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Drzymalla E, Crider KS, Wang A, Marta G, Khoury MJ, Rasooly D. Epigenome-wide association studies of prenatal maternal mental health and infant epigenetic profiles: a systematic review. Transl Psychiatry 2023; 13:377. [PMID: 38062042 PMCID: PMC10703876 DOI: 10.1038/s41398-023-02620-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 10/01/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
Prenatal stress and poor maternal mental health are associated with adverse offspring outcomes; however, the biological mechanisms are unknown. Epigenetic modification has linked maternal health with offspring development. Epigenome-wide association studies (EWAS) have examined offspring DNA methylation profiles for association with prenatal maternal mental health to elucidate mechanisms of these complex relationships. The objective of this study is to provide a comprehensive, systematic review of EWASs of infant epigenetic profiles and prenatal maternal anxiety, depression, or depression treatment. We conducted a systematic literature search following PRISMA guidelines for EWAS studies between prenatal maternal mental health and infant epigenetics through May 22, 2023. Of 645 identified articles, 20 fulfilled inclusion criteria. We assessed replication of CpG sites among studies, conducted gene enrichment analysis, and evaluated the articles for quality and risk of bias. We found one repeated CpG site among the maternal depression studies; however, nine pairs of overlapping differentially methylatd regions were reported in at least two maternal depression studies. Gene enrichment analysis found significant pathways for maternal depression but not for any other maternal mental health category. We found evidence that these EWAS present a medium to high risk of bias. Exposure to prenatal maternal depression and anxiety or treatment for such was not consistently associated with epigenetic changes in infants in this systematic review and meta-analysis. Small sample size, potential bias due to exposure misclassification and statistical challenges are critical to address in future efforts to explore epigenetic modification as a potential mechanism by which prenatal exposure to maternal mental health disorders leads to adverse infant outcomes.
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Affiliation(s)
- Emily Drzymalla
- Division of Blood Disorders and Public Health Genomics, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Krista S Crider
- Infant Outcomes Research and Prevention Branch, Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Arick Wang
- Infant Outcomes Research and Prevention Branch, Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Muin J Khoury
- Division of Blood Disorders and Public Health Genomics, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Danielle Rasooly
- Division of Blood Disorders and Public Health Genomics, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Perez-Garcia J, Pino-Yanes M, Plender EG, Everman JL, Eng C, Jackson ND, Moore CM, Beckman KB, Medina V, Sharma S, Winnica DE, Holguin F, Rodríguez-Santana J, Villar J, Ziv E, Seibold MA, Burchard EG. Epigenomic response to albuterol treatment in asthma-relevant airway epithelial cells. Clin Epigenetics 2023; 15:156. [PMID: 37784136 PMCID: PMC10546710 DOI: 10.1186/s13148-023-01571-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Albuterol is the first-line asthma medication used in diverse populations. Although DNA methylation (DNAm) is an epigenetic mechanism involved in asthma and bronchodilator drug response (BDR), no study has assessed whether albuterol could induce changes in the airway epithelial methylome. We aimed to characterize albuterol-induced DNAm changes in airway epithelial cells, and assess potential functional consequences and the influence of genetic variation and asthma-related clinical variables. RESULTS We followed a discovery and validation study design to characterize albuterol-induced DNAm changes in paired airway epithelial cultures stimulated in vitro with albuterol. In the discovery phase, an epigenome-wide association study using paired nasal epithelial cultures from Puerto Rican children (n = 97) identified 22 CpGs genome-wide associated with repeated-use albuterol treatment (p < 9 × 10-8). Albuterol predominantly induced a hypomethylation effect on CpGs captured by the EPIC array across the genome (probability of hypomethylation: 76%, p value = 3.3 × 10-5). DNAm changes on the CpGs cg23032799 (CREB3L1), cg00483640 (MYLK4-LINC01600), and cg05673431 (KSR1) were validated in nasal epithelia from 10 independent donors (false discovery rate [FDR] < 0.05). The effect on the CpG cg23032799 (CREB3L1) was cross-tissue validated in bronchial epithelial cells at nominal level (p = 0.030). DNAm changes in these three CpGs were shown to be influenced by three independent genetic variants (FDR < 0.05). In silico analyses showed these polymorphisms regulated gene expression of nearby genes in lungs and/or fibroblasts including KSR1 and LINC01600 (6.30 × 10-14 ≤ p ≤ 6.60 × 10-5). Additionally, hypomethylation at the CpGs cg10290200 (FLNC) and cg05673431 (KSR1) was associated with increased gene expression of the genes where they are located (FDR < 0.05). Furthermore, while the epigenetic effect of albuterol was independent of the asthma status, severity, and use of medication, BDR was nominally associated with the effect on the CpG cg23032799 (CREB3L1) (p = 0.004). Gene-set enrichment analyses revealed that epigenomic modifications of albuterol could participate in asthma-relevant processes (e.g., IL-2, TNF-α, and NF-κB signaling pathways). Finally, nine differentially methylated regions were associated with albuterol treatment, including CREB3L1, MYLK4, and KSR1 (adjusted p value < 0.05). CONCLUSIONS This study revealed evidence of epigenetic modifications induced by albuterol in the mucociliary airway epithelium. The epigenomic response induced by albuterol might have potential clinical implications by affecting biological pathways relevant to asthma.
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Grants
- R01 ES015794 NIEHS NIH HHS
- R01 HL120393 NHLBI NIH HHS
- R01ES015794, R21ES24844 NIEHS NIH HHS
- UM1 HG008901 NHGRI NIH HHS
- R01MD010443, R56MD013312 NIMHD NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R21 ES024844 NIEHS NIH HHS
- R01 HL117626 NHLBI NIH HHS
- R56 MD013312 NIMHD NIH HHS
- R01 MD010443 NIMHD NIH HHS
- R01 HL155024 NHLBI NIH HHS
- R01HL155024-01, HHSN268201600032I, 3R01HL-117626-02S1, HHSN268201800002I, 3R01HL117004-02S3, 3R01HL-120393-02S1, R01HL117004, R01HL128439, R01HL135156, X01HL134589 NHLBI NIH HHS
- HHSN268201600032C NHLBI NIH HHS
- U24 HG008956 NHGRI NIH HHS
- Ministerio de Universidades
- Ministerio de Ciencia e Innovación
- Instituto de Salud Carlos III
- National Heart, Lung, and Blood Institute
- National Human Genome Research Institute
- National Institute of Environmental Health Sciences
- National Institute on Minority Health and Health Disparities
- The Centers for Common Disease Genomics of the Genome Sequencing Program
- Tobacco-Related Disease Research Program
- Sandler Family Foundation
- American Asthma Foundation
- Amos Medical Faculty Development Program from the Robert Wood Johnson Foundation
- Harry Wm. and Diana V. Hind Distinguished Professor in Pharmaceutical Sciences II
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Affiliation(s)
- Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Canary Islands, Spain.
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Canary Islands, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), La Laguna, Spain.
| | - Elizabeth G Plender
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Jamie L Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Camille M Moore
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Biomedical Research, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado, Denver, CO, USA
| | - Kenneth B Beckman
- University of Minnesota Genomics Center (UMNGC), Minneapolis, MN, USA
| | | | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daniel Efrain Winnica
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Fernando Holguin
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Multidisciplinary Organ Dysfunction Evaluation Research Network (MODERN), Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
- Li Ka Shing Knowledge Institute at the St. Michael's Hospital, Toronto, ON, Canada
| | - Elad Ziv
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco (UCSF), San Francisco, CA, USA
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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: 5] [Impact Index Per Article: 5.0] [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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4
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Perez-Garcia J, Herrera-Luis E, Li A, Mak ACY, Huntsman S, Oh SS, Elhawary JR, Eng C, Beckman KB, Hu D, Lorenzo-Diaz F, Lenoir MA, Rodriguez-Santana J, Zaitlen N, Villar J, Borrell LN, Burchard EG, Pino-Yanes M. Multi-omic approach associates blood methylome with bronchodilator drug response in pediatric asthma. J Allergy Clin Immunol 2023; 151:1503-1512. [PMID: 36796456 DOI: 10.1016/j.jaci.2023.01.026] [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: 05/04/2022] [Revised: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Albuterol is the drug most widely used as asthma treatment among African Americans despite having a lower bronchodilator drug response (BDR) than other populations. Although BDR is affected by gene and environmental factors, the influence of DNA methylation is unknown. OBJECTIVE This study aimed to identify epigenetic markers in whole blood associated with BDR, study their functional consequences by multi-omic integration, and assess their clinical applicability in admixed populations with a high asthma burden. METHODS We studied 414 children and young adults (8-21 years old) with asthma in a discovery and replication design. We performed an epigenome-wide association study on 221 African Americans and replicated the results on 193 Latinos. Functional consequences were assessed by integrating epigenomics with genomics, transcriptomics, and environmental exposure data. Machine learning was used to develop a panel of epigenetic markers to classify treatment response. RESULTS We identified 5 differentially methylated regions and 2 CpGs genome-wide significantly associated with BDR in African Americans located in FGL2 (cg08241295, P = 6.8 × 10-9) and DNASE2 (cg15341340, P = 7.8 × 10-8), which were regulated by genetic variation and/or associated with gene expression of nearby genes (false discovery rate < 0.05). The CpG cg15341340 was replicated in Latinos (P = 3.5 × 10-3). Moreover, a panel of 70 CpGs showed good classification for those with response and nonresponse to albuterol therapy in African American and Latino children (area under the receiver operating characteristic curve for training, 0.99; for validation, 0.70-0.71). The DNA methylation model showed similar discrimination as clinical predictors (P > .05). CONCLUSIONS We report novel associations of epigenetic markers with BDR in pediatric asthma and demonstrate for the first time the applicability of pharmacoepigenetics in precision medicine of respiratory diseases.
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Affiliation(s)
- Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain
| | - Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain
| | - Annie Li
- Department of Medicine, University of California, San Francisco, Calif
| | - Angel C Y Mak
- Department of Medicine, University of California, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, Calif
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, Calif
| | | | - Celeste Eng
- Department of Medicine, University of California, San Francisco, Calif
| | | | - Donglei Hu
- Department of Medicine, University of California, San Francisco, Calif
| | - Fabian Lorenzo-Diaz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain; Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), ULL, Santa Cruz de Tenerife, Spain
| | | | | | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, Calif; Department of Computational Medicine, University of California, Los Angeles, Calif
| | - Jesús Villar
- Multidisciplinary Organ Dysfunction Evaluation Research Network (MODERN), Research Unit, Hospital Universitario Dr Negrín, Las Palmas de Gran Canaria, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Luisa N Borrell
- Department of Epidemiology and Biostatistics, Graduate School of Public Health and Health Policy, City University of New York, New York, NY
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Tecnologías Biomédicas, ULL, La Laguna, Spain.
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5
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Martin-Almeida M, Perez-Garcia J, Herrera-Luis E, Rosa-Baez C, Gorenjak M, Neerincx AH, Sardón-Prado O, Toncheva AA, Harner S, Wolff C, Brandstetter S, Valletta E, Abdel-Aziz MI, Hashimoto S, Berce V, Corcuera-Elosegui P, Korta-Murua J, Buntrock-Döpke H, Vijverberg SJH, Verster JC, Kerssemakers N, Hedman AM, Almqvist C, Villar J, Kraneveld AD, Potočnik U, Kabesch M, der Zee AHMV, Pino-Yanes M, Consortium OBOTS. Epigenome-Wide Association Studies of the Fractional Exhaled Nitric Oxide and Bronchodilator Drug Response in Moderate-to-Severe Pediatric Asthma. Biomedicines 2023; 11:biomedicines11030676. [PMID: 36979655 PMCID: PMC10044864 DOI: 10.3390/biomedicines11030676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/14/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023] Open
Abstract
Asthma is the most prevalent pediatric chronic disease. Bronchodilator drug response (BDR) and fractional exhaled nitric oxide (FeNO) are clinical biomarkers of asthma. Although DNA methylation (DNAm) contributes to asthma pathogenesis, the influence of DNAm on BDR and FeNO is scarcely investigated. This study aims to identify DNAm markers in whole blood associated either with BDR or FeNO in pediatric asthma. We analyzed 121 samples from children with moderate-to-severe asthma. The association of genome-wide DNAm with BDR and FeNO has been assessed using regression models, adjusting for age, sex, ancestry, and tissue heterogeneity. Cross-tissue validation was assessed in 50 nasal samples. Differentially methylated regions (DMRs) and enrichment in traits and biological pathways were assessed. A false discovery rate (FDR) < 0.1 and a genome-wide significance threshold of p < 9 × 10−8 were used to control for false-positive results. The CpG cg12835256 (PLA2G12A) was genome-wide associated with FeNO in blood samples (coefficient= −0.015, p = 2.53 × 10−9) and nominally associated in nasal samples (coefficient = −0.015, p = 0.045). Additionally, three CpGs were suggestively associated with BDR (FDR < 0.1). We identified 12 and four DMRs associated with FeNO and BDR (FDR < 0.05), respectively. An enrichment in allergic and inflammatory processes, smoking, and aging was observed. We reported novel associations of DNAm markers associated with BDR and FeNO enriched in asthma-related processes.
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Affiliation(s)
- Mario Martin-Almeida
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
| | - Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
| | - Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
| | - Carlos Rosa-Baez
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Anne H. Neerincx
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Olaia Sardón-Prado
- Division of Pediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain
- Department of Pediatrics, University of the Basque Country (UPV/EHU), 48013 San Sebastián, Spain
| | - Antoaneta A. Toncheva
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Susanne Harner
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Christine Wolff
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Susanne Brandstetter
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Elisa Valletta
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Mahmoud I. Abdel-Aziz
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Clinical Pharmacy, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt
| | - Simone Hashimoto
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Pediatric Respiratory Medicine, Emma Children’s Hospital, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
- Clinic of Pediatrics, University Medical Centre Maribor, 2000 Maribor, Slovenia
| | - Paula Corcuera-Elosegui
- Division of Pediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain
| | - Javier Korta-Murua
- Division of Pediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain
- Department of Pediatrics, University of the Basque Country (UPV/EHU), 48013 San Sebastián, Spain
| | - Heike Buntrock-Döpke
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Susanne J. H. Vijverberg
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Joris C. Verster
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands
- Centre for Human Psychopharmacology, Swinburne University, Melbourne, VIC 3122, Australia
| | - Nikki Kerssemakers
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Anna M Hedman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, 171 77 Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, 171 77 Stockholm, Sweden
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Multidisciplinary Organ Dysfunction Evaluation Research Network, Research Unit, Hospital Universitario Dr. Negrín, 35010 Las Palmas de Gran Canaria, Spain
| | - Aletta D. Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
- Clinic of Pediatrics, University Medical Centre Maribor, 2000 Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology, and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, 2000 Maribor, Slovenia
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, D-93049 Regensburg, Germany
| | - Anke H. Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam University Medical Centres—Loc. AMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Department of Pediatric Respiratory Medicine, Emma Children’s Hospital, Amsterdam UMC, 1105 AZ Amsterdam, The Netherlands
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), 38200 San Cristóbal de La Laguna, Spain
- Correspondence: ; Tel.: +34-9223-16502-6343
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6
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Stikker BS, Hendriks RW, Stadhouders R. Decoding the genetic and epigenetic basis of asthma. Allergy 2023; 78:940-956. [PMID: 36727912 DOI: 10.1111/all.15666] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
Asthma is a complex and heterogeneous chronic inflammatory disease of the airways. Alongside environmental factors, asthma susceptibility is strongly influenced by genetics. Given its high prevalence and our incomplete understanding of the mechanisms underlying disease susceptibility, asthma is frequently studied in genome-wide association studies (GWAS), which have identified thousands of genetic variants associated with asthma development. Virtually all these genetic variants reside in non-coding genomic regions, which has obscured the functional impact of asthma-associated variants and their translation into disease-relevant mechanisms. Recent advances in genomics technology and epigenetics now offer methods to link genetic variants to gene regulatory elements embedded within non-coding regions, which have started to unravel the molecular mechanisms underlying the complex (epi)genetics of asthma. Here, we provide an integrated overview of (epi)genetic variants associated with asthma, focusing on efforts to link these disease associations to biological insight into asthma pathophysiology using state-of-the-art genomics methodology. Finally, we provide a perspective as to how decoding the genetic and epigenetic basis of asthma has the potential to transform clinical management of asthma and to predict the risk of asthma development.
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Affiliation(s)
- Bernard S Stikker
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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7
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Kelly L, Barrett P, McCarthy FP, O'Keeffe GW, Maher GM, Khashan AS. The association between hypertensive disorders of pregnancy and childhood asthma. Pediatr Res 2022; 92:1188-1194. [PMID: 35079113 DOI: 10.1038/s41390-022-01935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/11/2021] [Accepted: 12/18/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Asthma is a chronic long-term inflammatory disease of the airways and is a major global health challenge. The primary aim of this study was to investigate the association between hypertensive disorders of pregnancy (HDP) and the risk of asthma at or before the age of seven years using the UK Millennium Cohort Study (MCS). METHODS Overall, 18,552 families were recruited for wave one of the MCS when the child was 9 months old, and subsequently participated in waves two, three and four when they were three, five and seven years respectively. HDP were self-reported by mothers in wave one. The primary outcome was a parent-reported diagnosis of "ever asthma" at seven years, based on responses to a validated questionnaire. RESULTS Following adjustment for a range of potential confounding factors, HDP was found to be associated with asthma in the offspring (adjusted odds ratio (AOR 1.35; 95% CI: 1.15-1.59)). A larger effect estimate was observed amongst children exposed to HDP and born preterm (AOR 1.81; 95% CI: 1.25-2.61) or small for gestational age (SGA) (AOR = 1.58; (95% CI: 1.15-2.18)). CONCLUSIONS In conclusion, children exposed to HDP may be at increased odds of asthma diagnosis by age seven, particularly if they were born preterm or SGA. IMPACT There is a paucity of data investigating the relationship between hypertensive disorders of pregnancy and childhood asthma, with recent studies showing conflicting results. Our study investigated this relationship using a large cohort with ample information on a wide range of confounding factors. Our study showed that individuals exposed to HDP may be at increased odds of asthma diagnosis by age seven years, particularly if they were also born SGA or preterm.
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Affiliation(s)
- Louise Kelly
- School of Public Health, University College Cork, Cork, Ireland.
| | - Peter Barrett
- School of Public Health, University College Cork, Cork, Ireland.,INFANT Research Centre, University College Cork, Cork, Ireland
| | - Fergus P McCarthy
- INFANT Research Centre, University College Cork, Cork, Ireland.,Department of Obstetrics and Gynaecology, University College Cork, Cork, Ireland
| | - Gerard W O'Keeffe
- INFANT Research Centre, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Gillian M Maher
- School of Public Health, University College Cork, Cork, Ireland.,INFANT Research Centre, University College Cork, Cork, Ireland
| | - Ali S Khashan
- School of Public Health, University College Cork, Cork, Ireland.,INFANT Research Centre, University College Cork, Cork, Ireland
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8
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Saferali A, Hersh CP. Genetic Determinants in Airways Obstructive Diseases: The Case of Asthma Chronic Obstructive Pulmonary Disease Overlap. Immunol Allergy Clin North Am 2022; 42:559-573. [PMID: 35965045 PMCID: PMC9379112 DOI: 10.1016/j.iac.2022.03.003] [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] [Indexed: 11/05/2022]
Abstract
Genome-wide association studies (GWAS) of asthma and chronic obstructive pulmonary disease (COPD) with ever-increasing sample sizes have found multiple genetic loci associated with either disease. However, there are few intersecting loci between asthma and COPD. GWAS specifically focused on asthma-COPD overlap (ACO) have been limited by smaller sample sizes and the lack of a consistent definition of ACO that has also hampered clinical and epidemiologic studies. Other genomic techniques, such as gene expression profiling, are feasible with smaller sample sizes. Genetic analyses of objective measures of airway reactivity and allergy/T2 inflammation biomarkers in COPD studies may be another strategy to overcome limitations in ACO definitions.
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Affiliation(s)
- Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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9
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Tuazon JA, Kilburg-Basnyat B, Oldfield LM, Wiscovitch-Russo R, Dunigan-Russell K, Fedulov AV, Oestreich KJ, Gowdy KM. Emerging Insights into the Impact of Air Pollution on Immune-Mediated Asthma Pathogenesis. Curr Allergy Asthma Rep 2022; 22:77-92. [PMID: 35394608 PMCID: PMC9246904 DOI: 10.1007/s11882-022-01034-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Increases in ambient levels of air pollutants have been linked to lung inflammation and remodeling, processes that lead to the development and exacerbation of allergic asthma. Conventional research has focused on the role of CD4+ T helper 2 (TH2) cells in the pathogenesis of air pollution-induced asthma. However, much work in the past decade has uncovered an array of air pollution-induced non-TH2 immune mechanisms that contribute to allergic airway inflammation and disease. RECENT FINDINGS In this article, we review current research demonstrating the connection between common air pollutants and their downstream effects on non-TH2 immune responses emerging as key players in asthma, including PRRs, ILCs, and non-TH2 T cell subsets. We also discuss the proposed mechanisms by which air pollution increases immune-mediated asthma risk, including pre-existing genetic risk, epigenetic alterations in immune cells, and perturbation of the composition and function of the lung and gut microbiomes. Together, these studies reveal the multifaceted impacts of various air pollutants on innate and adaptive immune functions via genetic, epigenetic, and microbiome-based mechanisms that facilitate the induction and worsening of asthma.
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Affiliation(s)
- J A Tuazon
- Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
- Medical Scientist Training Program, The Ohio State University, Columbus, OH, 43210, USA
| | - B Kilburg-Basnyat
- Department of Pharmacology and Toxicology, East Carolina University, Greenville, NC, 27858, USA
| | - L M Oldfield
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
- Department of Synthetic Genomics, Replay Holdings LLC, San Diego, 92121, USA
| | - R Wiscovitch-Russo
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - K Dunigan-Russell
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, OH, 43210, USA
| | - A V Fedulov
- Division of Surgical Research, Department of Surgery, Alpert Medical School, Brown University, Rhode Island Hospital, Providence, RI, 02903, USA
| | - K J Oestreich
- Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, The James Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - K M Gowdy
- Division of Pulmonary, Critical Care, and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, OH, 43210, USA.
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10
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Legaki E, Arsenis C, Taka S, Papadopoulos NG. DNA methylation biomarkers in asthma and rhinitis: Are we there yet? Clin Transl Allergy 2022; 12:e12131. [PMID: 35344303 PMCID: PMC8967268 DOI: 10.1002/clt2.12131] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/01/2022] [Accepted: 02/22/2022] [Indexed: 12/16/2022] Open
Abstract
The study of epigenetics has improved our understanding of mechanisms underpinning gene‐environment interactions and is providing new insights in the pathophysiology of respiratory allergic diseases. We reviewed the literature on DNA methylation patterns across different tissues in asthma and/or rhinitis and attempted to elucidate differentially methylated loci that could be used to characterize asthma or rhinitis. Although nasal and bronchial epithelia are similar in their histological structure and cellular composition, genetic and epigenetic regulation may differ across tissues. Advanced methods have enabled comprehensive, high‐throughput methylation profiling of different tissues (bronchial or nasal epithelial cells, whole blood or isolated mononuclear cells), in subjects with respiratory conditions, aiming to elucidate gene regulation mechanisms and identify new biomarkers. Several genes and CpGs have been suggested as asthma biomarkers, though research on allergic rhinitis is still lacking. The most common differentially methylated loci presented in both blood and nasal samples are ACOT7, EPX, KCNH2, SIGLEC8, TNIK, FOXP1, ATPAF2, ZNF862, ADORA3, ARID3A, IL5RA, METRNL and ZFPM1. Overall, there is substantial variation among studies, (i.e. sample sizes, age groups and disease phenotype). Greater variability of analysis method detailed phenotypic characterization and age stratification should be taken into account in future studies.
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Affiliation(s)
- Evangelia Legaki
- Allergy and Clinical Immunology Unit Second Pediatric Clinic National and Kapodistrian University of Athens Athens Greece
| | - Christos Arsenis
- Allergy and Clinical Immunology Unit Second Pediatric Clinic National and Kapodistrian University of Athens Athens Greece
| | - Styliani Taka
- Allergy and Clinical Immunology Unit Second Pediatric Clinic National and Kapodistrian University of Athens Athens Greece
| | - Nikolaos G. Papadopoulos
- Allergy and Clinical Immunology Unit Second Pediatric Clinic National and Kapodistrian University of Athens Athens Greece
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11
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Kothalawala DM, Kadalayil L, Curtin JA, Murray CS, Simpson A, Custovic A, Tapper WJ, Arshad SH, Rezwan FI, Holloway JW. Integration of Genomic Risk Scores to Improve the Prediction of Childhood Asthma Diagnosis. J Pers Med 2022; 12:75. [PMID: 35055391 PMCID: PMC8777841 DOI: 10.3390/jpm12010075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/18/2021] [Accepted: 12/31/2021] [Indexed: 01/24/2023] Open
Abstract
Genome-wide and epigenome-wide association studies have identified genetic variants and differentially methylated nucleotides associated with childhood asthma. Incorporation of such genomic data may improve performance of childhood asthma prediction models which use phenotypic and environmental data. Using genome-wide genotype and methylation data at birth from the Isle of Wight Birth Cohort (n = 1456), a polygenic risk score (PRS), and newborn (nMRS) and childhood (cMRS) methylation risk scores, were developed to predict childhood asthma diagnosis. Each risk score was integrated with two previously published childhood asthma prediction models (CAPE and CAPP) and were validated in the Manchester Asthma and Allergy Study. Individually, the genomic risk scores demonstrated modest-to-moderate discriminative performance (area under the receiver operating characteristic curve, AUC: PRS = 0.64, nMRS = 0.55, cMRS = 0.54), and their integration only marginally improved the performance of the CAPE (AUC: 0.75 vs. 0.71) and CAPP models (AUC: 0.84 vs. 0.82). The limited predictive performance of each genomic risk score individually and their inability to substantially improve upon the performance of the CAPE and CAPP models suggests that genetic and epigenetic predictors of the broad phenotype of asthma are unlikely to have clinical utility. Hence, further studies predicting specific asthma endotypes are warranted.
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Affiliation(s)
- Dilini M. Kothalawala
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - John A. Curtin
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, Manchester University Hospital NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; (J.A.C.); (C.S.M.); (A.S.)
| | - Clare S. Murray
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, Manchester University Hospital NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; (J.A.C.); (C.S.M.); (A.S.)
| | - Angela Simpson
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, Manchester University Hospital NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; (J.A.C.); (C.S.M.); (A.S.)
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College of Science, Technology, and Medicine, London SW3 6LY, UK;
| | - William J. Tapper
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
| | - S. Hasan Arshad
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- The David Hide Asthma and Allergy Research Centre, St. Mary’s Hospital, Isle of Wight PO30 5TG, UK
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, UK
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
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12
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Agache I, Palmer E, Sanver D, Kirtland M, Shamji MH. Molecular allergology approach to allergic asthma. Mol Aspects Med 2021; 85:101027. [PMID: 34579961 DOI: 10.1016/j.mam.2021.101027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 07/26/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022]
Abstract
Allergic asthma is a frequently encountered and well described asthma phenotype. However, its precise mechanisms are less known. The tools for targeted selection of patients for an optimal response to intervention (prevention or treatment) are also lacking. Here we explore the potential of the molecular allergology approach to achieve a better understanding of allergic asthma mechanisms, a precise diagnosis and an optimal management of these patients.
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Affiliation(s)
- Ioana Agache
- Faculty of Medicine, Transylvania University, Brasov, Romania.
| | - Elizabeth Palmer
- Imperial College, Faculty of Medicine, National Heart & Lung Institute, London, UK
| | - Didem Sanver
- Imperial College, Faculty of Medicine, National Heart & Lung Institute, London, UK; Necmettin Erbakan University, Engineering & Architecture Faculty, Department of Food Engineering, Konya, Turkey
| | - Max Kirtland
- Imperial College, Faculty of Medicine, National Heart & Lung Institute, London, UK
| | - Mohamed H Shamji
- Imperial College, Faculty of Medicine, National Heart & Lung Institute, London, UK
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13
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Komlósi ZI, van de Veen W, Kovács N, Szűcs G, Sokolowska M, O'Mahony L, Akdis M, Akdis CA. Cellular and molecular mechanisms of allergic asthma. Mol Aspects Med 2021; 85:100995. [PMID: 34364680 DOI: 10.1016/j.mam.2021.100995] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 12/21/2022]
Abstract
Asthma is a chronic disease of the airways, which affects more than 350 million people worldwide. It is the most common chronic disease in children, affecting at least 30 million children and young adults in Europe. Asthma is a complex, partially heritable disease with a marked heterogeneity. Its development is influenced both by genetic and environmental factors. The most common, as well as the most well characterized subtype of asthma is allergic eosinophilic asthma, which is characterized by a type 2 airway inflammation. The prevalence of asthma has substantially increased in industrialized countries during the last 60 years. The mechanisms underpinning this phenomenon are incompletely understood, however increased exposure to various environmental pollutants probably plays a role. Disease inception is thought to be enabled by a disadvantageous shift in the balance between protective and harmful lifestyle and environmental factors, including exposure to protective commensal microbes versus infection with pathogens, collectively leading to airway epithelial cell damage and disrupted barrier integrity. Epithelial cell-derived cytokines are one of the main drivers of the type 2 immune response against innocuous allergens, ultimately leading to infiltration of lung tissue with type 2 T helper (TH2) cells, type 2 innate lymphoid cells (ILC2s), M2 macrophages and eosinophils. This review outlines the mechanisms responsible for the orchestration of type 2 inflammation and summarizes the novel findings, including but not limited to dysregulated epithelial barrier integrity, alarmin release and innate lymphoid cell stimulation.
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Affiliation(s)
- Zsolt I Komlósi
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary.
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Nóra Kovács
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary; Lung Health Hospital, Munkácsy Mihály Str. 70, 2045, Törökbálint, Hungary
| | - Gergő Szűcs
- Department of Genetics, Cell- and Immunobiology, Semmelweis University, Nagyvárad Sqr. 4, 1089, Budapest, Hungary; Department of Pulmonology, Semmelweis University, Tömő Str. 25-29, 1083, Budapest, Hungary
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Liam O'Mahony
- Department of Medicine and School of Microbiology, APC Microbiome Ireland, University College Cork, Ireland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), Hermann-Burchard Strasse 9, CH7265, Davos Wolfgand, Switzerland; Christine Kühne - Center for Allergy Research and Education, Davos, Switzerland
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14
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Huang Y, Sun X, Jiang H, Yu S, Robins C, Armstrong MJ, Li R, Mei Z, Shi X, Gerasimov ES, De Jager PL, Bennett DA, Wingo AP, Jin P, Wingo TS, Qin ZS. A machine learning approach to brain epigenetic analysis reveals kinases associated with Alzheimer's disease. Nat Commun 2021; 12:4472. [PMID: 34294691 PMCID: PMC8298578 DOI: 10.1038/s41467-021-24710-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
Alzheimer's disease (AD) is influenced by both genetic and environmental factors; thus, brain epigenomic alterations may provide insights into AD pathogenesis. Multiple array-based Epigenome-Wide Association Studies (EWASs) have identified robust brain methylation changes in AD; however, array-based assays only test about 2% of all CpG sites in the genome. Here, we develop EWASplus, a computational method that uses a supervised machine learning strategy to extend EWAS coverage to the entire genome. Application to six AD-related traits predicts hundreds of new significant brain CpGs associated with AD, some of which are further validated experimentally. EWASplus also performs well on data collected from independent cohorts and different brain regions. Genes found near top EWASplus loci are enriched for kinases and for genes with evidence for physical interactions with known AD genes. In this work, we show that EWASplus implicates additional epigenetic loci for AD that are not found using array-based AD EWASs.
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Affiliation(s)
- Yanting Huang
- Department of Computer Science, Emory University, Atlanta, GA, USA
| | - Xiaobo Sun
- Department of Mathematical and Statistical Finance, School of Statistics and Mathematics, Zhongnan University of Economics and Laws, Wuhan, Hubei, China.
| | - Huige Jiang
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Shaojun Yu
- Department of Computer Science, Emory University, Atlanta, GA, USA
| | - Chloe Robins
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Matthew J Armstrong
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ronghua Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Zhen Mei
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Xiaochuan Shi
- Department of Statistics, University of Washington, Seattle, WA, USA
| | | | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Aliza P Wingo
- Division of Mental Health, Atlanta VA Medical Center, Decatur, GA, USA
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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15
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Boyle RJ, Shamji MH. Evidence Synthesis in Allergy - A call for submissions. Clin Exp Allergy 2021; 51:868-869. [PMID: 34180092 DOI: 10.1111/cea.13963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert J Boyle
- National Heart and Lung Institute, Wright Fleming Institute, Imperial College London, London, UK
| | - Mohamed H Shamji
- National Heart and Lung Institute, Wright Fleming Institute, Imperial College London, London, UK
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16
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Söderhäll C, Reinius LE, Salmenperä P, Gentile M, Acevedo N, Konradsen JR, Nordlund B, Hedlin G, Scheynius A, Myllykangas S, Kere J. High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3. Clin Epigenetics 2021; 13:106. [PMID: 33971943 PMCID: PMC8111952 DOI: 10.1186/s13148-021-01093-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methylation of DNA at CpG sites is an epigenetic modification and a potential modifier of disease risk, possibly mediating environmental effects. Currently, DNA methylation is commonly assessed using specific microarrays that sample methylation at a few % of all methylated sites. METHODS To understand if significant information on methylation can be added by a more comprehensive analysis of methylation, we set up a quantitative method, bisulfite oligonucleotide-selective sequencing (Bs-OS-seq), and compared the data with microarray-derived methylation data. We assessed methylation at two asthma-associated genes, IL13 and ORMDL3, in blood samples collected from children with and without asthma and fractionated white blood cell types from healthy adult controls. RESULTS Our results show that Bs-OS-seq can uncover vast amounts of methylation variation not detected by commonly used array methods. We found that high-density methylation information from even one gene can delineate the main white blood cell lineages. CONCLUSIONS We conclude that high-resolution methylation studies can yield clinically important information at selected specific loci missed by array-based methods, with potential implications for future studies of methylation-disease associations.
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Affiliation(s)
- Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden. .,Department of Women's and Children's Health, Karolinska Institutet, Bioclinicum J9:30, Visionsgatan 4, 171 64, Stockholm, Sweden. .,Department of Pediatric Allergy and Pulmonology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.
| | - Lovisa E Reinius
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Nathalie Acevedo
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, 118 83, Stockholm, Sweden.,Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | - Jon R Konradsen
- Department of Women's and Children's Health, Karolinska Institutet, Bioclinicum J9:30, Visionsgatan 4, 171 64, Stockholm, Sweden.,Department of Pediatric Allergy and Pulmonology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Björn Nordlund
- Department of Women's and Children's Health, Karolinska Institutet, Bioclinicum J9:30, Visionsgatan 4, 171 64, Stockholm, Sweden.,Department of Pediatric Allergy and Pulmonology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Gunilla Hedlin
- Department of Women's and Children's Health, Karolinska Institutet, Bioclinicum J9:30, Visionsgatan 4, 171 64, Stockholm, Sweden.,Department of Pediatric Allergy and Pulmonology, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Annika Scheynius
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs' Children and Youth Hospital, Södersjukhuset, 118 83, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
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17
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Lee YS, Zhang H, Jiang Y, Kadalayil L, Karmaus W, Ewart SL, H Arshad S, Holloway JW. Epigenome-scale comparison of DNA methylation between blood leukocytes and bronchial epithelial cells. Epigenomics 2021; 13:485-498. [PMID: 33736458 DOI: 10.2217/epi-2020-0384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: Agreement in DNA methylation (DNAm) at the genome scale between blood leukocytes (BL) and bronchial epithelial cells (BEC) is unknown. We examine as to what extent DNAm in BL is comparable with that in BEC and serves as a surrogate for BEC. Materials & methods: Overall agreement (paired t-tests with false discovery rate adjusted p > 0.05) and consistency (Pearson's correlation coefficients >0.5) between two tissues, at each of the 767,412 CpGs, were evaluated. Results: We identified 247,721 CpGs showing overall agreement and 47,371 CpGs showing consistency in DNAm. Identified CpGs are involved in certain immune pathways, indicating the potential of using blood as a biomarker for BEC at those CpGs in lower airway-related diseases. Conclusion: CpGs showing overall agreement and those without overall agreement are distributed differently on the genome.
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Affiliation(s)
- Yu-Sheng Lee
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Latha Kadalayil
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Susan L Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Syed H Arshad
- David Hide Asthma & Allergy Research Centre, St Mary's Hospital, Newport, Isle of Wight, UK.,Clinical & Experimental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
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18
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Chen YC, Tsai YH, Wang CC, Liu SF, Chen TW, Fang WF, Lee CP, Hsu PY, Chao TY, Wu CC, Wei YF, Chang HC, Tsen CC, Chang YP, Lin MC. Epigenome-wide association study on asthma and chronic obstructive pulmonary disease overlap reveals aberrant DNA methylations related to clinical phenotypes. Sci Rep 2021; 11:5022. [PMID: 33658578 PMCID: PMC7930096 DOI: 10.1038/s41598-021-83185-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
We hypothesized that epigenetics is a link between smoking/allergen exposures and the development of Asthma and chronic obstructive pulmonary disease (ACO). A total of 75 of 228 COPD patients were identified as ACO, which was independently associated with increased exacerbations. Microarray analysis identified 404 differentially methylated loci (DML) in ACO patients, and 6575 DML in those with rapid lung function decline in a discovery cohort. In the validation cohort, ACO patients had hypermethylated PDE9A (+ 30,088)/ZNF323 (− 296), and hypomethylated SEPT8 (− 47) genes as compared with either pure COPD patients or healthy non-smokers. Hypermethylated TIGIT (− 173) gene and hypomethylated CYSLTR1 (+ 348)/CCDC88C (+ 125,722)/ADORA2B (+ 1339) were associated with severe airflow limitation, while hypomethylated IFRD1 (− 515) gene with frequent exacerbation in all the COPD patients. Hypermethylated ZNF323 (− 296) / MPV17L (+ 194) and hypomethylated PTPRN2 (+ 10,000) genes were associated with rapid lung function decline. In vitro cigarette smoke extract and ovalbumin concurrent exposure resulted in specific DNA methylation changes of the MPV17L / ZNF323 genes, while 5-aza-2′-deoxycytidine treatment reversed promoter hypermethylation-mediated MPV17L under-expression accompanied with reduced apoptosis and decreased generation of reactive oxygen species. Aberrant DNA methylations may constitute a determinant for ACO, and provide a biomarker of airflow limitation, exacerbation, and lung function decline.
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Affiliation(s)
- Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan. .,Medical Department, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Ying-Huang Tsai
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Chin-Chou Wang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan.,Chang Gung University of Science and Technology, Chia-Yi, Taiwan
| | - Shih-Feng Liu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan.,Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Wen-Feng Fang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan.,Chang Gung University of Science and Technology, Chia-Yi, Taiwan
| | - Chiu-Ping Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Po-Yuan Hsu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Tung-Ying Chao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Chao-Chien Wu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Yu-Feng Wei
- Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Huang-Chih Chang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Chia-Cheng Tsen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Yu-Ping Chang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan. .,Medical Department, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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19
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Wang M, Ibeagha-Awemu EM. Impacts of Epigenetic Processes on the Health and Productivity of Livestock. Front Genet 2021; 11:613636. [PMID: 33708235 PMCID: PMC7942785 DOI: 10.3389/fgene.2020.613636] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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20
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Koo HK, Song P, Lee JH. Novel association between asthma and osteoarthritis: a nationwide health and nutrition examination survey. BMC Pulm Med 2021; 21:59. [PMID: 33593334 PMCID: PMC7885236 DOI: 10.1186/s12890-021-01425-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Background Asthma and osteoarthritis (OA) are medical conditions that inhibit physical activity and adversely affect quality of life. Despite the high prevalence, there are limited studies focusing on the comorbid condition and association between asthma and OA. The aim of this study was to assess the prevalence of OA co-occurring with asthma and to identify the relevant clinical considerations. Methods Adult participants aged over 40 years who completed questionnaire assessments and spirometry tests were enrolled from the Korean National Health and Nutrition Examination Survey. Asthma and OA were defined based on the medical history of a diagnosis made by a doctor. Radiographic severities of OA were measured using the Kellgren–Lawrence grading system. Chronic obstructive pulmonary disease (COPD), as a comparative respiratory disease, was diagnosed based on the spirometric results. Results A total of 9344 subjects were enrolled, and the prevalence of asthma and COPD were 4.6% ± 0.3% and 12.0% ± 0.5%, respectively. The prevalence of OA in the asthma group was 31.9% ± 2.8%, which was significantly higher than that in the COPD (17.8% ± 1.5%) or control (16.2% ± 0.6%) groups. OA was more prevalent in patients with asthma after adjusting for age, sex, body mass index, and smoking status (OR 1.65; 95% CI 1.27–2.13). Furthermore, after adjustment of this model for the prescription of OA medication, OA remained independently associated with asthma (OR 1.56; 95% CI 1.10–2.20). Conversely, the relationship of OA medication with asthma was not significant (P = 0.64). This relationship was evident in patients with asthma without airflow limitation measured by spirometry (OR 1.97; 95% CI 1.32–2.93). Moreover, the radiographic severity of knee OA correlated with asthma (OR 1.10; 95% CI 1.0–1.21). Conclusions OA shows a high prevalence in patients with asthma, higher than in patients with COPD or the controls. The comorbid characteristics of these two conditions need to be considered in clinical practice.
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Affiliation(s)
- Hyeon-Kyoung Koo
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Inje University Ilsan Paik Hospital, Goyang, Korea
| | - Pamela Song
- Department of Neurology, Inje University Ilsan Paik Hospital, Goyang, Korea
| | - Joo-Hyun Lee
- Division of Rheumatology, Department of Internal Medicine, Inje University Ilsan Paik Hospital, Goyang, 10380, Korea.
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21
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Abstract
PURPOSE OF REVIEW Asthma is a common disease worldwide, however, its pathogenesis has not been fully elucidated. Emerging evidence suggests that epigenetic modifications may play a role in the development and natural history of asthma. The aim of this review is to highlight recent progress in research on epigenetic mechanisms in asthma. RECENT FINDINGS Over the past years, epigenetic studies, in particular DNA methylation studies, have added to the growing body of evidence supporting a link between epigenetic regulation of gene expression and asthma. Recent studies demonstrate that epigenetic mechanisms also play a role in asthma remission. Although most existing studies in this field have been conducted on blood cells, recent evidence suggests that epigenetic signatures are also crucial for the regulation of airway epithelial cells. Studies conducted on nasal epithelium revealed highly replicable epigenetic patterns that could be used for diagnostic purposes. SUMMARY Further research is needed to explore the diagnostic and therapeutic potential of epigenetic modifications in asthma. Multiomics studies on asthma will become increasingly important for a better understanding of etiology, heterogeneity, and severity of asthma, as well as establishing molecular biomarkers that could be combined with clinical information to improve the management of asthma patients.
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22
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Edris A, de Roos EW, McGeachie MJ, Verhamme KMC, Brusselle GG, Tantisira KG, Iribarren C, Lu M, Wu AC, Stricker BH, Lahousse L. Pharmacogenetics of inhaled corticosteroids and exacerbation risk in adults with asthma. Clin Exp Allergy 2021; 52:33-45. [PMID: 33428814 DOI: 10.1111/cea.13829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inhaled corticosteroids (ICS) are a cornerstone of asthma treatment. However, their efficacy is characterized by wide variability in individual responses. OBJECTIVE We investigated the association between genetic variants and risk of exacerbations in adults with asthma and how this association is affected by ICS treatment. METHODS We investigated the pharmacogenetic effect of 10 single nucleotide polymorphisms (SNPs) selected from the literature, including SNPs previously associated with response to ICS (assessed by change in lung function or exacerbations) and novel asthma risk alleles involved in inflammatory pathways, within all adults with asthma from the Dutch population-based Rotterdam study with replication in the American GERA cohort. The interaction effects of the SNPs with ICS on the incidence of asthma exacerbations were assessed using hurdle models adjusting for age, sex, BMI, smoking and treatment step according to the GINA guidelines. Haplotype analyses were also conducted for the SNPs located on the same chromosome. RESULTS rs242941 (CRHR1) homozygotes for the minor allele (A) showed a significant, replicated increased risk for frequent exacerbations (RR = 6.11, P < 0.005). In contrast, rs1134481 T allele within TBXT (chromosome 6, member of a family associated with embryonic lung development) showed better response with ICS. rs37973 G allele (GLCCI1) showed a significantly poorer response on ICS within the discovery cohort, which was also significant but in the opposite direction in the replication cohort. CONCLUSION rs242941 in CRHR1 was associated with poor ICS response. Conversely, TBXT variants were associated with improved ICS response. These associations may reveal specific endotypes, potentially allowing prediction of exacerbation risk and ICS response.
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Affiliation(s)
- Ahmed Edris
- Department of Bioanalysis, Ghent University, Ghent, Belgium.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Emmely W de Roos
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Katia M C Verhamme
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Guy G Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,University of California San Diego, CA, USA
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Meng Lu
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Ann Chen Wu
- Department of Population Medicine, Precision Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, MA, USA
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ghent, Belgium.,Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
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23
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Affiliation(s)
- G Roberts
- Clinical and Experimental Sciences and Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK.,The David Hide Asthma and Allergy Research Centre, St Mary's Hospital, Isle of Wight, UK
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24
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Hoang TT, Sikdar S, Xu CJ, Lee MK, Cardwell J, Forno E, Imboden M, Jeong A, Madore AM, Qi C, Wang T, Bennett BD, Ward JM, Parks CG, Beane-Freeman LE, King D, Motsinger-Reif A, Umbach DM, Wyss AB, Schwartz DA, Celedón JC, Laprise C, Ober C, Probst-Hensch N, Yang IV, Koppelman GH, London SJ. Epigenome-wide association study of DNA methylation and adult asthma in the Agricultural Lung Health Study. Eur Respir J 2020; 56:13993003.00217-2020. [PMID: 32381493 PMCID: PMC7469973 DOI: 10.1183/13993003.00217-2020] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022]
Abstract
Epigenome-wide studies of methylation in children support a role for epigenetic mechanisms in asthma; however, studies in adults are rare and few have examined non-atopic asthma. We conducted the largest epigenome-wide association study (EWAS) of blood DNA methylation in adults in relation to non-atopic and atopic asthma. We measured DNA methylation in blood using the Illumina MethylationEPIC array among 2286 participants in a case-control study of current adult asthma nested within a United States agricultural cohort. Atopy was defined by serum specific immunoglobulin E (IgE). Participants were categorised as atopy without asthma (n=185), non-atopic asthma (n=673), atopic asthma (n=271), or a reference group of neither atopy nor asthma (n=1157). Analyses were conducted using logistic regression. No associations were observed with atopy without asthma. Numerous cytosine–phosphate–guanine (CpG) sites were differentially methylated in non-atopic asthma (eight at family-wise error rate (FWER) p<9×10−8, 524 at false discovery rate (FDR) less than 0.05) and implicated 382 novel genes. More CpG sites were identified in atopic asthma (181 at FWER, 1086 at FDR) and implicated 569 novel genes. 104 FDR CpG sites overlapped. 35% of CpG sites in non-atopic asthma and 91% in atopic asthma replicated in studies of whole blood, eosinophils, airway epithelium, or nasal epithelium. Implicated genes were enriched in pathways related to the nervous system or inflammation. We identified numerous, distinct differentially methylated CpG sites in non-atopic and atopic asthma. Many CpG sites from blood replicated in asthma-relevant tissues. These circulating biomarkers reflect risk and sequelae of disease, as well as implicate novel genes associated with non-atopic and atopic asthma. Distinct methylation signals are found in non-atopic and atopic asthma. Most are related to gene expression and are replicated in asthma-relevant tissues, confirming the value of blood DNA methylation for identifying novel genes linked in asthma pathogenesis.https://bit.ly/2VnbJg3
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Affiliation(s)
- Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA.,Joint first authors
| | - Sinjini Sikdar
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA.,Dept of Mathematics and Statistics, Old Dominion University, Norfolk, VA, USA.,Joint first authors
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Centre for Experimental and Clinical Infection Research (TWINCORE), Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Joint first authors
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Jonathan Cardwell
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Erick Forno
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.,Dept of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Medea Imboden
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Dept of Public Health, University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Dept of Public Health, University of Basel, Basel, Switzerland
| | - Anne-Marie Madore
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Cancan Qi
- Dept of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital and GRIAC Research Institute, Groningen, The Netherlands
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Brian D Bennett
- Integrative Bioinformatics Support Group, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - James M Ward
- Integrative Bioinformatics Support Group, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Christine G Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Laura E Beane-Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Debra King
- Clinical Pathology Group, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
| | - David A Schwartz
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Juan C Celedón
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.,Dept of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Centre Intersectoriel en Santé Durable, Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Dept of Pediatrics, Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Saguenay, QC, Canada
| | - Carole Ober
- Dept of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Nicole Probst-Hensch
- Chronic Disease Epidemiology Unit, Dept of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Dept of Public Health, University of Basel, Basel, Switzerland
| | - Ivana V Yang
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gerard H Koppelman
- Dept of Pediatric Pulmonology and Pediatric Allergy, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital and GRIAC Research Institute, Groningen, The Netherlands
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, USA
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25
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Sugita K, Soyka MB, Wawrzyniak P, Rinaldi AO, Mitamura Y, Akdis M, Akdis CA. Outside-in hypothesis revisited: The role of microbial, epithelial, and immune interactions. Ann Allergy Asthma Immunol 2020; 125:517-527. [PMID: 32454094 DOI: 10.1016/j.anai.2020.05.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/14/2020] [Accepted: 05/17/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Our understanding of the origin of allergic diseases has increased in recent years, highlighting the importance of microbial dysbiosis and epithelial barrier dysfunction in affected tissues. Exploring the microbial-epithelial-immune crosstalk underlying the mechanisms of allergic diseases will allow the development of novel prevention and treatment strategies for allergic diseases. DATA SOURCES This review summarizes the recent advances in microbial, epithelial, and immune interactions in atopic dermatitis, allergic rhinitis, chronic rhinosinusitis, and asthma. STUDY SELECTIONS We performed a literature search, identifying relevant recent primary articles and review articles. RESULTS Dynamic crosstalk between the environmental factors and microbial, epithelial, and immune cells in the development of atopic dermatitis, allergic rhinitis, chronic rhinosinusitis, and asthma underlies the pathogenesis of these diseases. There is substantial evidence in the literature suggesting that environmental factors directly affect barrier function of the epithelium. In addition, T-helper 2 (TH2) cells, type 2 innate lymphoid cells, and their cytokine interleukin 13 (IL-13) damage skin and lung barriers. The effects of environmental factors may at least in part be mediated by epigenetic mechanisms. Histone deacetylase activation by type 2 immune response has a major effect on leaky barriers and blocking of histone deacetylase activity corrects the defective barrier in human air-liquid interface cultures and mouse models of allergic asthma with rhinitis. We also present and discuss a novel device to detect and monitor skin barrier dysfunction, which provides an opportunity to rapidly and robustly assess disease severity. CONCLUSION A complex interplay between environmental factors, epithelium, and the immune system is involved in the development of systemic allergic diseases.
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Affiliation(s)
- Kazunari Sugita
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland; Division of Dermatology, Department of Medicine of Sensory and Motor Organs, Faculty of Medicine, Tottori University, Yonago, Japan.
| | - Michael B Soyka
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Department of Otorhinolaryngology, Head and Neck Surgery, University and University Hospital of Zurich, Zurich, Switzerland
| | - Paulina Wawrzyniak
- Division of Clinical Chemistry and Biochemistry and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Arturo O Rinaldi
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Yasutaka Mitamura
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland
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26
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Kabesch M, Tost J. Recent findings in the genetics and epigenetics of asthma and allergy. Semin Immunopathol 2020; 42:43-60. [PMID: 32060620 PMCID: PMC7066293 DOI: 10.1007/s00281-019-00777-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 12/22/2019] [Indexed: 12/16/2022]
Abstract
In asthma and allergy genetics, a trend towards a few main topics developed over the last 2 years. First, a number of studies have been published recently which focus on overlapping and/or very specific phenotypes: within the allergy spectrum but also reaching beyond, looking for common genetic traits shared between different diseases or disease entities. Secondly, an urgently needed focus has been put on asthma and allergy genetics in populations genetically different from European ancestry. This acknowledges that the majority of new asthma patients today are not white and asthma is a truly worldwide disease. In epigenetics, recent years have seen several large-scale epigenome-wide association studies (EWAS) being published and a further focus was on the interaction between the environment and epigenetic signatures. And finally, the major trends in current asthma and allergy genetics and epigenetics comes from the field of pharmacogenetics, where it is necessary to understand the susceptibility for and mechanisms of current asthma and allergy therapies while at the same time, we need to have scientific answers to the recent availability of novel drugs that hold the promise for a more individualized therapy.
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Affiliation(s)
- Michael Kabesch
- Department of Pediatric Pneumology and Allergy, St. Hedwig's Hospital of the order of St. John, University Children's Hospital Regensburg (KUNO), Steinmetzstr. 1-3, 93049, Regensburg, Germany.
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, 2 rue Gaston Crémieux, 91000, Evry, France
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Hudon Thibeault AA, Laprise C. Cell-Specific DNA Methylation Signatures in Asthma. Genes (Basel) 2019; 10:E932. [PMID: 31731604 PMCID: PMC6896152 DOI: 10.3390/genes10110932] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022] Open
Abstract
Asthma is a complex trait, often associated with atopy. The genetic contribution has been evidenced by familial occurrence. Genome-wide association studies allowed for associating numerous genes with asthma, as well as identifying new loci that have a minor contribution to its phenotype. Considering the role of environmental exposure on asthma development, an increasing amount of literature has been published on epigenetic modifications associated with this pathology and especially on DNA methylation, in an attempt to better understand its missing heritability. These studies have been conducted in different tissues, but mainly in blood or its peripheral mononuclear cells. However, there is growing evidence that epigenetic changes that occur in one cell type cannot be directly translated into another one. In this review, we compare alterations in DNA methylation from different cells of the immune system and of the respiratory tract. The cell types in which data are obtained influences the global status of alteration of DNA methylation in asthmatic individuals compared to control (an increased or a decreased DNA methylation). Given that several genes were cell-type-specific, there is a great need for comparative studies on DNA methylation from different cells, but from the same individuals in order to better understand the role of epigenetics in asthma pathophysiology.
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Affiliation(s)
- Andrée-Anne Hudon Thibeault
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada;
- Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada
- Quebec Respiratory Health Network, Quebec, G1V 4G5 QC, Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada;
- Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada
- Quebec Respiratory Health Network, Quebec, G1V 4G5 QC, Canada
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