study will establish the molecular basis of this disease in Tunisia.
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21
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Forno E, Celedón JC. Epigenomics and Transcriptomics in the Prediction and Diagnosis of Childhood Asthma: Are We There Yet? Front Pediatr 2019; 7:115. [PMID: 31001502 PMCID: PMC6454089 DOI: 10.3389/fped.2019.00115] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/11/2019] [Indexed: 01/15/2023] Open
Abstract
Asthma is the most common non-communicable chronic disease of childhood. Despite its high prevalence, to date we lack methods that are both efficient and accurate in diagnosing asthma. Most traditional approaches have been based on garnering clinical evidence, such as risk factors and exposures. Given the high heritability of asthma, more recent approaches have looked at genetic polymorphisms as potential "risk factors." However, genetic variants explain only a small proportion of asthma risk, and have been less than optimal at predicting risk for individual subjects. Epigenomic studies offer significant advantages over previous approaches. Epigenetic regulation is highly tissue-specific, and can induce both short- and long-term changes in gene expression. Such changes can start in utero, can vary throughout the life span, and in some instances can be passed on from one generation to another. Most importantly, the epigenome can be modified by environmental factors and exposures, and thus epigenetic and transcriptomic profiling may yield the most accurate risk estimates for a given patient by incorporating environmental (and treatment) effects throughout the lifespan. Here we will review the most recent advances in the use of epigenetic and transcriptomic analysis for the early diagnosis of asthma and atopy, as well as challenges and future directions in the field as it moves forward. We will particularly focus on DNA methylation, the most studied mechanism of epigenetic regulation.
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Affiliation(s)
- Erick Forno
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Juan C Celedón
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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22
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Reese SE, Xu CJ, den Dekker HT, Lee MK, Sikdar S, Ruiz-Arenas C, Merid SK, Rezwan FI, Page CM, Ullemar V, Melton PE, Oh SS, Yang IV, Burrows K, Söderhäll C, Jima DD, Gao L, Arathimos R, Küpers LK, Wielscher M, Rzehak P, Lahti J, Laprise C, Madore AM, Ward J, Bennett BD, Wang T, Bell DA, Vonk JM, Håberg SE, Zhao S, Karlsson R, Hollams E, Hu D, Richards AJ, Bergström A, Sharp GC, Felix JF, Bustamante M, Gruzieva O, Maguire RL, Gilliland F, Baïz N, Nohr EA, Corpeleijn E, Sebert S, Karmaus W, Grote V, Kajantie E, Magnus MC, Örtqvist AK, Eng C, Liu AH, Kull I, Jaddoe VWV, Sunyer J, Kere J, Hoyo C, Annesi-Maesano I, Arshad SH, Koletzko B, Brunekreef B, Binder EB, Räikkönen K, Reischl E, Holloway JW, Jarvelin MR, Snieder H, Kazmi N, Breton CV, Murphy SK, Pershagen G, Anto JM, Relton CL, Schwartz DA, Burchard EG, Huang RC, Nystad W, Almqvist C, Henderson AJ, Melén E, Duijts L, Koppelman GH, London SJ. Epigenome-wide meta-analysis of DNA methylation and childhood asthma. J Allergy Clin Immunol 2018; 143:2062-2074. [PMID: 30579849 DOI: 10.1016/j.jaci.2018.11.043] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/01/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Epigenetic mechanisms, including methylation, can contribute to childhood asthma. Identifying DNA methylation profiles in asthmatic patients can inform disease pathogenesis. OBJECTIVE We sought to identify differential DNA methylation in newborns and children related to childhood asthma. METHODS Within the Pregnancy And Childhood Epigenetics consortium, we performed epigenome-wide meta-analyses of school-age asthma in relation to CpG methylation (Illumina450K) in blood measured either in newborns, in prospective analyses, or cross-sectionally in school-aged children. We also identified differentially methylated regions. RESULTS In newborns (8 cohorts, 668 cases), 9 CpGs (and 35 regions) were differentially methylated (epigenome-wide significance, false discovery rate < 0.05) in relation to asthma development. In a cross-sectional meta-analysis of asthma and methylation in children (9 cohorts, 631 cases), we identified 179 CpGs (false discovery rate < 0.05) and 36 differentially methylated regions. In replication studies of methylation in other tissues, most of the 179 CpGs discovered in blood replicated, despite smaller sample sizes, in studies of nasal respiratory epithelium or eosinophils. Pathway analyses highlighted enrichment for asthma-relevant immune processes and overlap in pathways enriched both in newborns and children. Gene expression correlated with methylation at most loci. Functional annotation supports a regulatory effect on gene expression at many asthma-associated CpGs. Several implicated genes are targets for approved or experimental drugs, including IL5RA and KCNH2. CONCLUSION Novel loci differentially methylated in newborns represent potential biomarkers of risk of asthma by school age. Cross-sectional associations in children can reflect both risk for and effects of disease. Asthma-related differential methylation in blood in children was substantially replicated in eosinophils and respiratory epithelium.
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Affiliation(s)
- Sarah E Reese
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Cheng-Jian Xu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Herman T den Dekker
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mi Kyeong Lee
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Sinjini Sikdar
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Carlos Ruiz-Arenas
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon K Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Phillip E Melton
- Curtin/UWA Centre for Genetic Origins of Health and Disease, Faculty of Health and Medical Sciences, University of Western Australia, Crawley, Australia; School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia
| | - Sam S Oh
- Department of Medicine, University of California San Francisco, San Francisco, Calif
| | - Ivana V Yang
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Kimberley Burrows
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Dereje D Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC
| | - Lu Gao
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Calif
| | - Ryan Arathimos
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Leanne K Küpers
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Peter Rzehak
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland; Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki, Finland
| | - Catherine Laprise
- Centre intégré universitaire de santé et de services sociaux du Saguenay, Saguenay, Quebec, Canada; Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Quebec, Canada
| | - Anne-Marie Madore
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Quebec, Canada
| | - James Ward
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Brian D Bennett
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Tianyuan Wang
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Douglas A Bell
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | | | - Judith M Vonk
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Siri E Håberg
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Shanshan Zhao
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Elysia Hollams
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, Calif
| | - Adam J Richards
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Gemma C Sharp
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mariona Bustamante
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Rachel L Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC; Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | - Frank Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Calif
| | - Nour Baïz
- Epidemiology of Allergic and Respiratory Diseases Department, IPLESP, INSERM and UPMC Sorbonne Université, Paris, France
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sylvain Sebert
- Biocenter Oulu, University of Oulu, Oulu, Finland; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland; Department of Genomics of Complex Diseases, School of Public Health, Imperial College London, London, United Kingdom
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, Tenn
| | - Veit Grote
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Eero Kajantie
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland; Department of Obstetrics and Gynaecology, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland; Hospital for Children and Adolescents, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Maria C Magnus
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Anne K Örtqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, Calif
| | | | - Inger Kull
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children's Hospital, Södersjukhuset, Stockholm, Sweden
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jordi Sunyer
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC; Department of Biological Sciences, North Carolina State University, Raleigh, NC
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic and Respiratory Diseases Department, IPLESP, INSERM and UPMC Sorbonne Université, Paris, France
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; David Hide Asthma and Allergy Research Centre, Isle of Wight, United Kingdom
| | - Berthold Koletzko
- Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians Universität München (LMU), Munich, Germany
| | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elisabeth B Binder
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Ga; Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum Muenchen, Munich, Germany
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, United Kingdom; Biocenter Oulu, University of Oulu, Oulu, Finland; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nabila Kazmi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom; School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Calif
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC; Nicholas School of the Environment, Duke University, Durham, NC
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Josep Maria Anto
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Caroline L Relton
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom; Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - David A Schwartz
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, Calif
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Wenche Nystad
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - A John Henderson
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Sachs' Children's Hospital, Södersjukhuset, Stockholm, Sweden
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine and Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands; Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC.
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Zhang X, Biagini Myers JM, Burleson JD, Ulm A, Bryan KS, Chen X, Weirauch MT, Baker TA, Butsch Kovacic MS, Ji H. Nasal DNA methylation is associated with childhood asthma. Epigenomics 2018; 10:629-641. [PMID: 29692198 DOI: 10.2217/epi-2017-0127] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
AIM We aim to study DNA methylation (DNAm) variations associated with childhood asthma. METHODS Nasal DNAm was compared between sibling pairs discordant for asthma, 29 sib pairs for genome-wide association studies and 54 sib pairs for verification by pyrosequencing. Associations of methylation with asthma symptoms, allergy and environmental exposures were evaluated. In vitro experiments and functional genomic analyses were performed to explore biologic relevance. RESULTS Three CpGs were associated with asthma. cg14830002 was associated with allergies in nonasthmatics. cg23602092 was associated with asthma symptoms. cg14830002 and cg23602092 were associated with traffic-related air pollution exposure. Nearby genes were transcriptionally regulated by diesel exhaust, house dust mite and 5-aza-2'-deoxycytidine. Active chromatin marks and transcription factor binding were found around these sites. CONCLUSION We identified novel DNAm variations associated with childhood asthma and suggested new disease-contributing epigenetic mechanisms.
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Affiliation(s)
- Xue Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jocelyn M Biagini Myers
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - J D Burleson
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ashley Ulm
- Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kelly S Bryan
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA.,Center for Autoimmune Genomics & Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Divisions of Biomedical Informatics & Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Theresa A Baker
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Melinda S Butsch Kovacic
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA.,Division of Biostatistics & Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Hong Ji
- Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
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24
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Mei M, Song H, Chen L, Hu B, Bai R, Xu D, Liu Y, Zhao Y, Chen C. Early-life exposure to three size-fractionated ultrafine and fine atmospheric particulates in Beijing exacerbates asthma development in mature mice. Part Fibre Toxicol 2018. [PMID: 29540228 PMCID: PMC5851307 DOI: 10.1186/s12989-018-0249-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Epidemiological studies have suggested that elevated levels of air pollution contribute to an increased incidence or severity of asthma. Although late-onset adult asthma seems to be more attributable to environmental risk factors, limited data is available on the impact of early-life exposure to size-fractionated ambient particulate matter (PM) on asthma in adults. We aimed to determine the effect on the development and exacerbation of asthma in the adult after the mice were exposed as juveniles to three size-fractionated ambient particulates collected from Beijing. METHODS The three size-fractionated ambient particulates were collected from urban Beijing in winter, heavily affected by traffic and coal-fired emissions. The typical morphological and major chemical components of the PM were characterized first. Oxidative stress and expression of DNA methyltransferases (DNMTs) were then examined in vitro and in the lungs of mouse pups 48 h after exposure to PM by oropharyngeal aspiration. When the exposed and control juvenile mice matured to adulthood, an antigen-induced asthma model was established and relevant bio-indices were assessed. RESULTS PM with different granularities can induce oxidative stress; in particular, F1, with the smallest size (< 0.49 μm), decreased the mRNA expression of DNMTs in vitro and in vivo the most significantly. In an asthma model of adult mice, previous exposure as juveniles to size-fractionated PM caused increased peribronchiolar inflammation, increased airway mucus secretion, and increased production of Th2 cytokines and chemokines. In general, F1 and F2 (aerodynamic diameter < 0.95 μm) particulates affected murine adult asthma development more seriously than F3 (0.95-1.5 μm). Moreover, F1 led to airway inflammation in the form of both increased neutrophils and eosinophils in BALF. The activation of the TGF-β1/Smad2 and Smad3/Stat3 signaling pathways leading to airway fibrosis was more profoundly induced by F1. CONCLUSION This study demonstrated that exposure to ambient PM in juvenile mice enhanced adult asthma development, as shown by increased Th2 responses, which might be associated with the persistent effects resulting from the oxidative stress and decreased gene expression of DNMTs induced by PM exposure. The observed differences between the effects of three size-fractionated particulates were attributed to particle sizes and chemical constituents, including heavy metals and also PAHs, since the amounts of PAH associated with more severe toxicity were enriched equivalently in the F1 and F2 fractions. Relative to the often mentioned PM2.5, PM with an aerodynamic diameter smaller than 0.95 μm had a more aggravating effect on asthma development.
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Affiliation(s)
- Mei Mei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience & Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology of China and University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Haojun Song
- Division of Nuclear Technology and Applications, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Lina Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience & Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology of China and University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Bin Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience & Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology of China and University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ru Bai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience & Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology of China and University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Diandou Xu
- Division of Nuclear Technology and Applications, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Ying Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience & Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology of China and University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience & Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology of China and University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience & Beijing Key Laboratory of Ambient Particles Health Effects and Prevention Techniques, National Center for Nanoscience and Technology of China and University of Chinese Academy of Sciences, Beijing, 100190, China.
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25
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Mohandas N, Bass-Stringer S, Maksimovic J, Crompton K, Loke YJ, Walstab J, Reid SM, Amor DJ, Reddihough D, Craig JM. Epigenome-wide analysis in newborn blood spots from monozygotic twins discordant for cerebral palsy reveals consistent regional differences in DNA methylation. Clin Epigenetics 2018; 10:25. [PMID: 29484035 PMCID: PMC5824607 DOI: 10.1186/s13148-018-0457-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/12/2018] [Indexed: 12/21/2022] Open
Abstract
Background Cerebral palsy (CP) is a clinical description for a group of motor disorders that are heterogeneous with respect to causes, symptoms and severity. A diagnosis of CP cannot usually be made at birth and in some cases may be delayed until 2–3 years of age. This limits opportunities for early intervention that could otherwise improve long-term outcomes. CP has been recorded in monozygotic twins discordant for the disorder, indicating a potential role of non-genetic factors such as intrauterine infection, hypoxia-ischaemia, haemorrhage and thrombosis. The aim of this exploratory study was to utilise the discordant monozygotic twin model to understand and measure epigenetic changes associated with the development of CP. Methods We performed a genome-wide analysis of DNA methylation using the Illumina Infinium Human Methylation 450 BeadChip array with DNA from newborn blood spots of 15 monozygotic twin pairs who later became discordant for CP. Quality control and data preprocessing were undertaken using the minfi R package. Differential methylation analysis was performed using the remove unwanted variation (RUVm) method, taking twin pairing into account in order to identify CP-specific differentially methylated probes (DMPs), and bumphunter was performed to identify differentially methylated regions (DMRs). Results We identified 33 top-ranked DMPs based on a nominal p value cut-off of p < 1 × 10−4 and two DMRs (p < 1 × 10−3) associated with CP. The top-ranked probes related to 25 genes including HNRNPL, RASSF5, CD3D and KALRN involved in immune signalling pathways, in addition to TBC1D24, FBXO9 and VIPR2 previously linked to epileptic encephalopathy. Gene ontology and pathway analysis of top-ranked DMP-associated genes revealed enrichment of inflammatory signalling pathways, regulation of cytokine secretion and regulation of leukocyte-mediated immunity. We also identified two top-ranked DMRs including one on chromosome 6 within the promoter region of LTA gene encoding tumour necrosis factor-beta (TNF-β), an important regulator of inflammation and brain development. The second was within the transcription start site of the LIME1 gene, which plays a key role in inflammatory pathways such as MAPK signalling. CP-specific differential DNA methylation within one of our two top DMRs was validated using an independent platform, MassArray EpiTyper. Conclusions Ours is the first epigenome-wide association study of CP in disease-discordant monozygotic twin pairs and suggests a potential role for immune dysfunction in this condition. Electronic supplementary material The online version of this article (10.1186/s13148-018-0457-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Namitha Mohandas
- Environmental and Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia.,2Department of Paediatrics, The University of Melbourne, Flemington Road, Parkville, Victoria 3052 Australia
| | - Sebastian Bass-Stringer
- Environmental and Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia
| | - Jovana Maksimovic
- 2Department of Paediatrics, The University of Melbourne, Flemington Road, Parkville, Victoria 3052 Australia.,Bioinformatics Group, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia
| | - Kylie Crompton
- 2Department of Paediatrics, The University of Melbourne, Flemington Road, Parkville, Victoria 3052 Australia.,4Developmental Disability and Rehabilitation Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria 3052 Australia.,5Neurodevelopment and Disability, The Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia
| | - Yuk J Loke
- Environmental and Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia
| | - Janet Walstab
- 2Department of Paediatrics, The University of Melbourne, Flemington Road, Parkville, Victoria 3052 Australia.,4Developmental Disability and Rehabilitation Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria 3052 Australia
| | - Susan M Reid
- 2Department of Paediatrics, The University of Melbourne, Flemington Road, Parkville, Victoria 3052 Australia.,4Developmental Disability and Rehabilitation Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria 3052 Australia.,5Neurodevelopment and Disability, The Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia
| | - David J Amor
- 2Department of Paediatrics, The University of Melbourne, Flemington Road, Parkville, Victoria 3052 Australia.,4Developmental Disability and Rehabilitation Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria 3052 Australia.,5Neurodevelopment and Disability, The Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia
| | - Dinah Reddihough
- 2Department of Paediatrics, The University of Melbourne, Flemington Road, Parkville, Victoria 3052 Australia.,4Developmental Disability and Rehabilitation Research, Murdoch Children's Research Institute, Flemington Road, Parkville, Victoria 3052 Australia.,5Neurodevelopment and Disability, The Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia
| | - Jeffrey M Craig
- Environmental and Genetic Epidemiology Research, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052 Australia.,2Department of Paediatrics, The University of Melbourne, Flemington Road, Parkville, Victoria 3052 Australia.,6Centre for Molecular and Medical Research, School of Medicine, Deakin University, Geelong, Victoria 3220 Australia
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Pacholewska A, Kraft MF, Gerber V, Jagannathan V. Differential Expression of Serum MicroRNAs Supports CD4⁺ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma. Genes (Basel) 2017; 8:E383. [PMID: 29231896 PMCID: PMC5748701 DOI: 10.3390/genes8120383] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/21/2017] [Accepted: 12/01/2017] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) regulate post-transcriptional gene expression and may be exported from cells via exosomes or in partnership with RNA-binding proteins. MiRNAs in body fluids can act in a hormone-like manner and play important roles in disease initiation and progression. Hence, miRNAs are promising candidates as biomarkers. To identify serum miRNA biomarkers in the equine model of asthma we investigated small RNA derived from the serum of 34 control and 37 asthmatic horses. These samples were used for next generation sequencing, novel miRNA identification and differential miRNA expression analysis. We identified 11 significantly differentially expressed miRNAs between case and control horses: eca-miR-128, eca-miR-744, eca-miR-197, eca-miR-103, eca-miR-107a, eca-miR-30d, eca-miR-140-3p, eca-miR-7, eca-miR-361-3p, eca-miR-148b-3p and eca-miR-215. Pathway enrichment using experimentally validated target genes of the human homologous miRNAs showed a significant enrichment in the regulation of epithelial-to-mesenchymal transition (key player in airway remodeling in asthma) and the phosphatidylinositol (3,4,5)-triphosphate (PIP3) signaling pathway (modulator of CD4⁺ T cell maturation and function). Downregulated miR-128 and miR-744 supports a Th2/Th17 type immune response in severe equine asthma.
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Affiliation(s)
- Alicja Pacholewska
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Länggassstrasse 124, 3012 Bern, Switzerland.
- Department of Clinical Research and Veterinary Public Health, Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109A, 3012 Bern, Switzerland.
| | - Matthias F Kraft
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Länggassstrasse 124, 3012 Bern, Switzerland.
- Department of Clinical Research and Veterinary Public Health, Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109A, 3012 Bern, Switzerland.
| | - Vincent Gerber
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Länggassstrasse 124, 3012 Bern, Switzerland.
| | - Vidhya Jagannathan
- Department of Clinical Research and Veterinary Public Health, Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109A, 3012 Bern, Switzerland.
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27
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Zhang X, Biagini Myers JM, Yadagiri VK, Ulm A, Chen X, Weirauch MT, Khurana Hershey GK, Ji H. Nasal DNA methylation differentiates corticosteroid treatment response in pediatric asthma: A pilot study. PLoS One 2017; 12:e0186150. [PMID: 29028809 PMCID: PMC5640236 DOI: 10.1371/journal.pone.0186150] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/26/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Treatment response to systemic corticosteroid in asthmatic children is heterogeneous and may be mediated by epigenetic mechanism(s). We aim to identify DNA methylation (DNAm) changes responsive to steroid, and DNAm biomarkers that distinguish treatment response. MATERIALS AND METHODS We followed 33 children (ages 5-18) presenting to the Emergency Department (ED) for asthma exacerbation. Based on whether they met discharge criteria in ≤24 hours, participants were grouped into good and poor responders to steroid treatment. Nasal samples were collected upon presentation to the ED (T0) and 18-24 hours later (T1). Genome-wide DNAm was measured for both time points in 20 subjects, and compared between T0 and T1 in good and poor responders respectively. DNAm at T1 was also compared between two responder groups. DNAm of selected CpGs was verified in the complete cohort, and expression of associated genes was examined. Interactions between DNAm, common single nucleotide polymorphism (SNP) located at the CpG sites and treatment responses were assessed. RESULTS Three CpGs located in the OTX2 promoter showed responder-specific DNAm changes from T0 to T1, in which DNAm decreased in good but not in poor responders. Good and poor responders showed differential DNAm at T1 in 127 CpGs without and 182 CpGs with common SNP co-localization. Negative correlations between DNAm and gene expression were observed at CpGs located within the LDHC promoter, suggesting an impact of DNAm on gene regulation. Interactions between SNPs, DNAm and treatment response were detected. CONCLUSION Acute systemic steroid treatment modifies nasal DNAm in good responders. Nasal DNAm, dependent or independent of SNPs, can differentiate response to treatment in acute asthmatic children.
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Affiliation(s)
- Xue Zhang
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Pyrosequencing lab for genomic and epigenomic research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jocelyn M. Biagini Myers
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Veda K. Yadagiri
- Pyrosequencing lab for genomic and epigenomic research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Ashley Ulm
- Pyrosequencing lab for genomic and epigenomic research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Matthew T. Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Gurjit K. Khurana Hershey
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Hong Ji
- Pyrosequencing lab for genomic and epigenomic research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
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28
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Kim SK, Seok H, Park HJ, Han K, Kang SW, Ban JY, Jung HJ, Kim KI, Lee BJ, Kim J, Chung JH. Association Between Secretoglobin Family 3A Member 2 (SCGB3A2) Gene Polymorphisms and Asthma in a Korean Population. Med Sci Monit 2017; 23:1880-1885. [PMID: 28422086 PMCID: PMC5405786 DOI: 10.12659/msm.903983] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background Secretoglobin family 3A member 2 (SCGB3A2) plays an important role in secreting lung surfactant protein, which is a downstream target of thyroid transcription factor. Material/Methods We investigated whether single-nucleotide polymorphisms (SNPs) of SCGB3A2 gene contribute to susceptibility to asthma. To explore this possible association, 2 promoter SNPs (rs6882292, 659 G/A and rs1368408, −112 G/A) and missense SNP (rs151333009, stop codon) were tested in SCGB3A2 gene in 101 asthma patients and 377 healthy control subjects. SNPStats was used to obtain odds ratio (OR), 95% confidence intervals (CI), and P value adjusted for age and sex as covariables. Logistic regression method in each model (dominant, recessive, and log-additive) was applied to analyze genetic data. Results rs151333009 SNP showed a monomorphic genotype. Two promoter SNPs (rs6882292, −659 G/A and rs1368408, −112 G/A) showed significant association with asthma (rs6882292, OR=2.66, 95% CI=1.42–5.01, p=0.0033 in dominant model, OR=2.45, 95% CI=1.33–4.54, p=0.0055 in log-additive model; rs1368408, OR=1.59, 95% CI=1.02–2.49, p=0.041 in dominant model, OR=3.02, 95% CI=1.15–7.90, p=0.03 in recessive model, OR=1.63, 95% CI=1.63, 95% CI=1.12–2.37, p=0.012 in log-additive model). Conclusions These results suggest that the promoter SNPs (rs6882292 and rs1368408) of SCGB3A2 gene may contribute to susceptibility to asthma in a Korean population.
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Affiliation(s)
- Su Kang Kim
- Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, South Korea
| | - Hosik Seok
- Department of Pharmacology, Graduate School, Kyung Hee University, Seoul, South Korea
| | - Hae Jeong Park
- Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, South Korea
| | - Kyuup Han
- Department of Pharmacology, Graduate School, Kyung Hee University, Seoul, South Korea
| | - Sang Wook Kang
- Department of Dental Pharmacology, School of Dentistry, Dankook University, Cheonan, South Korea
| | - Ju Yeon Ban
- Department of Dental Pharmacology, School of Dentistry, Dankook University, Cheonan, South Korea
| | - Hee-Jae Jung
- Division of Allergy and Respiratory System, Department of Korean Internal Medicine, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Kwan-Il Kim
- Division of Allergy and Respiratory System, Department of Korean Internal Medicine, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Beom-Joon Lee
- Division of Allergy and Respiratory System, Department of Korean Internal Medicine, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Jinju Kim
- Department of Korean Physiology, College of Pharmacy, Kyung Hee University, Seoul, South Korea
| | - Joo-Ho Chung
- Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, South Korea
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29
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Dose- and time- effect responses of DNA methylation and histone H3K9 acetylation changes induced by traffic-related air pollution. Sci Rep 2017; 7:43737. [PMID: 28256616 PMCID: PMC5335614 DOI: 10.1038/srep43737] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/30/2017] [Indexed: 11/08/2022] Open
Abstract
As an important risk factor of respiratory disorders, traffic-related air pollution (TRAP) has caused extensive concerns. Epigenetic change has been considered a link between TRAP and respiratory diseases. However, the exact effects of TRAP on epigenetic changes are still unclear. Here we investigated the dose- and time- effect responses of TRAP on DNA methylations and H3K9 acetylation (H3K9ac) in both blood and lung tissues of rats. The findings showed that every 1 μg/m3 increase of TRAP components were associated with changes in %5 mC (95% CI) in LINE-1, iNOS, p16CDKN2A, and APC ranging from −0.088% (−0.150, −0.026) to 0.102 (0.049, 0.154), as well as 0.276 (0.053, 0.498) to 0.475 (0.103, 0.848) ng/mg increase of H3K9ac. In addition, every 1 more day exposure at high level of TRAP (in tunnel) also significantly changed the levels of DNA methylation (ranging from −0.842% to 0.248%) and H3K9ac (16.033 and 15.718 ng/mg pro in PBMC and lung tissue, respectively) changes. Season and/or sex could interact with air pollutants in affecting DNA methylation and H3K9ac. The findings showed that TRAP exposure is dose- and time- dependently associated with the changes of DNA methylation and H3K9ac.
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Ji H, Biagini Myers JM, Brandt EB, Brokamp C, Ryan PH, Khurana Hershey GK. Air pollution, epigenetics, and asthma. Allergy Asthma Clin Immunol 2016; 12:51. [PMID: 27777592 PMCID: PMC5069789 DOI: 10.1186/s13223-016-0159-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022] Open
Abstract
Exposure to traffic-related air pollution (TRAP) has been implicated in asthma development, persistence, and exacerbation. This exposure is highly significant as large segments of the global population resides in zones that are most impacted by TRAP and schools are often located in high TRAP exposure areas. Recent findings shed new light on the epigenetic mechanisms by which exposure to traffic pollution may contribute to the development and persistence of asthma. In order to delineate TRAP induced effects on the epigenome, utilization of newly available innovative methods to assess and quantify traffic pollution will be needed to accurately quantify exposure. This review will summarize the most recent findings in each of these areas. Although there is considerable evidence that TRAP plays a role in asthma, heterogeneity in both the definitions of TRAP exposure and asthma outcomes has led to confusion in the field. Novel information regarding molecular characterization of asthma phenotypes, TRAP exposure assessment methods, and epigenetics are revolutionizing the field. Application of these new findings will accelerate the field and the development of new strategies for interventions to combat TRAP-induced asthma.
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Affiliation(s)
- Hong Ji
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave. MLC 7037, Cincinnati, OH 45229 USA ; Pyrosequencing lab for Genomic and Epigenomic research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Jocelyn M Biagini Myers
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave. MLC 7037, Cincinnati, OH 45229 USA
| | - Eric B Brandt
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave. MLC 7037, Cincinnati, OH 45229 USA
| | - Cole Brokamp
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Patrick H Ryan
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave. MLC 7037, Cincinnati, OH 45229 USA
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Fuchs O, Bahmer T, Rabe KF, von Mutius E. Asthma transition from childhood into adulthood. THE LANCET RESPIRATORY MEDICINE 2016; 5:224-234. [PMID: 27666650 DOI: 10.1016/s2213-2600(16)30187-4] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 06/13/2016] [Accepted: 06/23/2016] [Indexed: 12/11/2022]
Abstract
Asthma is the most prevalent chronic respiratory disease both in children and adults and resembles a complex syndrome rather than a single disease. Different methods have been developed to better characterise distinct asthma phenotypes in childhood and adulthood. In studies of adults, most phenotyping relies on biomaterials from the lower airways; however, this information is missing in paediatric studies because of restricted accessibility. Few patients show symptoms throughout childhood, adolescence, and adulthood. Risk factors for this might be genetics, family history of asthma and atopy, infections early in life, allergic diseases, and lung function deficits. In turn, a large proportion of children with asthma lose their symptoms during school age and adolescence. This improved prognosis, which might also reflect a better treatment response, is associated with being male and with milder and less allergic disease. Importantly, whether clinical remission of symptoms equals the disappearance of underlying pathology is unknown. In fact, airway hyper-responsiveness and airway inflammation might remain despite the absence of overt symptoms. Additionally, a new-onset of asthma symptoms is apparent in adulthood, especially in women and in the case of impaired lung function. However, many patients do not remember childhood symptoms, which might reflect relapse rather than true initiation. Both relapse and adult-onset of asthma symptoms have been associated with allergic disease and sensitisation in addition to airway hyper-responsiveness. Thus, asthma symptoms beginning in adults might have originated in childhood. Equivocally, persistence into, relapse, and new-onset of symptoms in adulthood have all been related to active smoking. However, underlying mechanisms for the associations remain unclear, and future asthma research should therefore integrate standardised molecular approaches in identical ways in both paediatric and adult populations and in longitudinal studies.
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Affiliation(s)
- Oliver Fuchs
- Division of Paediatric Allergology, Dr von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany; Comprehensive Pneumology Centre Munich (CPC-M), Munich, Germany; German Centre for Lung Research (DZL).
| | - Thomas Bahmer
- LungenClinic Grosshansdorf, Grosshansdorf, Germany; Airway Research Centre North (ARCN), Lubeck, Germany; ARCN, Kiel, Germany; ARCN, Grosshansdorf, Germany; German Centre for Lung Research (DZL)
| | - Klaus F Rabe
- LungenClinic Grosshansdorf, Grosshansdorf, Germany; Department of Medicine, Christian-Albrechts-University, Kiel, Germany; Airway Research Centre North (ARCN), Lubeck, Germany; ARCN, Kiel, Germany; ARCN, Grosshansdorf, Germany; German Centre for Lung Research (DZL)
| | - Erika von Mutius
- Division of Paediatric Allergology, Dr von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany; Comprehensive Pneumology Centre Munich (CPC-M), Munich, Germany; German Centre for Lung Research (DZL)
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Agache I, Akdis CA. Endotypes of allergic diseases and asthma: An important step in building blocks for the future of precision medicine. Allergol Int 2016; 65:243-52. [PMID: 27282212 DOI: 10.1016/j.alit.2016.04.011] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 04/25/2016] [Indexed: 02/07/2023] Open
Abstract
Discoveries from basic science research in the last decade have brought significant progress in knowledge of pathophysiologic processes of allergic diseases, with a compelling impact on understanding of the natural history, risk prediction, treatment selection or mechanism-specific prevention strategies. The view of the pathophysiology of allergic diseases developed from a mechanistic approach, with a focus on symptoms and organ function, to the recognition of a complex network of immunological pathways. Several subtypes of inflammation and complex immune-regulatory networks and the reasons for their failure are now described, that open the way for the development of new diagnostic tools and innovative targeted-treatments. An endotype is a subtype of a disease condition, which is defined by a distinct pathophysiological mechanism, whereas a disease phenotype defines any observable characteristic of a disease without any implication of a mechanism. Another key word linked to disease endotyping is biomarker that is measured and evaluated to examine any biological or pathogenic processes, including response to a therapeutic intervention. These three keywords will be discussed more and more in the future with the upcoming efforts to revolutionize patient care in the direction of precision medicine and precision health. The understanding of disease endotypes based on pathophysiological principles and their validation across clinically meaningful outcomes in asthma, allergic rhinitis, chronic rhinosinusitis, atopic dermatitis and food allergy will be crucial for the success of precision medicine as a new approach to patient management.
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