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Han R, Zhu D, Sha J, Zhao B, Jin P, Meng C. Decoding the role of DNA methylation in allergic diseases: from pathogenesis to therapy. Cell Biosci 2024; 14:89. [PMID: 38965641 PMCID: PMC11225420 DOI: 10.1186/s13578-024-01270-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Allergic diseases, characterized by a broad spectrum of clinical manifestations and symptoms, encompass a significant category of IgE-mediated atopic disorders, including asthma, allergic rhinitis, atopic dermatitis, and food allergies. These complex conditions arise from the intricate interplay between genetic and environmental factors and are known to contribute to socioeconomic burdens globally. Recent advancements in the study of allergic diseases have illuminated the crucial role of DNA methylation (DNAm) in their pathogenesis. This review explores the factors influencing DNAm in allergic diseases and delves into their mechanisms, offering valuable perspectives for clinicians. Understanding these epigenetic modifications aims to lay the groundwork for improved early prevention strategies. Moreover, our analysis of DNAm mechanisms in these conditions seeks to enhance diagnostic and therapeutic approaches, paving the way for more effective management of allergic diseases in the future.
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Affiliation(s)
- Ruiming Han
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Dongdong Zhu
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Precise Diagnosis and Treatment of Upper Airway Allergic Diseases, Changchun, China
| | - Jichao Sha
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
- Jilin Provincial Key Laboratory of Precise Diagnosis and Treatment of Upper Airway Allergic Diseases, Changchun, China
| | - Boning Zhao
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, 615 Michael ST NE, Atlanta, GA, 30322, USA.
| | - Cuida Meng
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.
- Jilin Provincial Key Laboratory of Precise Diagnosis and Treatment of Upper Airway Allergic Diseases, Changchun, China.
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Stefanović M, Stojković L, Životić I, Dinčić E, Stanković A, Živković M. Expression levels of GSDMB and ORMDL3 are associated with relapsing-remitting multiple sclerosis and IKZF3 rs12946510 variant. Heliyon 2024; 10:e25033. [PMID: 38314276 PMCID: PMC10837620 DOI: 10.1016/j.heliyon.2024.e25033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/06/2024] Open
Abstract
Multiple sclerosis (MS), a noncurable autoimmune neurodegenerative disease, requires constant research that could improve understanding of both environmental and genetic factors that lead to its occurrence and/or progression. Recognition of the genetic basis of MS further leads to an investigation of the regulatory role of genetic variants on gene expression. Among risk variants for MS, Ikaros zinc finger 3 (IKZF3) gene variant rs12946510 was identified as one of the top-ranked and the expression quantitative trait loci (eQTL) for genes residing in chromosomal locus 17q12-21. The study aimed to investigate the association of gene expression of the immunologically relevant genes, which map to indicated locus, ORMDL3, GSDMB, and IKZF3, with MS and rs12946510 genotype, taking into account disease phase, clinical parameters of disease progression, and severity and immunomodulatory therapy. We used TaqMan® technology for both allelic discrimination and gene expression determination in 67 relapsing MS patients and 50 healthy controls. Decreased ORMDL3 and GSDMB mRNA levels had significant associations with MS and rs12946510 TT rare homozygote among patients. Significant positive correlations between ORMDL3 and GSDMB mRNA expression were observed in both patients and controls. We detected the significant between-effect of sex and rs12946510 on the expression of ORMDL3 in the patient group and interferon β therapy and rs12946510 on GSDMB expression. Our results show the association of ORMDL3 and GSDMB mRNA expression with the clinical manifestation of MS and confirm that IKZF3 rs12946510 exerts the eQTL effect on both genes in multiple sclerosis. Besides providing novel insight related to MS phases and interferon β therapy, the study results confirm previous studies on regulatory genetic variants, autoimmunity, and MS.
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Affiliation(s)
- Milan Stefanović
- VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, Laboratory for Radiobiology and Molecular Genetics, University of Belgrade, Belgrade, Serbia
| | - Ljiljana Stojković
- VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, Laboratory for Radiobiology and Molecular Genetics, University of Belgrade, Belgrade, Serbia
| | - Ivan Životić
- VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, Laboratory for Radiobiology and Molecular Genetics, University of Belgrade, Belgrade, Serbia
| | - Evica Dinčić
- Military Medical Academy, Clinic for Neurology, Belgrade, Serbia
| | - Aleksandra Stanković
- VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, Laboratory for Radiobiology and Molecular Genetics, University of Belgrade, Belgrade, Serbia
| | - Maja Živković
- VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, Laboratory for Radiobiology and Molecular Genetics, University of Belgrade, Belgrade, Serbia
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3
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Chen LN, Shou ZX, Jin X. Interaction Between Genetic Susceptibility and COVID-19 Pathogenesis in Pediatric Multisystem Inflammatory Disorders: The Role of Immune Responses. Viral Immunol 2024; 37:1-11. [PMID: 38271561 DOI: 10.1089/vim.2023.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Abstract
Numerous studies have highlighted the emergence of coronavirus disease (COVID-19) symptoms reminiscent of Kawasaki disease in children, including fever, heightened multisystem inflammation, and multiorgan involvement, posing a life-threatening complication. Consequently, extensive research endeavors in pediatric have aimed to elucidate the intricate relationship between COVID-19 infection and the immune system. COVID-19 profoundly impacts immune cells, culminating in a cytokine storm that particularly inflicts damage on the pulmonary system. The gravity and vulnerability to COVID-19 are closely intertwined with the vigor of the immune response. In this context, the human leukocyte antigen (HLA) molecule assumes pivotal significance in shaping immune responses. Genetic scrutiny of HLA has unveiled the presence of at least one deleterious allele in children afflicted with multisystem inflammatory syndrome in children (MIS-C). Furthermore, research has demonstrated that COVID-19 exploits the angiotensin-converting enzyme 2 (ACE-2) receptor, transmembrane serine protease type 2, and various other genes to gain entry into host cells, with individuals harboring ACE-2 polymorphisms being at higher risk. Pediatric studies have employed diverse genetic methodologies, such as genome-wide association studies (GWAS) and whole exome sequencing, to scrutinize target genes. These investigations have pinpointed two specific genomic loci linked to the severity and susceptibility of COVID-19, with the HLA locus emerging as a notable risk factor. In this comprehensive review article, we endeavor to assess the available evidence and consolidate data, offering insights into current clinical practices and delineating avenues for future research. Our objective is to advance early diagnosis, stabilization, and appropriate management strategies to mitigate genetic susceptibility's impact on the incidence of COVID-19 in pediatric patients with multisystem inflammation.
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Affiliation(s)
- Li-Na Chen
- Department of Pediatric, Affiliated Hospital of Shaoxing University, Shaoxing, China
| | - Zhang-Xuan Shou
- Department of Pharmacy, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xue Jin
- Department of Pharmacy, Center for Clinical Pharmacy, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
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Brown AP, Parameswaran S, Cai L, Elston S, Pham C, Barski A, Weirauch MT, Ji H. TET1 regulates responses to house dust mite by altering chromatin accessibility, DNA methylation, and gene expression in airway epithelial cells. RESEARCH SQUARE 2023:rs.3.rs-3726852. [PMID: 38168374 PMCID: PMC10760239 DOI: 10.21203/rs.3.rs-3726852/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background Previous studies have identified TET1 as a potential key regulator of genes linked to asthma. TET1 has been shown to transcriptionally respond to house dust mite extract, an allergen known to directly cause allergic asthma development, and regulate the expression of genes involved in asthma. How TET1 regulates expression of these genes, however, is unknown. TET1 is a DNA demethylase; therefore, most prior research on TET1-based gene regulation has focused on how TET1 affects methylation. However, TET1 can also interact directly with transcription factors and histone modifiers to regulate gene expression. Understanding how TET1 regulates expression to contribute to allergic responses and asthma development thus requires a comprehensive approach. To this end, we measured mRNA expression, DNA methylation, chromatin accessibility and histone modifications in control and TET1 knockdown human bronchial epithelial cells treated or untreated with house dust mite extract. Results Throughout our analyses, we detected strong similarities between the effects of TET1 knockdown alone and the effects of HDM treatment alone. One especially striking pattern was that both TET1 knockdown and HDM treatment generally led to decreased chromatin accessibility at largely the same genomic loci. Transcription factor enrichment analyses indicated that altered chromatin accessibility following the loss of TET1 may affect, or be affected by, CTCF and CEBP binding. TET1 loss also led to changes in DNA methylation, but these changes were generally in regions where accessibility was not changing. Conclusions TET1 regulates gene expression through different mechanisms (DNA methylation and chromatin accessibility) in different parts of the genome in the airway epithelial cells, which mediates inflammatory responses to allergen. Collectively, our data suggest novel molecular mechanisms through which TET1 regulates critical pathways following allergen challenges and contributes to the development of asthma.
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Affiliation(s)
| | | | | | | | | | | | | | - Hong Ji
- University of California Davis
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Odimba U, Senthilselvan A, Farrell J, Gao Z. Sex-Specific Genetic Determinants of Asthma-COPD Phenotype and COPD in Middle-Aged and Older Canadian Adults: An Analysis of CLSA Data. COPD 2023; 20:233-247. [PMID: 37466093 DOI: 10.1080/15412555.2023.2229906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/22/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023]
Abstract
The etiology of sex differences in the risk of asthma-COPD phenotype and COPD is still not completely understood. Genetic and environmental risk factors are commonly believed to play an important role. This study aims to identify sex-specific genetic markers associated with asthma-COPD phenotype and COPD using the Canadian Longitudinal Study on Aging (CLSA) Baseline Comprehensive and Genomic data. There were a total of 1,415 COPD cases. Out of them, 504 asthma-COPD phenotype cases were identified. 20,524 participants without a diagnosis of asthma and COPD served as controls. We performed genome-wide SNP-by-sex interaction analysis. SNPs with an interaction p-value < 10-5 were included in a sex-stratified multivariable logistic regression for asthma-COPD phenotype and COPD outcomes. 18 and 28 SNPs had a significant interaction term p-value < 10-5 with sex in the regression analyses of asthma-COPD phenotype and COPD outcomes, respectively. Sex-stratified multivariable analysis of asthma-COPD phenotype showed that 7 SNPs in/near SMYD3, FHIT, ZNF608, RIMBP2, ZNF133, BPIFB1, and S100B loci were significant in males. Sex-stratified multivariable analysis of COPD showed that 8 SNPs in/near MAGI1, COX18, OSTC, ELOVL5, C7orf72 FGF14, and NKAIN4 were significant in males, and 4 SNPs in/near genes CAMTA1, SATB2, PDE10A, and LINC00908 were significant in females. An SNP in the ZPBP gene was associated with COPD in both males and females. Identification of sex-specific loci associated with asthma-COPD phenotype and COPD may offer valuable evidence toward a better understanding of the sex-specific differences in the pathophysiology of the diseases.
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Affiliation(s)
- Ugochukwu Odimba
- Clinical Epidemiology Unit, Division of Community Health and Humanities, Faculty of Medicine, Memorial University, St. John's, Canada
| | | | - Jamie Farrell
- Clinical Epidemiology Unit, Division of Community Health and Humanities, Faculty of Medicine, Memorial University, St. John's, Canada
- Faculty of Medicine, Health Sciences Centre (Respirology Department), Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Zhiwei Gao
- Clinical Epidemiology Unit, Division of Community Health and Humanities, Faculty of Medicine, Memorial University, St. John's, Canada
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Kim SR, Eom Y, Lee SH. Comprehensive analysis of sex differences in the function and ultrastructure of hippocampal presynaptic terminals. Neurochem Int 2023; 169:105570. [PMID: 37451344 DOI: 10.1016/j.neuint.2023.105570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/08/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
Sex differences in the brain, encompassing variations in specific brain structures, size, cognitive function, and synaptic connections, have been identified across numerous species. While previous research has explored sex differences in postsynaptic structures, synaptic plasticity, and hippocampus-dependent functions, the hippocampal presynaptic terminals remain largely uninvestigated. The hippocampus is a critical structure responsible for multiple brain functions. This study examined presynaptic differences in cultured hippocampal neurons derived from male and female mice using a combination of biochemical assays, functional analyses measuring exocytosis and endocytosis of synaptic vesicle proteins, ultrastructural analyses via electron microscopy, and presynaptic Ca2+-specific optical probes. Our findings revealed that female neurons exhibited a higher number of synaptic vesicles at presynaptic terminals compared to male neurons. However, no significant differences were observed in presynaptic protein expression, presynaptic terminal ultrastructure, synaptic vesicle exocytosis and endocytosis, or presynaptic Ca2+ alterations between male and female neurons.
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Affiliation(s)
- Sung Rae Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea; Brain Research Core Facilities of Korea Brain Research Institute (KBRI), Daegu 41068, Republic of Korea.
| | - Yunkyung Eom
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
| | - Sung Hoon Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea.
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Nowakowska J, Olechnowicz A, Langwiński W, Koteluk O, Lemańska Ż, Jóźwiak K, Kamiński K, Łosiewski W, Stegmayr J, Wagner D, Alsafadi HN, Lindstedt S, Dziuba M, Bielicka A, Graczyk Z, Szczepankiewicz A. Increased expression of ORMDL3 in allergic asthma: a case control and in vitro study. J Asthma 2023; 60:458-467. [PMID: 35321632 DOI: 10.1080/02770903.2022.2056896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Asthma is the most frequent chronic disease in children. One of the most replicated genetic findings in childhood asthma is the ORMDL3 gene confirmed in several GWA studies in several pediatric populations. OBJECTIVES The purpose of this study was to analyze ORMDL3 variants and expression in childhood asthma in the Polish population. METHODS In the study we included 416 subject, 223 asthmatic children and 193 healthy control subjects. The analysis of two SNPs (rs3744246 and rs8076131) was performed using genotyping with TaqMan probes. The methylation of the ORMDL3 promoter was examined with Methylation Sensitive HRM (MS-HRM), covering 9 CpG sites. The expression of ORMDL3 was analyzed in PBMCs from pediatric patients diagnosed with allergic asthma and primary human bronchial epithelial cells derived from healthy subjects treated with IL-13, IL-4, or co-treatment with both cytokines to model allergic airway inflammation. RESULTS We found that ORMDL3 expression was increased in allergic asthma both in PBMCs from asthmatic patients as well as in human bronchial epithelial cells stimulated with the current cytokines. We did not observe significant differences between cases and controls either in the genotype distribution of analyzed SNPs (rs3744246 and rs8076131) nor in the level of promoter methylation. CONCLUSIONS Increased ORMDL3 expression is associated with pediatric allergic asthma and upregulated in the airways upon Th2-cytokines stimulation, but further functional studies are required to fully understand its role in this disease.
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Affiliation(s)
- Joanna Nowakowska
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Olechnowicz
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Wojciech Langwiński
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Oliwia Koteluk
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Żaneta Lemańska
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Kacper Jóźwiak
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Kacper Kamiński
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Wojciech Łosiewski
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - John Stegmayr
- Lung Bioengineering and Regeneration, Department of Experimental Medical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Darcy Wagner
- Lung Bioengineering and Regeneration, Department of Experimental Medical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Hani N Alsafadi
- Lung Bioengineering and Regeneration, Department of Experimental Medical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Sandra Lindstedt
- Lung Bioengineering and Regeneration, Department of Experimental Medical Sciences, Faculty of Medicine, Lund University, Lund, Sweden
| | - Maria Dziuba
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Antonina Bielicka
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Zuzanna Graczyk
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | - Aleksandra Szczepankiewicz
- Molecular and Cell Biology Unit, Department of Pediatric Pulmonology, Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
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8
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Latour M, Lal D, Yim MT. Sex Differences in Airway Diseases. Otolaryngol Clin North Am 2023; 56:55-63. [DOI: 10.1016/j.otc.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Deciphering genetic causes for sex differences in human health through drug metabolism and transporter genes. Nat Commun 2023; 14:175. [PMID: 36635277 PMCID: PMC9837057 DOI: 10.1038/s41467-023-35808-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Sex differences have been widely observed in human health. However, little is known about the underlying mechanism behind these observed sex differences. We hypothesize that sex-differentiated genetic effects are contributors of these phenotypic differences. Focusing on a collection of drug metabolism enzymes and transporters (DMET) genes, we discover sex-differentiated genetic regulatory mechanisms between these genes and human complex traits. Here, we show that sex-differentiated genetic effects were present at genome-level and at DMET gene regions for many human complex traits. These sex-differentiated regulatory mechanisms are reflected in the levels of gene expression and endogenous serum biomarkers. Through Mendelian Randomization analysis, we identify putative sex-differentiated causal effects in each sex separately. Furthermore, we identify and validate sex differential gene expression of a subset of DMET genes in human liver samples. We observe higher protein abundance and enzyme activity of CYP1A2 in male-derived liver microsomes, which leads to higher level of an active metabolite formation of clozapine, a commonly prescribed antipsychotic drug. Taken together, our results demonstrate the presence of sex-differentiated genetic effects on DMET gene regulation, which manifest in various phenotypic traits including disease risks and drug responses.
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10
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Maggi E, Parronchi P, Azzarone BG, Moretta L. A pathogenic integrated view explaining the different endotypes of asthma and allergic disorders. Allergy 2022; 77:3267-3292. [PMID: 35842745 DOI: 10.1111/all.15445] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 01/28/2023]
Abstract
The inflammation of allergic diseases is characterized by a complex interaction between type 2 and type 3 immune responses, explaining clinical symptoms and histopathological patterns. Airborne stimuli activate the mucosal epithelium to release a number of molecules impacting the activity of resident immune and environmental cells. Signals from the mucosal barrier, regulatory cells, and the inflamed tissue are crucial conditions able to modify innate and adaptive effector cells providing the selective homing of eosinophils or neutrophils. The high plasticity of resident T- and innate lymphoid cells responding to external signals is the prerequisite to explain the multiplicity of endotypes of allergic diseases. This notion paved the way for the huge use of specific biologic drugs interfering with pathogenic mechanisms of inflammation. Based on the response of the epithelial barrier, the activity of resident regulatory cells, and functions of structural non-lymphoid environmental cells, this review proposes some immunopathogenic scenarios characterizing the principal endotypes which can be associated with a precise phenotype of asthma. Recent literature indicates that similar concepts can also be applied to the inflammation of other non-respiratory allergic disorders. The next challenges will consist in defining specific biomarker(s) of each endotype allowing for a quick diagnosis and the most effective personalized therapy.
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Affiliation(s)
- Enrico Maggi
- Department of Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Paola Parronchi
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | | | - Lorenzo Moretta
- Department of Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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11
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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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12
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Role of Epigenetics in the Pathogenesis, Treatment, Prediction, and Cellular Transformation of Asthma. Mediators Inflamm 2021; 2021:9412929. [PMID: 34566492 PMCID: PMC8457970 DOI: 10.1155/2021/9412929] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
Asthma is a mysterious disease with heterogeneity in etiology, pathogenesis, and clinical phenotypes. Although ongoing studies have provided a better understanding of asthma, its natural history, progression, pathogenesis, diversified phenotypes, and even the exact epigenetic linkage between childhood asthma and adult-onset/old age asthma remain elusive in many aspects. Asthma heritability has been established through genetic studies, but genetics is not the only influencing factor in asthma. The increasing incidence and some unsolved queries suggest that there may be other elements related to asthma heredity. Epigenetic mechanisms link genetic and environmental factors with developmental trajectories in asthma. This review provides an overview of asthma epigenetics and its components, including several epigenetic studies on asthma, and discusses the epigenetic linkage between childhood asthma and adult-onset/old age asthma. Studies involving asthma epigenetics present valuable novel approaches to solve issues related to asthma. Asthma epigenetic research guides us towards gene therapy and personalized T cell therapy, directs the discovery of new therapeutic agents, predicts long-term outcomes in severe cases, and is also involved in the cellular transformation of childhood asthma to adult-onset/old age asthma.
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13
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Migliore L, Nicolì V, Stoccoro A. Gender Specific Differences in Disease Susceptibility: The Role of Epigenetics. Biomedicines 2021; 9:652. [PMID: 34200989 PMCID: PMC8228628 DOI: 10.3390/biomedicines9060652] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 01/08/2023] Open
Abstract
Many complex traits or diseases, such as infectious and autoimmune diseases, cancer, xenobiotics exposure, neurodevelopmental and neurodegenerative diseases, as well as the outcome of vaccination, show a differential susceptibility between males and females. In general, the female immune system responds more efficiently to pathogens. However, this can lead to over-reactive immune responses, which may explain the higher presence of autoimmune diseases in women, but also potentially the more adverse effects of vaccination in females compared with in males. Many clinical and epidemiological studies reported, for the SARS-CoV-2 infection, a gender-biased differential response; however, the majority of reports dealt with a comparable morbidity, with males, however, showing higher COVID-19 adverse outcomes. Although gender differences in immune responses have been studied predominantly within the context of sex hormone effects, some other mechanisms have been invoked: cellular mosaicism, skewed X chromosome inactivation, genes escaping X chromosome inactivation, and miRNAs encoded on the X chromosome. The hormonal hypothesis as well as other mechanisms will be examined and discussed in the light of the most recent epigenetic findings in the field, as the concept that epigenetics is the unifying mechanism in explaining gender-specific differences is increasingly emerging.
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Affiliation(s)
- Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy; (V.N.); (A.S.)
- Department of Laboratory Medicine, Azienda Ospedaliero Universitaria Pisana, 56124 Pisa, Italy
| | - Vanessa Nicolì
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy; (V.N.); (A.S.)
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy; (V.N.); (A.S.)
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14
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Sheikhpour M, Maleki M, Ebrahimi Vargoorani M, Amiri V. A review of epigenetic changes in asthma: methylation and acetylation. Clin Epigenetics 2021; 13:65. [PMID: 33781317 PMCID: PMC8008616 DOI: 10.1186/s13148-021-01049-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/04/2021] [Indexed: 12/30/2022] Open
Abstract
Several studies show that childhood and adulthood asthma and its symptoms can be modulated through epigenetic modifications. Epigenetic changes are inheritable modifications that can modify the gene expression without changing the DNA sequence. The most common epigenetic alternations consist of DNA methylation and histone modifications. How these changes lead to asthmatic phenotype or promote the asthma features, in particular by immune pathways regulation, is an understudied topic. Since external effects, like exposure to tobacco smoke, air pollution, and drugs, influence both asthma development and the epigenome, elucidating the role of epigenetic changes in asthma is of great importance. This review presents available evidence on the epigenetic process that drives asthma genes and pathways, with a particular focus on DNA methylation, histone methylation, and acetylation. We gathered and assessed studies conducted in this field over the past two decades. Our study examined asthma in different aspects and also shed light on the limitations and the important factors involved in the outcomes of the studies. To date, most of the studies in this area have been carried out on DNA methylation. Therefore, the need for diagnostic and therapeutic applications through this molecular process calls for more research on the histone modifications in this disease.
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Affiliation(s)
- Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Mobina Maleki
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Ebrahimi Vargoorani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, College of Basic Sciences, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Vahid Amiri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
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15
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Owora AH, Zhang Y. Childhood wheeze trajectory-specific risk factors: A systematic review and meta-analysis. Pediatr Allergy Immunol 2021; 32:34-50. [PMID: 32668501 DOI: 10.1111/pai.13313] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND There is growing interest in the use of latent trajectory methodology to identify wheeze patterns in heterogeneous populations of children. This study systematically reviewed and meta-analyzed childhood wheeze trajectory studies to identify childhood wheeze trajectory group-specific risk factors among children from birth through to adolescence. METHODS We included studies that used latent trajectory methodology to identify wheeze trajectories and associated risk factors. We searched PubMed, EMBASE, and Google Scholar from 2000 through September 30, 2019, for relevant studies. The study was conducted according to the PRISMA recommendations. RESULTS Thirteen cohort studies conducted in eleven high-income countries were included in our meta-analysis with the length of follow-up ranging from 3 to 18 years. Five distinct latent wheeze trajectory groups were identified: Never/Infrequent, Early-Transient, Early-Persistent, Intermediate-Onset, and Late-Onset. We found moderate-to-strong evidence that family history of asthma predicted persistent childhood wheezing among male children but with lower risk among first-born children. There was weak-to-moderate evidence for childhood atopy, male sex, short duration of breastfeeding, tobacco exposure, daycare attendance, and having siblings as risk factors for Early-Transient wheezing; except for breastfeeding, these factors were also associated with intermediate and Late-Onset wheezing with varying effect sizes in high-risk vs general population cohorts. CONCLUSIONS Our findings confirm the consistency of wheeze trajectory groups defined by onset, peak prevalence, and duration; we also suggest a common nomenclature for future trajectory studies. With the exception of the relationship between a family history of asthma and persistent childhood wheezing, commonly suspected wheeze risk factors (childhood atopy, male sex, short duration of breastfeeding, tobacco exposure, daycare attendance, and having siblings) are not trajectory-specific and have varying effects in high-risk vs general population cohorts. Delineation of time-varying risk factor effects may be critical to the specificity of wheeze trajectory group prediction to better inform prognosis and targeted early preventive intervention among at-risk children.
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Affiliation(s)
- Arthur H Owora
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University, Bloomington, IN, USA
| | - Yijia Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University, Bloomington, IN, USA
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16
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Helling BA, Sobreira DR, Hansen GT, Sakabe NJ, Luo K, Billstrand C, Laxman B, Nicolae RI, Nicolae DL, Bochkov YA, Gern JE, Nobrega MA, White SR, Ober C. Altered transcriptional and chromatin responses to rhinovirus in bronchial epithelial cells from adults with asthma. Commun Biol 2020; 3:678. [PMID: 33188283 PMCID: PMC7666152 DOI: 10.1038/s42003-020-01411-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
There is a life-long relationship between rhinovirus (RV) infection and the development and clinical manifestations of asthma. In this study we demonstrate that cultured primary bronchial epithelial cells from adults with asthma (n = 9) show different transcriptional and chromatin responses to RV infection compared to those without asthma (n = 9). Both the number and magnitude of transcriptional and chromatin responses to RV were muted in cells from asthma cases compared to controls. Pathway analysis of the transcriptionally responsive genes revealed enrichments of apoptotic pathways in controls but inflammatory pathways in asthma cases. Using promoter capture Hi-C we tethered regions of RV-responsive chromatin to RV-responsive genes and showed enrichment of these regions and genes at asthma GWAS loci. Taken together, our studies indicate a delayed or prolonged inflammatory state in cells from asthma cases and highlight genes that may contribute to genetic risk for asthma.
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Affiliation(s)
- Britney A Helling
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Grace T Hansen
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Noboru J Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Kaixuan Luo
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | | | - Bharathi Laxman
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Raluca I Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Dan L Nicolae
- Department of Statistics, University of Chicago, Chicago, IL, 60637, USA
| | - Yury A Bochkov
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Marcelo A Nobrega
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Steven R White
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
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17
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Long A, Bunning B, Sampath V, DeKruyff RH, Nadeau KC. Epigenetics and the Environment in Airway Disease: Asthma and Allergic Rhinitis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1253:153-181. [PMID: 32445095 DOI: 10.1007/978-981-15-3449-2_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Asthma and rhinitis are complex, heterogeneous diseases characterized by chronic inflammation of the upper and lower airways. While genome-wide association studies (GWAS) have identified a number of susceptible loci and candidate genes associated with the pathogenesis of asthma and allergic rhinitis (AR), the risk-associated alleles account for only a very small percent of the genetic risk. In allergic airway and other complex diseases, it is thought that epigenetic modifications, including DNA methylation, histone modifications, and non-coding microRNAs, caused by complex interactions between the underlying genome and the environment may account for some of this "missing heritability" and may explain the high degree of plasticity in immune responses. In this chapter, we will focus on the current knowledge of classical epigenetic modifications, DNA methylation and histone modifications, and their potential role in asthma and AR. In particular, we will review epigenetic variations associated with maternal airway disease, demographics, environment, and non-specific associations. The role of specific genetic haplotypes in environmentally induced epigenetic changes are also discussed. A major limitation of many of the current studies of asthma epigenetics is that they evaluate epigenetic modifications in both allergic and non-allergic asthma, making it difficult to distinguish those epigenetic modifications that mediate allergic asthma from those that mediate non-allergic asthma. Additionally, most DNA methylation studies in asthma use peripheral or cord blood due to poor accessibility of airway cells or tissue. Unlike DNA sequences, epigenetic alterations are quite cell- and tissue-specific, and epigenetic changes found in airway tissue or cells may be discordant from that of circulating blood. These two confounding factors should be considered when reviewing epigenetic studies in allergic airway disease.
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Affiliation(s)
- Andrew Long
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.,Department of Pharmacy, Lucile Packard Children's Hospital, Stanford, CA, 94304, USA
| | - Bryan Bunning
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Vanitha Sampath
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Rosemarie H DeKruyff
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Kari C Nadeau
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.
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18
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Chang ML, Moussette S, Gamero-Estevez E, Gálvez JH, Chiwara V, Gupta IR, Ryan AK, Naumova AK. Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock. PLoS One 2019; 14:e0223212. [PMID: 31560728 PMCID: PMC6764692 DOI: 10.1371/journal.pone.0223212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/15/2019] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association study (GWAS) loci for several immunity-mediated diseases (early onset asthma, inflammatory bowel disease (IBD), primary biliary cholangitis, and rheumatoid arthritis) map to chromosomal region 17q12-q21. The predominant view is that association between 17q12-q21 alleles and increased risk of developing asthma or IBD is due to regulatory variants. ORM sphingolipid biosynthesis regulator (ORMDL3) residing in this region is the most promising gene candidate for explaining association with disease. However, the relationship between 17q12-q21 alleles and disease is complex suggesting contributions from other factors, such as trans-acting genetic and environmental modifiers or circadian rhythms. Circadian rhythms regulate expression levels of thousands of genes and their dysregulation is implicated in the etiology of several common chronic inflammatory diseases. However, their role in the regulation of the 17q12-q21 genes has not been investigated. Moreover, the core clock gene nuclear receptor subfamily 1, group D, member 1 (NR1D1) resides about 200 kb distal to the GWAS region. We hypothesized that circadian rhythms influenced gene expression levels in 17q12-q21 region and conversely, regulatory elements in this region influenced transcription of the core clock gene NR1D1 in cis. To test these hypotheses, we examined the diurnal expression profiles of zona pellucida binding protein 2 (ZPBP2/Zpbp2), gasdermin B (GSDMB), and ORMDL3/Ormdl3 in human and mouse tissues and analyzed the impact of genetic variation in the ZPBP2/Zpbp2 region on NR1D1/Nr1d1 expression. We found that Ormdl3 and Zpbp2 were controlled by the circadian clock in a tissue-specific fashion. We also report that deletion of the Zpbp2 region altered the expression profile of Nr1d1 in lungs and ileum in a time-dependent manner. In liver, the deletion was associated with enhanced expression of Ormdl3. We provide the first evidence that disease-associated genes Zpbp2 and Ormdl3 are regulated by circadian rhythms and the Zpbp2 region influences expression of the core clock gene Nr1d1.
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Affiliation(s)
- Matthew L. Chang
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Sanny Moussette
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | | | - Victoria Chiwara
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Indra R. Gupta
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Paediatrics, McGill University, Montreal, Quebec, Canada
| | - Aimee K. Ryan
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Paediatrics, McGill University, Montreal, Quebec, Canada
| | - Anna K. Naumova
- The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Obstetrics and Gynecology, McGill University, Montreal, Quebec, Canada
- * E-mail:
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19
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Jansen RJ, Tong L, Argos M, Jasmine F, Rakibuz-Zaman M, Sarwar G, Islam MT, Shahriar H, Islam T, Rahman M, Yunus M, Kibriya MG, Baron JA, Ahsan H, Pierce BL. The effect of age on DNA methylation in whole blood among Bangladeshi men and women. BMC Genomics 2019; 20:704. [PMID: 31506065 PMCID: PMC6734473 DOI: 10.1186/s12864-019-6039-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/16/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND It is well-known that methylation changes occur as humans age, however, understanding how age-related changes in DNA methylation vary by sex is lacking. In this study, we characterize the effect of age on DNA methylation in a sex-specific manner and determine if these effects vary by genomic context. We used the Illumina HumanMethylation 450 K array and DNA derived from whole blood for 400 adult participants (189 males and 211 females) from Bangladesh to identify age-associated CpG sites and regions and characterize the location of these age-associated sites with respect to CpG islands (vs. shore, shelf, or open sea) and gene regions (vs. intergenic). We conducted a genome-wide search for age-associated CpG sites (among 423,604 sites) using a reference-free approach to adjust for cell type composition (the R package RefFreeEWAS) and performed an independent replication analysis of age-associated CpGs. RESULTS The number of age-associated CpGs (p < 5 x 10- 8) were 986 among men and 3479 among women of which 2027(63.8%) and 572 (64.1%) replicated (using Bonferroni adjusted p < 1.2 × 10- 5). For both sexes, age-associated CpG sites were more likely to be hyper-methylated with increasing age (compared to hypo-methylated) and were enriched in CpG islands and promoter regions compared with other locations and all CpGs on the array. Although we observed strong correlation between chronological age and previously-developed epigenetic age models (r ≈ 0.8), among our top (based on lowest p-value) age-associated CpG sites only 12 for males and 44 for females are included in these prediction models, and the median chronological age compared to predicted age was 44 vs. 51.7 in males and 45 vs. 52.1 in females. CONCLUSIONS Our results describe genome-wide features of age-related changes in DNA methylation. The observed associations between age and methylation were generally consistent for both sexes, although the associations tended to be stronger among women. Our population may have unique age-related methylation changes that are not captured in the established methylation-based age prediction model we used, which was developed to be non-tissue-specific.
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Affiliation(s)
- Rick J Jansen
- Department of Public Health, North Dakota State University, Fargo, ND, USA
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Biostatistics Core Facility, North Dakota State University, Fargo, ND, USA
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA
| | - Maria Argos
- Divison of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA
| | | | - Golam Sarwar
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
| | | | - Hasan Shahriar
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
| | - Tariqul Islam
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
| | - Mahfuzar Rahman
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
- Research and Evaluation Division BRAC, Mohakhali, Dhaka, 1212, Bangladesh
| | - Md Yunus
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, 1000, Bangladesh
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA
| | - John A Baron
- Department of Epidemiology, Gillings School of Global Public Health, University of North Caroline, Chapel Hill, NC, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA.
- Department of Medicine, The University of Chicago, Chicago, IL, USA.
- Department of Human Genetics and Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA.
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA.
- Department of Human Genetics and Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA.
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20
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Everson TM, Zhang H, Lockett GA, Kaushal A, Forthofer M, Ewart SL, Burrows K, Relton CL, Sharp GC, Henderson AJ, Patil VK, Rezwan FI, Arshad SH, Holloway JW, Karmaus W. Epigenome-wide association study of asthma and wheeze characterizes loci within HK1. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2019; 15:43. [PMID: 31367216 PMCID: PMC6657035 DOI: 10.1186/s13223-019-0356-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/12/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND To identify novel epigenetic markers of adolescent asthma and replicate findings in an independent cohort, then explore whether such markers are detectable at birth, predictive of early-life wheeze, and associated with gene expression in cord blood. METHODS We performed epigenome-wide screening with recursive random forest feature selection and internal validation in the IOW birth cohort. We then tested whether we could replicate these findings in the independent cohort ALSPAC and followed-up our top finding with children of the IOW cohort. RESULTS We identified 10 CpG sites associated with adolescent asthma at a 5% false discovery rate (IOW, n = 370), five of which exhibited evidence of associations in the replication study (ALSPAC, n = 720). One site, cg16658191, within HK1 displayed particularly strong associations after cellular heterogeneity adjustments in both cohorts (ORIOW = 0.17, 95% CI 0.04-0.57) (ORALSPAC = 0.57, 95% CI 0.38-0.87). Additionally, higher expression of HK1 (OR = 3.81, 95% CI 1.41-11.77) in cord blood was predictive of wheezing in infancy (n = 82). CONCLUSION We identified novel associations between asthma and wheeze with methylation at cg16658191 and the expression of HK1, which may serve as markers of, predictors of, and potentially etiologic factors involved in asthma and early life wheeze.
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Affiliation(s)
- Todd M. Everson
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene Street, Columbia, SC 29208 USA
- Present Address: Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd, Atlanta, GA 30322 USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA
| | - Gabrielle A. Lockett
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK
| | - Akhilesh Kaushal
- Center for Precision and Environmental Health, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030 USA
| | - Melinda Forthofer
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, 915 Greene Street, Columbia, SC 29208 USA
- Present Address: Department of Public Health Sciences at the College of Health and Human Services, University of North Carolina Charlotte, 9201 University City Boulevard, Charlotte, NC 28223 USA
| | - Susan L. Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI USA
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - Gemma C. Sharp
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - A. John Henderson
- Avon Longitudinal Study of Parents and Children, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN UK
| | - Veeresh K. Patil
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight UK
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK
| | - S. Hasan Arshad
- Clinical and Experimental Sciences Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight UK
- NIHR Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton, UK
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK
- Clinical and Experimental Sciences Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, SO16 6YD UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152 USA
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21
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Alag A. Machine learning approach yields epigenetic biomarkers of food allergy: A novel 13-gene signature to diagnose clinical reactivity. PLoS One 2019; 14:e0218253. [PMID: 31216310 PMCID: PMC6584060 DOI: 10.1371/journal.pone.0218253] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 05/29/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Current laboratory tests are less than 50% accurate in distinguishing between people who have food allergies (FA) and those who are merely sensitized to foods, resulting in the use of expensive and potentially dangerous Oral Food Challenges. This study presents a purely-computational machine learning approach, conducted using DNA Methylation (DNAm) data, to accurately diagnose food allergies and potentially find epigenetic targets for the disease. METHODS AND RESULTS An unbiased feature-selection pipeline was created that narrowed down 405,000+ potential CpG biomarkers to 18. Machine-learning models that utilized subsets of this 18-feature aggregate achieved perfect classification accuracy on completely hidden test cohorts (on an 8-fold hidden dataset). Ensemble classification was also shown to be effective for this High Dimension Low Sample Size (HDLSS) DNA methylation dataset. The efficacy of these machine learning classifiers and the 18 CpGs was further validated by their high accuracy on a large number of hidden data permutations, where the samples in the training, cross-validation, and hidden sets were repeatedly randomly allocated. The 18-CpG signature mapped to 13 genes, on which biological insights were collected. Notably, many of the FA-discriminating genes found in this study were strongly associated with the immune system, and seven of the 13 genes were previously associated with FA. CONCLUSIONS Previous studies have also created highly-accurate classifiers for this dataset, using both data-driven and a priori biological insights to construct a 96-CpG signature. This research builds on previous work because it uses a completely computational approach to obtain a perfect classification accuracy while using only 18 highly discriminating CpGs (0.005% of the total available features). In machine learning, simpler models, as used in this study, are generally preferred over more complex ones (other things being equal). Lastly, the completely data-driven methodology presented in this research eliminates the need for a priori biological information and allows for generalizability to other DNAm classification problems.
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Affiliation(s)
- Ayush Alag
- The Harker School, San Jose, CA, United States of America
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22
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Wu CC, Hsu TY, Chang JC, Ou CY, Kuo HC, Liu CA, Wang CL, Chuang H, Chen CP, Yang KD. Paternal Tobacco Smoke Correlated to Offspring Asthma and Prenatal Epigenetic Programming. Front Genet 2019; 10:471. [PMID: 31214241 PMCID: PMC6554446 DOI: 10.3389/fgene.2019.00471] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/01/2019] [Indexed: 12/15/2022] Open
Abstract
Rationale: Little is known about effects of paternal tobacco smoke (PTS) on the offspring's asthma and its prenatal epigenetic programming. Objective: To investigate whether PTS exposure was associated with the offspring's asthma and correlated to epigenetic CG methylation of potential tobacco-related immune genes: LMO2, GSTM1 or/and IL-10 genes. Measurements and Main Results: In a birth cohort of 1,629 newborns, we measured exposure rates of PTS (23%) and maternal tobacco smoke (MTS, 0.2%), cord blood DNA methylation, infant respiratory tract infection, childhood DNA methylation, and childhood allergic diseases. Infants with prenatal PTS exposure had a significantly higher risk of asthma by the age of 6 than those without (p = 0.026). The PTS exposure doses at 0, <20, and ≧20 cigarettes per day were significantly associated with the trend of childhood asthma and the increase of LMO2-E148 (p = 0.006), and IL10_P325 (p = 0.008) CG methylation. The combination of higher CG methylation levels of LMO2_E148, IL10_P325, and GSTM1_P266 corresponded to the highest risk of asthma by 43.48%, compared to other combinations (16.67-23.08%) in the 3-way multi-factor dimensionality reduction (MDR) analysis. The LMO2_P794 and GSTM1_P266 CG methylation levels at age 0 were significantly correlated to those at age of 6. Conclusions: Prenatal PTS exposure increases CG methylation contents of immune genes, such as LMO2 and IL-10, which significantly retained from newborn stage to 6 years of age and correlated to development of childhood asthma. Modulation of the LMO2 and IL-10 CG methylation and/or their gene expression may provide a regimen for early prevention of PTS-associated childhood asthma. Descriptor number: 1.10 Asthma Mediators. Scientific Knowledge on the Subject: It has been better known that maternal tobacco smoke (MTS) has an impact on the offspring's asthma via epigenetic modification. Little is known about effects of paternal tobacco smoke (PTS) on the offspring's asthma and its prenatal epigenetic programming. What This Study Adds to the Field: Prenatal tobacco smoke (PTS) can program epigenetic modifications in certain genes, such as LMO2 and IL-10, and that these modifications are correlated to childhood asthma development. The higher the PTS exposure dose the higher the CG methylation levels are found. The combination of higher CG methylation levels of LMO2_E148, IL10_P325 and GSTM1_P266 corresponded to the highest risk of asthma. Measuring the DNA methylation levels of certain genes might help to predict high-risk populations for childhood asthma and provide a potential target to prevent the development of childhood asthma.
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Affiliation(s)
- Chih-Chiang Wu
- Department of Pediatrics, Po-Zen Hospital, Kaohsiung, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Te-Yao Hsu
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Jen-Chieh Chang
- Genomic and Proteomic Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Yu Ou
- Department of Obstetrics, Po-Zen Hospital, Kaohsiung, Taiwan
| | - Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chieh-An Liu
- Department of Pediatrics, Po-Zen Hospital, Kaohsiung, Taiwan
| | - Chih-Lu Wang
- Department of Pediatrics, Po-Zen Hospital, Kaohsiung, Taiwan
| | - Hau Chuang
- Genomic and Proteomic Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chie-Pein Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Kuender D Yang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan.,Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan.,Institute of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
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23
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Farzan N, Vijverberg SJ, Kabesch M, Sterk PJ, Maitland-van der Zee AH. The use of pharmacogenomics, epigenomics, and transcriptomics to improve childhood asthma management: Where do we stand? Pediatr Pulmonol 2018; 53:836-845. [PMID: 29493882 DOI: 10.1002/ppul.23976] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/01/2018] [Indexed: 01/11/2023]
Abstract
Asthma is a complex multifactorial disease and it is the most common chronic disease in children. There is a high variability in response to asthma treatment, even in patients with good adherence to maintenance treatment, and a correct inhalation technique. Distinct underlying disease mechanisms in childhood asthma might be the reason of this heterogeneity. A deeper knowledge of the underlying molecular mechanisms of asthma has led to the recent development of advanced and mechanism-based treatments such as biologicals. However, biologicals are recommended only for patients with specific asthma phenotypes who remain uncontrolled despite high dosages of conventional asthma treatment. One of the main unmet needs in their application is lack of clinically available biomarkers to individualize pediatric asthma management and guide treatment. Pharmacogenomics, epigenomics, and transcriptomics are three omics fields that are rapidly advancing and can provide tools to identify novel asthma mechanisms and biomarkers to guide treatment. Pharmacogenomics focuses on variants in the DNA, epigenomics studies heritable changes that do not involve changes in the DNA sequence but lead to alteration of gene expression, and transcriptomics investigates gene expression by studying the complete set of mRNA transcripts in a cell or a population of cells. Advances in high-throughput technologies and statistical tools together with well-phenotyped patient inclusion and collaborations between different centers will expand our knowledge of underlying molecular mechanisms involved in disease onset and progress. Furthermore, it could help to select and stratify appropriate therapeutic strategies for subgroups of patients and hopefully bring precision medicine to daily practice.
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Affiliation(s)
- Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
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24
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Kanagaratham C, Chiwara V, Ho B, Moussette S, Youssef M, Venuto D, Jeannotte L, Bourque G, de Sanctis JB, Radzioch D, Naumova AK. Loss of the zona pellucida-binding protein 2 (Zpbp2) gene in mice impacts airway hypersensitivity and lung lipid metabolism in a sex-dependent fashion. Mamm Genome 2018. [PMID: 29536159 DOI: 10.1007/s00335-018-9743-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The human chromosomal region 17q12-q21 is one of the best replicated genome-wide association study loci for childhood asthma. The associated SNPs span a large genomic interval that includes several protein-coding genes. Here, we tested the hypothesis that the zona pellucida-binding protein 2 (ZPBP2) gene residing in this region contributes to asthma pathogenesis using a mouse model. We tested the lung phenotypes of knock-out (KO) mice that carry a deletion of the Zpbp2 gene. The deletion attenuated airway hypersensitivity (AHR) in female, but not male, mice in the absence of allergic sensitization. Analysis of the lipid profiles of their lungs showed that female, but not male, KO mice had significantly lower levels of sphingosine-1-phosphate (S1P), very long-chain ceramides (VLCCs), and higher levels of long-chain ceramides compared to wild-type controls. Furthermore, in females, lung resistance following methacholine challenge correlated with lung S1P levels (Pearson correlation coefficient 0.57) suggesting a link between reduced AHR in KO females, Zpbp2 deletion, and S1P level regulation. In livers, spleens and blood plasma, however, VLCC, S1P, and sphingosine levels were reduced in both KO females and males. We also find that the Zpbp2 deletion was associated with gain of methylation in the adjacent DNA regions. Thus, we demonstrate that the mouse ortholog of ZPBP2 has a role in controlling AHR in female mice. Our data also suggest that Zpbp2 may act through regulation of ceramide metabolism. These findings highlight the importance of phospholipid metabolism for sexual dimorphism in AHR.
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Affiliation(s)
| | - Victoria Chiwara
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Bianca Ho
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sanny Moussette
- The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mina Youssef
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - David Venuto
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Lucie Jeannotte
- Département de Biologie moléculaire, Biochimie medicale & Pathologie, Faculté de médecine, Université Laval, Québec, QC, Canada.,Centre de recherche sur le cancer de l'Université Laval, CRCHU de Québec-Université Laval, L'Hôtel-Dieu de Québec, Québec, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Juan Bautista de Sanctis
- Institute of Immunology, Faculty of Medicine, Universidad Central de Venezuela, Sabana Grande, Caracas, Venezuela
| | - Danuta Radzioch
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada.,Infectious Diseases and Immunity in Global Health Program (IDIGH), The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Anna K Naumova
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,The Research Institute of the McGill University Health Centre, Montreal, QC, Canada. .,Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada.
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25
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Ho B, Greenlaw K, Al Tuwaijri A, Moussette S, Martínez F, Giorgio E, Brusco A, Ferrero GB, Linhares ND, Valadares ER, Svartman M, Kalscheuer VM, Rodríguez Criado G, Laprise C, Greenwood CMT, Naumova AK. X chromosome dosage and presence of SRY shape sex-specific differences in DNA methylation at an autosomal region in human cells. Biol Sex Differ 2018; 9:10. [PMID: 29463315 PMCID: PMC5819645 DOI: 10.1186/s13293-018-0169-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/31/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Sexual dimorphism in DNA methylation levels is a recurrent epigenetic feature in different human cell types and has been implicated in predisposition to disease, such as psychiatric and autoimmune disorders. To elucidate the genetic origins of sex-specific DNA methylation, we examined DNA methylation levels in fibroblast cell lines and blood cells from individuals with different combinations of sex chromosome complements and sex phenotypes focusing on a single autosomal region--the differentially methylated region (DMR) in the promoter of the zona pellucida binding protein 2 (ZPBP2) as a reporter. RESULTS Our data show that the presence of the sex determining region Y (SRY) was associated with lower methylation levels, whereas higher X chromosome dosage in the absence of SRY led to an increase in DNA methylation levels at the ZPBP2 DMR. We mapped the X-linked modifier of DNA methylation to the long arm of chromosome X (Xq13-q21) and tested the impact of mutations in the ATRX and RLIM genes, located in this region, on methylation levels. Neither ATRX nor RLIM mutations influenced ZPBP2 methylation in female carriers. CONCLUSIONS We conclude that sex-specific methylation differences at the autosomal locus result from interaction between a Y-linked factor SRY and at least one X-linked factor that acts in a dose-dependent manner.
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Affiliation(s)
- Bianca Ho
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Abeer Al Tuwaijri
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Sanny Moussette
- The Research Institute of the McGill University Health Centre (MUHC), 1001 Decarie Blvd., Bloc E, Room EM03226, Montreal, Quebec, H4A 3J1, Canada
| | - Francisco Martínez
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, 46026, Valencia, Spain
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, 10126, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126, Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy
| | | | - Natália D Linhares
- Setor de Citogenética, Laboratório Central do Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eugênia R Valadares
- Departamento de Propedêutica Complementar, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Ambulatório de Erros Inatos do Metabolismo, Hospital das Clínicas da Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marta Svartman
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Centre intégré universitaire de santé et services sociaux du Saguenay, Lac-Saint-Jean, Saguenay, Quebec, Canada
- Centre de santé et de services sociaux de Chicoutimi, Saguenay, Québec, Canada
| | - Celia M T Greenwood
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Research Institute, Montréal, Quebec, Canada
- Departments of Oncology and Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Anna K Naumova
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
- The Research Institute of the McGill University Health Centre (MUHC), 1001 Decarie Blvd., Bloc E, Room EM03226, Montreal, Quebec, H4A 3J1, Canada.
- Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada.
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26
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Choleris E, Galea LAM, Sohrabji F, Frick KM. Sex differences in the brain: Implications for behavioral and biomedical research. Neurosci Biobehav Rev 2018; 85:126-145. [PMID: 29287628 PMCID: PMC5751942 DOI: 10.1016/j.neubiorev.2017.07.005] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 07/16/2017] [Indexed: 01/11/2023]
Abstract
Biological differences between males and females are found at multiple levels. However, females have too often been under-represented in behavioral neuroscience research, which has stymied the study of potential sex differences in neurobiology and behavior. This review focuses on the study of sex differences in the neurobiology of social behavior, memory, emotions, and recovery from brain injury, with particular emphasis on the role of estrogens in regulating forebrain function. This work, presented by the authors at the 2016 meeting of the International Behavioral Neuroscience Society, emphasizes varying approaches from several mammalian species in which sex differences have not only been documented, but also become the focus of efforts to understand the mechanistic basis underlying them. This information may provide readers with useful experimental tools to successfully address recently introduced regulations by granting agencies that either require (e.g. the National Institutes of Health in the United States and the Canadian Institutes of Health Research in Canada) or recommend (e.g. Horizon 2020 in Europe) the inclusion of both sexes in biomedical research.
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Affiliation(s)
- Elena Choleris
- Department of Psychology and Neuroscience Program, University of Guelph, MacKinnon Bldg. Room 4020, Guelph, ON N1G 2W1, Canada.
| | - Liisa A M Galea
- Department of Psychology, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T1Z3, Canada
| | - Farida Sohrabji
- Women's Health in Neuroscience Program, Department of Neuroscience and Experimental Therapeutics, Texas A&M HSC College of Medicine, Bryan, TX 77807, United States
| | - Karyn M Frick
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, United States
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27
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Hizawa N. Clinical approaches towards asthma and chronic obstructive pulmonary disease based on the heterogeneity of disease pathogenesis. Clin Exp Allergy 2017; 46:678-87. [PMID: 27009427 DOI: 10.1111/cea.12731] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Asthma and chronic obstructive pulmonary disease (COPD) are each heterogeneous disease classifications that include several clinical and pathophysiological phenotypes. This heterogeneity complicates characterization of each disease and, in some cases, hinders the selection of appropriate treatment. Therefore, in recent years, emphasis has been placed on improving our understanding of the various phenotypes of asthma and of COPD and identifying biomarkers for each phenotype. Likewise, the concept of the endotype has been gaining acceptance; an endotype is a disease subtype that is defined by unique or distinctive functional or pathophysiological mechanisms. Endotypes of asthma or COPD may be primarily characterized by increased susceptibility to type 2 inflammation, increased susceptibility to viral infections, bacterial colonization or impaired lung development. The 'Dutch hypothesis' is as follows: gene variants underlying particular endotypes interact with detrimental environmental stimuli (e.g. smoking, viral infection and air pollution) and contribute to the ultimate development of asthma, COPD or both. Novel approaches that involve multidimensional assessment should facilitate identification and management of the components that generate this heterogeneity. Ultimately, patients with chronic inflammatory lung diseases may be treated based on these endotypes as determined by the respective biomarkers that correspond to individual endotypes instead of on disease labels such as asthma, COPD or even asthma-COPD overlap syndrome (ACOS).
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Affiliation(s)
- N Hizawa
- Faculty of Medicine, Department of Pulmonary Medicine, University of Tsukuba, Tsukuba, Japan
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28
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Chesi A, Mitchell JA, Kalkwarf HJ, Bradfield JP, Lappe JM, Cousminer DL, Roy SM, McCormack SE, Gilsanz V, Oberfield SE, Hakonarson H, Shepherd JA, Kelly A, Zemel BS, Grant SF. A Genomewide Association Study Identifies Two Sex-Specific Loci, at SPTB and IZUMO3, Influencing Pediatric Bone Mineral Density at Multiple Skeletal Sites. J Bone Miner Res 2017; 32:1274-1281. [PMID: 28181694 PMCID: PMC5466475 DOI: 10.1002/jbmr.3097] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 01/21/2017] [Accepted: 01/25/2017] [Indexed: 12/27/2022]
Abstract
Failure to achieve optimal bone mineral accretion during childhood and adolescence results in subsequent suboptimal peak bone mass, contributing to osteoporosis risk later in life. To identify novel genetic factors that influence pediatric bone mass at discrete skeletal sites, we performed a sex-stratified genomewide association study of areal bone mineral density (BMD) measured by dual-energy X-ray absorptiometry at the 1/3 distal radius, spine, total hip, and femoral neck in a cohort of 933 healthy European American children. We took forward signals with p < 5 × 10-5 and minor allele frequency (MAF) >5% into an independent cohort of 486 European American children in search of replication. In doing so, we identified five loci that achieved genome wide significance in the combined cohorts (nearest genes: CPED1, IZUMO3, RBFOX1, SPBT, and TBPL2), of which the last four were novel and two were sex-specific (SPTB in females and IZUMO3 in males), with all of them yielding associations that were particularly strong at a specific skeletal site. Annotation of potential regulatory function, expression quantitative trait loci (eQTL) effects and pathway analyses identified several potential target genes at these associated loci. This study highlights the importance of sex-stratified analyses at discrete skeletal sites during the critical period of bone accrual, and identifies novel loci for further functional follow-up to pinpoint key genes and better understand the regulation of bone development in children. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Alessandra Chesi
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jonathan A. Mitchell
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Heidi J. Kalkwarf
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Jonathan P. Bradfield
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joan M. Lappe
- Division of Endocrinology, Department of Medicine, Creighton University, Omaha, NE, USA
| | - Diana L. Cousminer
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia
| | - Sani M. Roy
- Division of Endocrinology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shana E. McCormack
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Vicente Gilsanz
- Department of Radiology, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Sharon E. Oberfield
- Division of Pediatric Endocrinology, Diabetes, and Metabolism, Department of Pediatrics, Columbia University Medical Center, New York; NY, USA
| | - Hakon Hakonarson
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - John A. Shepherd
- Department of Radiology, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Kelly
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Babette S. Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Struan F.A. Grant
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Endocrinology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
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29
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Potaczek DP, Harb H, Michel S, Alhamwe BA, Renz H, Tost J. Epigenetics and allergy: from basic mechanisms to clinical applications. Epigenomics 2017; 9:539-571. [PMID: 28322581 DOI: 10.2217/epi-2016-0162] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Allergic diseases are on the rise in the Western world and well-known allergy-protecting and -driving factors such as microbial and dietary exposure, pollution and smoking mediate their influence through alterations of the epigenetic landscape. Here, we review key facts on the involvement of epigenetic modifications in allergic diseases and summarize and critically evaluate the lessons learned from epigenome-wide association studies. We show the potential of epigenetic changes for various clinical applications: as diagnostic tools, to assess tolerance following immunotherapy or possibly predict the success of therapy at an early time point. Furthermore, new technological advances such as epigenome editing and DNAzymes will allow targeted alterations of the epigenome in the future and provide novel therapeutic tools.
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Affiliation(s)
- Daniel P Potaczek
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany.,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN).,German Centre for Lung Research (DZL).,John Paul II Hospital, Krakow, Poland
| | - Hani Harb
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany.,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN).,German Centre for Lung Research (DZL)
| | - Sven Michel
- Secarna Pharmaceuticals GmbH & Co KG, Planegg, Germany
| | - Bilal Alashkar Alhamwe
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany.,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN).,German Centre for Lung Research (DZL)
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
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30
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Role of DNA methylation in expression control of the IKZF3-GSDMA region in human epithelial cells. PLoS One 2017; 12:e0172707. [PMID: 28241063 PMCID: PMC5328393 DOI: 10.1371/journal.pone.0172707] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 02/08/2017] [Indexed: 12/29/2022] Open
Abstract
Chromosomal region 17q12-q21 is associated with asthma and harbors regulatory polymorphisms that influence expression levels of all five protein-coding genes in the region: IKAROS family zinc finger 3 (Aiolos) (IKZF3), zona pellucida binding protein 2 (ZPBP2), ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3), and gasdermins A and B (GSDMA, GSDMB). Furthermore, DNA methylation in this region has been implicated as a potential modifier of the genetic risk of asthma development. To further characterize the effect of DNA methylation, we examined the impact of treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza-dC) that causes DNA demethylation, on expression and promoter methylation of the five 17q12-q21 genes in the human airway epithelium cell line NuLi-1, embryonic kidney epithelium cell line 293T and human adenocarcinoma cell line MCF-7. 5-aza-dC treatment led to upregulation of expression of GSDMA in all three cell lines. ZPBP2 was upregulated in NuLi-1, but remained repressed in 293T and MCF-7 cells, whereas ORMDL3 was upregulated in 293T and MCF-7 cells, but not NuLi-1. Upregulation of ZPBP2 and GSDMA was accompanied by a decrease in promoter methylation. Moreover, 5-aza-dC treatment modified allelic expression of ZPBP2 and ORMDL3 suggesting that different alleles may respond differently to treatment. We also identified a polymorphic CTCF-binding site in intron 1 of ORMDL3 carrying a CG SNP rs4065275 and determined its methylation level. The site’s methylation was unaffected by 5-aza-dC treatment in NuLi-1 cells. We conclude that modest changes (8–13%) in promoter methylation levels of ZPBP2 and GSDMA may cause substantial changes in RNA levels and that allelic expression of ZPBP2 and ORMDL3 is mediated by DNA methylation.
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31
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Abstract
PURPOSE OF REVIEW The goal of this review was to systematically analyze recent studies updating our knowledge on the role of epigenetic mechanisms in childhood asthma. RECENT FINDINGS A systematic literature search was conducted that identified 23 fresh articles published within the last 5 years reporting the results of human studies on the relationships between epigenetic modifications and childhood asthma or its/related phenotypes. In almost all these studies, meaningful associations between levels of epigenetic marks (DNA methylation and/or histone modifications) and pediatric asthma or its/related phenotypes have been observed. In addition, many studies identified by our screening analyzed those associations in the context of environmental factors, such as pollution, tobacco smoke, farming, or diet, showing in a huge majority a modifying effect of those exposures. SUMMARY The results of our systematic literature search provide a strong support for the role of epigenetic mechanisms in (mediating the effects of environmental exposure on) pediatric asthma. This knowledge may possibly be translated into diagnostic and/or therapeutic approaches.
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Tse SM, Rifas-Shiman SL, Coull BA, Litonjua AA, Oken E, Gold DR. Sex-specific risk factors for childhood wheeze and longitudinal phenotypes of wheeze. J Allergy Clin Immunol 2016; 138:1561-1568.e6. [PMID: 27246527 PMCID: PMC5083247 DOI: 10.1016/j.jaci.2016.04.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 04/05/2016] [Accepted: 04/13/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Although sexual dimorphism in wheeze and asthma prevalence are well documented, sex-specific risk factors for wheeze and longitudinal wheeze phenotypes have not been well elucidated. OBJECTIVE By using a large prebirth cohort, this study aimed to identify sex-specific risk factors for wheeze from birth through midchildhood and identify distinct longitudinal wheeze phenotypes and the sex-specific risk factors associated with these phenotypes. METHODS Mothers reported child wheeze symptoms over the past year approximately yearly on 9 occasions starting at age 1 year. We identified sex-specific predictors of wheeze, wheeze phenotypes, and sex-specific predictors of these phenotypes by using generalized estimating equations, latent class mixed models, and multinomial logistic analysis, respectively. RESULTS A total of 1623 children had information on wheeze at 1 or more time points. Paternal asthma was a stronger predictor of ever wheezing in boys (odds ratio [OR], 2.15; 95% CI, 1.74-2.66) than in girls (OR, 1.53; 95% CI, 1.19-1.96; P for sex by paternal asthma interaction = .03), whereas being black or Hispanic, birth weight for gestational age z score, and breast-feeding duration had stronger associations among girls. We identified 3 longitudinal wheeze phenotypes: never/infrequent wheeze (74.1%), early transient wheeze (12.7%), and persistent wheeze (13.1%). Compared with never/infrequent wheeze, maternal asthma, infant bronchiolitis, and atopic dermatitis were associated with persistent wheeze in both sexes, but paternal asthma was associated with persistent wheeze in boys only (OR, 4.27; 95% CI, 2.33-7.83; P for sex by paternal asthma interaction = .02), whereas being black or Hispanic was a predictor for girls only. CONCLUSION We identified sex-specific predictors of wheeze and longitudinal wheeze patterns, which might have important prognostic value and allow for a more personalized approach to wheeze and asthma treatment.
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Affiliation(s)
- Sze Man Tse
- Division of Respiratory Medicine, Department of Pediatrics, Sainte-Justine University Hospital Center and University of Montreal, Montreal, Quebec, Canada.
| | - Sheryl L Rifas-Shiman
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Mass
| | - Brent A Coull
- Department of Biostatistics, Harvard School of Public Health, Boston, Mass
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Mass
| | - Diane R Gold
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
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Petrus NCM, Henneman P, Venema A, Mul A, van Sinderen F, Haagmans M, Mook O, Hennekam RC, Sprikkelman AB, Mannens M. Cow's milk allergy in Dutch children: an epigenetic pilot survey. Clin Transl Allergy 2016; 6:16. [PMID: 27148440 PMCID: PMC4855719 DOI: 10.1186/s13601-016-0105-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/31/2016] [Indexed: 01/28/2023] Open
Abstract
Background Cow’s milk allergy (CMA) is a common disease in infancy. Early environmental factors are likely to contribute to CMA. It is known that epigenetic gene regulation can be altered by environmental factors. We have set up a proof of concept study, aiming to detect epigenetic associations specific with CMA. Methods We studied children from the Dutch EuroPrevall birth cohort study (N = 20 CMA, N = 23 controls, N = 10 tolerant boys), age and gender matched. CMA was challenge proven. Bisulfite converted DNA (blood) was analyzed using the 450K infinium DNA-methylation array. Four groups (combined, girls, boys and tolerant boys) were analysed between CMA and controls. Statistical analysis and pathway-analysis were performed in “R” using IMA, Minfi and the global-test package. Differentially methylated regions in DHX58, ZNF281, EIF42A and HTRA2 genes were validated by quantitative amplicon sequencing (ROCHE 454®). Results General hypermethylation was found in the CMA group compared to control children, while this effect was absent in the tolerant group. Methylation differences were, among others, found in regions of DHX58, ZNF281, EIF42A and HTRA2 genes. Several of these genes are known to be involved in immunological pathways and associated with other allergies. Conclusion We show that epigenetic associations are involved in CMA. Although, the statistical power of our study is limited and our sample was based on whole blood, we were still able to detect feasible loci and pathways. Therefore our findings might contribute to future diagnostic or therapeutic interventions for specific CMA. Further studies have to confirm the findings of our study.
Electronic supplementary material The online version of this article (doi:10.1186/s13601-016-0105-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicole C M Petrus
- Department of Pediatric Respiratory Medicine and Allergy, H7-270, Emma Children's Hospital Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, DNA-Diagnostics Laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, DNA-Diagnostics Laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Adri Mul
- Department of Clinical Genetics, DNA-Diagnostics Laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Femke van Sinderen
- Department of Clinical Genetics, DNA-Diagnostics Laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Martin Haagmans
- Department of Clinical Genetics, DNA-Diagnostics Laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Olaf Mook
- Department of Clinical Genetics, DNA-Diagnostics Laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Raoul C Hennekam
- Department of Pediatric Respiratory Medicine and Allergy, H7-270, Emma Children's Hospital Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Department of Clinical Genetics, DNA-Diagnostics Laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Aline B Sprikkelman
- Department of Pediatric Respiratory Medicine and Allergy, H7-270, Emma Children's Hospital Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marcel Mannens
- Department of Clinical Genetics, DNA-Diagnostics Laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
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Cousminer DL, Widén E, Palmert MR. The genetics of pubertal timing in the general population: recent advances and evidence for sex-specificity. Curr Opin Endocrinol Diabetes Obes 2016; 23:57-65. [PMID: 26574646 PMCID: PMC4734379 DOI: 10.1097/med.0000000000000213] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW This article overviews advances in the genetics of puberty based on studies in the general population, describes evidence for sex-specific genetic effects on pubertal timing, and briefly reviews possible mechanisms mediating sexually dimorphic genetic effects. RECENT FINDINGS Pubertal timing is highly polygenic, and many loci are conserved among ethnicities. A number of identified loci underlie both pubertal timing and related traits such as height and BMI. It is increasingly apparent that understanding the factors modulating the onset of puberty is important because the timing of this developmental stage is associated with a wider range of adult health outcomes than previously appreciated. Although most of the genetic effects underlying the timing of puberty are common between boys and girls, some effects show sex-specificity and many are epigenetically modulated. Several potential mechanisms, including hormone-independent ones, may be responsible for observed sex differences. SUMMARY Studies of pubertal timing in the general population have provided new knowledge about the genetic architecture of this complex trait. Increasing attention paid to sex-specific effects may provide key insights into the sexual dimorphism in pubertal timing and even into the associations between puberty and adult health risks by identifying common underlying biological pathways.
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Affiliation(s)
- Diana L. Cousminer
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elisabeth Widén
- Institute for Molecular Medicine, Finland, University of Helsinki, Helsinki, Finland
| | - Mark R. Palmert
- Division of Endocrinology, the Hospital for Sick Children
- The Departments of Pediatrics and Physiology, University of Toronto, Canada
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Raghavan D, Jain R. Increasing awareness of sex differences in airway diseases. Respirology 2015; 21:449-59. [PMID: 26677803 DOI: 10.1111/resp.12702] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 07/21/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022]
Abstract
There is growing epidemiologic data demonstrating sex differences with respect to prevalence and progression of airway diseases, including asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF) and non-CF-related bronchiectasis. In asthma, for example, young boys have increased exacerbations and higher morbidity than girls which distinctly reverses after adolescence and into adulthood. In COPD, a disease that was historically considered an illness of men, the number of women dying per year is now greater than in men. Finally, women with CF-related bronchiectasis have a decreased median life expectancy relative to men and a higher risk of respiratory infections despite equal prevalence of the disease. A number of studies now exist demonstrating mechanisms behind these sex differences, including influences of genetic predisposition, sex hormones and comorbidities. The notable sex disparity has potential diagnostic, therapeutic and prognostic implications and for the practicing respiratory or general physician, a familiarity with these distinctions may augment effective management of patients with airway diseases. This review seeks to concisely summarize the data regarding gender-based differences in airway diseases, outline the current understanding of contributing factors and discuss therapeutic implications for clinicians.
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Affiliation(s)
- Deepa Raghavan
- Division of Pulmonary and Critical Care, Department of Medicine, University of Arkansas Medical Sciences, Little Rock, Arkansas, USA
| | - Raksha Jain
- Division of Pulmonary and Critical Care, Department of Medicine, University of Texas Southwestern, Dallas, Texas, USA
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Al Tuwaijri A, Gagné-Ouellet V, Madore AM, Laprise C, Naumova AK. Local genotype influences DNA methylation at two asthma-associated regions, 5q31 and 17q21, in a founder effect population. J Med Genet 2015; 53:232-41. [PMID: 26671913 DOI: 10.1136/jmedgenet-2015-103313] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/14/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Two asthma-associated regions 17q12-q21 and 5q31.1 harbour genes that show strong effect of genotype on expression levels. DNA methylation has an important role in gene regulation; therefore, we examined DNA methylation at promoters of 12 genes from 5q31 and 17q12-q21 regions. Our goal was to determine whether DNA methylation was associated with predisposition to asthma and whether such a relationship was independent from genetic association. METHODS Using sodium bisulfite sequencing and pyrosequencing methylation assays, we examined the effect of genotype on DNA methylation in peripheral blood cells from individuals from the Saguenay-Lac-Saint-Jean asthma familial collection and lymphoblastoid cell lines. RESULTS The local genotype influenced methylation levels of solute carrier family 22 (organic 3 cation/carnitine transporter) member 5 (SLC22A5), zona pellucida binding protein 2 (ZPBP2) and gasdermin A (GSDMA) promoter regions. The genotype had a dominant effect on ZPBP2 and GSDMA methylation with lower methylation levels in individuals that carry the asthma-predisposing alleles. Males also had lower methylation at the ZPBP2 promoter than females. We did not observe an effect of asthma status that would be independent of the genotype and the sex effects in the GSDMA, ZPBP2 and SLC22A5 regions; however, GSDMA and ZPBP2 data were suggestive of interaction between asthma and methylation levels in females and SLC22A5 in males. CONCLUSIONS The local genotype influences methylation levels at SLC22A5 and ZPBP2 promoters independently of the asthma status. Further studies are necessary to confirm the relationship between GSDMA-ZPBP2 and SLC22A5 methylation and asthma in females and males separately.
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Affiliation(s)
- Abeer Al Tuwaijri
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Valérie Gagné-Ouellet
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Anne-Marie Madore
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Anna K Naumova
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada Department of Obstetrics and Gynecology, McGill University, Montreal, Quebec, Canada The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
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García-Sánchez A, Isidoro-García M, García-Solaesa V, Sanz C, Hernández-Hernández L, Padrón-Morales J, Lorente-Toledano F, Dávila I. Genome-wide association studies (GWAS) and their importance in asthma. Allergol Immunopathol (Madr) 2015; 43:601-8. [PMID: 25433770 DOI: 10.1016/j.aller.2014.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/21/2014] [Indexed: 12/16/2022]
Abstract
Asthma is a complex disease determined by the interaction of different genes and environmental factors. The first genetic investigations in asthma were candidate gene association studies and linkage studies. In recent years research has focused on association studies that scan the entire genome without any prior conditioning hypothesis: the so-called genome-wide association studies (GWAS). The first GWAS was published in 2007, and described a new locus associated to asthma in chromosome 17q12-q21, involving the ORMDL3, GSDMB and ZPBP2 genes (a description of the genes named in the manuscript are listed in Table 1). None of these genes would have been selected in a classical genetic association study since it was not known they could be implicated in asthma. To date, a number of GWAS studies in asthma have been made, with the identification of about 1000 candidate genes. Coordination of the different research groups in international consortiums and the application of new technologies such as new generation sequencing will help discover new implicated genes and improve our understanding of the molecular mechanisms underlying the disease.
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Affiliation(s)
- A García-Sánchez
- Departamento de Pediatría, Universidad de Salamanca, Spain; Grupo de Alergia, Instituto Biosanitario de Salamanca (IBSAL), Spain.
| | - M Isidoro-García
- Grupo de Alergia, Instituto Biosanitario de Salamanca (IBSAL), Spain; Servicio de Bioquímica Clínica, Complejo Asistencial Universitario de Salamanca, Spain; Departamento de Medicina, Universidad de Salamanca, Spain
| | - V García-Solaesa
- Grupo de Alergia, Instituto Biosanitario de Salamanca (IBSAL), Spain; Servicio de Bioquímica Clínica, Complejo Asistencial Universitario de Salamanca, Spain
| | - C Sanz
- Grupo de Alergia, Instituto Biosanitario de Salamanca (IBSAL), Spain; Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
| | - L Hernández-Hernández
- Departamento de Pediatría, Universidad de Salamanca, Spain; Grupo de Alergia, Instituto Biosanitario de Salamanca (IBSAL), Spain
| | - J Padrón-Morales
- Servicio de Bioquímica Clínica, Complejo Asistencial Universitario de Salamanca, Spain
| | - F Lorente-Toledano
- Departamento de Pediatría, Universidad de Salamanca, Spain; Grupo de Alergia, Instituto Biosanitario de Salamanca (IBSAL), Spain; Servicio de Pediatría, Hospital Universitario de Salamanca, Spain
| | - I Dávila
- Departamento de Pediatría, Universidad de Salamanca, Spain; Grupo de Alergia, Instituto Biosanitario de Salamanca (IBSAL), Spain; Servicio de Alergia, Complejo Asistencial Universitario de Salamanca, Spain
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Tse SM, Coull BA, Sordillo JE, Datta S, Gold DR. Gender- and age-specific risk factors for wheeze from birth through adolescence. Pediatr Pulmonol 2015; 50:955-62. [PMID: 25348842 PMCID: PMC4800823 DOI: 10.1002/ppul.23113] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/29/2014] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND OBJECTIVE Cross-sectional gender differences in wheeze are well documented, but few studies have examined the gender-specific risk factors for wheeze longitudinally. This study aims to identify gender- and age-specific risk factors for wheeze from birth through adolescence. METHODS The incidence of wheeze was ascertained every 6 months through age 14 years in a birth cohort consisting of 499 children with a parental history of atopy. Gender- and age-specific risk factors were identified through generalized estimating equations. RESULTS A total of 454 (91.0%) and 351 (70.3%) children were followed past age 7 and 13 years, respectively. Maternal asthma was a risk factor for wheeze in girls (OR = 2.05, 95% CI 1.44-2.91, P < 0.0001) and boys (OR = 1.79, 1.29-2.48, P = 0.0004) and had a similar effect on wheeze throughout the ages. Paternal asthma (OR = 1.83, 1.38-2.57, P = 0.0005) and infant bronchiolitis (OR = 2.15, 1.47-3.14, P < 0.0001) were risk factors for boys only, with similar effects throughout the ages. CONCLUSION Using a prospective cohort, we identified gender- and age-specific risk factors for wheeze. The identification of gender-specific early life risk factors may allow for timely interventions and a more personalized approach to the treatment of asthma.
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Affiliation(s)
- Sze Man Tse
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Pediatrics, Sainte-Justine University Hospital Center, Montreal, Quebec, Canada
| | - Brent A Coull
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusett
| | - Joanne E Sordillo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Soma Datta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Diane R Gold
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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Abstract
Recently, a new research agenda emphasizing interactions between social factors and health has emerged. The term social determinant of health often refers to any nonmedical factor directly influencing health. Health across the life span is strongly and adversely affected by social disadvantage. Research in epigenetics indicates that alterations in DNA methylation may provide a causal link between social adversity and health disparity. Likewise, accelerated loss of telomeres is correlated with chronic stress. Research is still required to develop an understanding of the role of epigenetics and perturbed telomere function in linking social adversity with health outcome.
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Affiliation(s)
- Daniel A Notterman
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Colter Mitchell
- Institute of Social Research, University of Michigan-Ann Arbor, 426 Thompson Street, 2264 ISR, Ann Arbor, MI 48106, USA
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Gagné-Ouellet V, Guay SP, Boucher-Lafleur AM, Bouchard L, Laprise C. DNA methylation signature of interleukin 1 receptor type II in asthma. Clin Epigenetics 2015; 7:80. [PMID: 26246860 PMCID: PMC4526162 DOI: 10.1186/s13148-015-0114-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/13/2015] [Indexed: 12/25/2022] Open
Abstract
Interleukin 1 and its receptors are associated with allergic diseases such as asthma. In the present study, we measured DNA methylation at the IL1R1 and IL1R2 gene loci and assessed for associations with asthma-related phenotypes and gene expressions. We found that asthmatic and atopic individuals have higher IL1R2 promoter DNA methylation than control subjects. Additionally, we observed a negative correlation between DNA methylation at the IL1R2 promoter and IL1R2 mRNA expression. These results suggest for the first time that IL1R2 promoter DNA methylation is associated with its gene repression in allergic diseases such as asthma.
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Affiliation(s)
- Valérie Gagné-Ouellet
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC Canada
| | - Simon-Pierre Guay
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC Canada ; ECOGENE-21 and Lipid Clinic, Hôpital de Chicoutimi, Saguenay, QC Canada
| | | | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC Canada ; ECOGENE-21 and Lipid Clinic, Hôpital de Chicoutimi, Saguenay, QC Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC Canada
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Guibas GV, Megremis S, West P, Papadopoulos NG. Contributing factors to the development of childhood asthma: working toward risk minimization. Expert Rev Clin Immunol 2015; 11:721-35. [PMID: 25873298 DOI: 10.1586/1744666x.2015.1035649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Asthma is the most common chronic disease in childhood, and considerable research has been undertaken to find ways to prevent its development and reduce its prevalence. For such interventions to be successful, risk factors for asthma emergence should be identified and clearly defined. Data are robust for some of them, including atopy, viral infections and exposure to airborne irritants, whereas it is less conclusive for others, such as aeroallergen exposure and bacterial infections. Several interventions for asthma prevention, including avoidance and pharmacotherapy, have been attempted. However, most of them have furnished equivocal results. Various issues hinder the establishment of risk factors for asthma development and reduce the effectiveness of interventions, including the complexity of the disease and the fluidity of the developing systems in childhood. In this review, we revisit the evidence on pediatric asthma risk factors and prevention and discuss issues that perplex this field.
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Affiliation(s)
- George V Guibas
- Centre for Pediatrics and Child Health, Institute of Human Development, University of Manchester, Manchester, UK
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Abstract
It is now becoming widely recognized that there are important sex differences in disease. These include rates of disease incidence, symptoms and age of onset. These differences between the sexes can be seen as a subset of the more general phenomenon of sexual dimorphism of quantitative phenotypes. From a genetic point of view, this is paradoxical, since the vast majority of genetic material is shared between the sexes. How can males and females differ in so many ways and yet have a common genetic code? Traditionally, the modifying action of hormones has been offered as a solution to this paradox, but experiments disentangling the effects of hormones and sex-chromosomes have shown that this cannot be the sole explanation. In this review, I outline current ideas about the evolutionary origins of sex differences in phenotypes, with a particular focus on how sex differences in disease can arise. I also discuss how sex differences in themselves can generate new risk factors for disease, in effect becoming a new environmental factor, as well as briefly reviewing more general evidence for sexually antagonistic selection and genetic variation within humans. Taking an evolutionary view on sex differences in disease provides an opportunity for greater understanding of mechanisms of disease and as such provides a clear motivation for clinicians to explore how therapies may be tailored to the individual in a sex-dependent way.
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Abstract
It is generally agreed that environmental factors trigger the onset and cause flares of inflammatory bowel disease. Although we have learned much about genetic susceptibility factors of inflammatory bowel disease in recent years, our knowledge on these environmental factors is limited. The sum of all environmental factors a human is exposed to during lifetime has been termed the exposome. The challenge of investigating the exposome is discussed in this overview. The environmental exposure of a subject causes changes in the intestinal microbiota and subsequently changes the epigenetic imprinting of the mucosa and the associated immune system. Some relevant environmental factors have been investigated in recent years in inflammatory bowel disease and other (auto)inflammatory disease. These factors can be categorized in air pollution, diet, drugs, stress, infections, water pollution, food additives, and lifestyle. Examples from those categories and their potential pathophysiological mechanism are discussed.
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Early origins of chronic obstructive lung diseases across the life course. Eur J Epidemiol 2014; 29:871-85. [PMID: 25537319 DOI: 10.1007/s10654-014-9981-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/06/2014] [Indexed: 12/12/2022]
Abstract
Chronic obstructive lung diseases, like asthma and chronic obstructive pulmonary disease, have high prevalences and are a major public health concern. Chronic obstructive lung diseases have at least part of their origins in early life. Exposure to an adverse environment during critical periods in early life might lead to permanent developmental adaptations which results in impaired lung growth with smaller airways and lower lung volume, altered immunological responses and related inflammation, and subsequently to increased risks of chronic obstructive lung diseases throughout the life course. Various pathways leading from early life factors to respiratory health outcomes in later life have been studied, including fetal and early infant growth patterns, preterm birth, maternal obesity, diet and smoking, children's diet, allergen exposure and respiratory tract infections, and genetic susceptibility. Data on potential adverse factors in the embryonic and preconception period and respiratory health outcomes are scarce. Also, the underlying mechanisms how specific adverse exposures in the fetal and early postnatal period lead to chronic obstructive lung diseases in later life are not yet fully understood. Current studies suggest that interactions between early environmental exposures and genetic factors such as changes in DNA-methylation and RNA expression patterns may explain the early development of chronic obstructive lung diseases. New well-designed epidemiological studies are needed to identify specific critical periods and to elucidate the mechanisms underlying the development of chronic obstructive lung disease throughout the life course.
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Lockett GA, Patil VK, Soto-Ramírez N, Ziyab AH, Holloway JW, Karmaus W. Epigenomics and allergic disease. Epigenomics 2014; 5:685-99. [PMID: 24283882 DOI: 10.2217/epi.13.68] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Allergic disease development is affected by both genes and the environment, and epigenetic mechanisms are hypothesized to mediate these environmental effects. In this article, we discuss the link between the environment, DNA methylation and allergic disease, as well as questions of causality inherent to analyses of DNA methylation. From the practical side, we describe characteristics of allergic phenotypes and contrast different epidemiologic study designs used in epigenetic research. We examine methodological considerations, how best to conduct preprocessing and analysis of DNA methylation data sets, and the latest methods, technologies and discoveries in this rapidly advancing field. DNA methylation and other epigenetic marks are firmly entwined with allergic disease, a link that may hold the basis for future allergic disease diagnosis and treatment.
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Affiliation(s)
- Gabrielle A Lockett
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
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Gilks WP, Abbott JK, Morrow EH. Sex differences in disease genetics: evidence, evolution, and detection. Trends Genet 2014; 30:453-63. [DOI: 10.1016/j.tig.2014.08.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/27/2014] [Accepted: 08/27/2014] [Indexed: 12/13/2022]
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Hong X, Wang X. Epigenetics and development of food allergy (FA) in early childhood. Curr Allergy Asthma Rep 2014; 14:460. [PMID: 25096861 DOI: 10.1007/s11882-014-0460-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review aims to highlight the latest advance on epigenetics in the development of food allergy (FA) and to offer future perspectives. FA, a condition caused by an immunoglobulin (Ig) E-mediated hypersensitivity reaction to food, has emerged as a major clinical and public health problem worldwide in light of its increasing prevalence, potential fatality, and significant medical and economic impact. Current evidence supports that epigenetic mechanisms are involved in immune regulation and that the epigenome may represent a key "missing piece" of the etiological puzzle for FA. There are a growing number of population-based epigenetic studies on allergy-related phenotypes, mostly focused on DNA methylation. Previous studies mostly applied candidate-gene approaches and have demonstrated that epigenetic marks are associated with multiple allergic diseases and/or with early-life exposures relevant to allergy development (such as early-life smoking exposure, air pollution, farming environment, and dietary fat). Rapid technological advancements have made unbiased genome-wide DNA methylation studies highly feasible, although there are substantial challenge in study design, data analyses, and interpretation of findings. In conclusion, epigenetics represents both an important knowledge gap and a promising research area for FA. Due to the early onset of FA, epigenetic studies of FA in prospective birth cohorts have the potential to better understand gene-environment interactions and underlying biological mechanisms in FA during critical developmental windows (preconception, in utero, and early childhood) and may lead to new paradigms in the diagnosis, prevention, and management of FA and provide novel targets for future drug discovery and therapies for FA.
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Affiliation(s)
- Xiumei Hong
- Center on the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, E4132, Baltimore, MD, 21205-2179, USA
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Abstract
PURPOSE OF REVIEW Epigenetic mechanisms such as DNA methylation, histone modification and microRNA control the accessibility of the genome and manage gene transcription in response to the environment in a heritable fashion. Recent evidence suggests that these mechanisms play a role in allergy and asthma. RECENT FINDINGS Here, we give an overview on recent developments in the field of asthma and allergy epigenetics with a special focus on the role of DNA methylation in these diseases, where finally, first pilot studies investigating differences in methylation pattern in patients have been published. Although these studies have to be interpreted with caution, it seems that methylation is affected by environmental stimuli such as prenatal smoke exposure and farming environments, whereas asthma status is associated with change in methylation in early childhood. SUMMARY Early stage data from population studies indicate a role of methylation differences in asthma and allergy, whereas the exact impact of these epigenetic mechanisms on disease development needs to be elucidated further.
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Abstract
Immune-mediated pulmonary diseases are a group of diseases that resulted from immune imbalance initiated by allergens or of unknown causes. Inflammatory responses without restrictions cause tissue damage and remodeling, which leads to airway hyperactivity, destruction of alveolar architecture, and a resultant loss of lung function. Epigenetic mechanisms have been demonstrated to be involved in inflammation, autoimmunity, and cancer. Recent studies have identified that epigenetic changes also regulate molecular pathways in immune-mediated lung diseases. Aberrant DNA methylation status, dysregulation of histone modifications, as well as altered microRNAs expression could change transcription activity of genes involved in the development of immune-mediated pulmonary diseases, which contributes to skewed differentiation of T cells and proliferation and activation of myofibroblasts, leading to overproduction of inflammatory cytokines and excessive accumulation of extracellular matrix, respectively. Aside from this, epigenetics also explains how environmental exposure influence on gene transcription without genetic changes. It acts as a mediator of the interaction between environmental factors and genetic factors. Identification of the abnormal epigenetic marks in diseases provides novel biomarkers for prediction and diagnosis and affords novel therapeutic targets for those difficult clinical problems, such as steroid-resistance and rapidly progressing fibrosis. In this review, we summarized the latest experimental and translational epigenetic studies in immune-mediated pulmonary diseases, including asthma, idiopathic pulmonary fibrosis, tuberculosis, sarcoidosis, and silicosis.
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Bégin P, Nadeau KC. Epigenetic regulation of asthma and allergic disease. Allergy Asthma Clin Immunol 2014; 10:27. [PMID: 24932182 PMCID: PMC4057652 DOI: 10.1186/1710-1492-10-27] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/18/2014] [Indexed: 01/18/2023] Open
Abstract
Epigenetics of asthma and allergic disease is a field that has expanded greatly in the last decade. Previously thought only in terms of cell differentiation, it is now evident the epigenetics regulate many processes. With T cell activation, commitment toward an allergic phenotype is tightly regulated by DNA methylation and histone modifications at the Th2 locus control region. When normal epigenetic control is disturbed, either experimentally or by environmental exposures, Th1/Th2 balance can be affected. Epigenetic marks are not only transferred to daughter cells with cell replication but they can also be inherited through generations. In animal models, with constant environmental pressure, epigenetically determined phenotypes are amplified through generations and can last up to 2 generations after the environment is back to normal. In this review on the epigenetic regulation of asthma and allergic diseases we review basic epigenetic mechanisms and discuss the epigenetic control of Th2 cells. We then cover the transgenerational inheritance model of epigenetic traits and discuss how this could relate the amplification of asthma and allergic disease prevalence and severity through the last decades. Finally, we discuss recent epigenetic association studies for allergic phenotypes and related environmental risk factors as well as potential underlying mechanisms for these associations.
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Affiliation(s)
- Philippe Bégin
- Allergy, Immunology, and Rheumatology Division, Stanford University, 269 Campus Drive, Stanford, California, USA
| | - Kari C Nadeau
- Allergy, Immunology, and Rheumatology Division, Stanford University, 269 Campus Drive, Stanford, California, USA
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