1
|
Zhang L, Xu Y, Li X, Yang F, Wang C, Yu C. Multivitamin consumption and childhood asthma: a cross-sectional study of the NHANES database. BMC Pediatr 2024; 24:84. [PMID: 38297283 PMCID: PMC10829257 DOI: 10.1186/s12887-024-04540-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Dietary intakes of vitamins are associated with asthma. However, previous studies mainly explored the association between a single vitamin intake and asthma, which did not take the multivitamins into consideration. Herein, this study aims to explore the overall effect of dietary multivitamins consumption on childhood asthma. METHODS Data of children and adolescents (aged 2-17 years old) were extracted from the National Health and Nutrition Examination Survey (NHANES) database in 2015-2018 in this cross-sectional study. Weighted univariate logistic regression analysis was used to screen covariates. The association between multivitamins (including vitamin A, C, D, E, B1, B2, B6, B12, K, niacin, folic acid, and choline) and childhood asthma was explored using univariate and multivariate logistic regression analyses. The evaluation indexes were odds ratio (OR) and 95% confidence interval (CI). We further introduced the Bayesian kernel machine regression (BKMR) to assess the joint effect of the twelve vitamins on childhood asthma, the impact of an individual vitamin as part of a vitamin mixture, and the potential interactions among different vitamins. RESULTS Among 4,715 eligible children and adolescents, 487 (10.3%) had asthma. After adjusting for covariates including race, family history of asthma, pregnant smoking, BMI Z-score, energy intake, breast feeding, and low birth weight, we found that for each 1-unit increase in vitamin K consumption, the odds of childhood asthma decreased 0.99 (P=0.028). The overall effect analysis reported a trend of negative relationship between the multivitamins and childhood asthma, especially at the 75th percentile and over. According to the BKMR models, when other vitamins are fixed at the median level, the odds of childhood asthma increased along with the elevated vitamin D (VD) and vitamin B2 (VB2), whereas along with the depressed vitamin C (VC). In addition, no potential interaction has been found between every two vitamins of multivitamins on childhood asthma. CONCLUSION Among children and adolescents who have high-risk of asthma, it may be beneficial to increase dietary consumption of multivitamins. Our findings recommended that children and adolescents should increase the intake of VC-rich foods, whereas control the dietary consumption of VD and VB2 in daily life.
Collapse
Affiliation(s)
- Li Zhang
- Department of Pediatrics, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401147, P.R. China
| | - Yali Xu
- Department of Pediatric Center, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, P.R. China
| | - Xuemei Li
- Department of Pediatrics, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401147, P.R. China
| | - Fan Yang
- Department of Pediatrics, The Fifth People's Hospital of Chongqing, No.24 Renji Road, Nanan District, Chongqing, 400062, P.R. China
| | - Chengxiu Wang
- Department of Pediatrics, The Fifth People's Hospital of Chongqing, No.24 Renji Road, Nanan District, Chongqing, 400062, P.R. China
| | - Chunmei Yu
- Department of Pediatrics, The Fifth People's Hospital of Chongqing, No.24 Renji Road, Nanan District, Chongqing, 400062, P.R. China.
| |
Collapse
|
2
|
Kim S, Qin Y, Park HJ, Yue M, Xu Z, Forno E, Chen W, Celedón JC. Methyl-TWAS: A powerful method for in silico transcriptome-wide association studies (TWAS) using long-range DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566586. [PMID: 38014125 PMCID: PMC10680683 DOI: 10.1101/2023.11.10.566586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
In silico transcriptome-wide association studies (TWAS) are commonly used to test whether expression of specific genes is linked to a complex trait. However, genotype-based in silico TWAS such as PrediXcan, exhibit low prediction accuracy for a majority of genes because genotypic data lack tissue- and disease-specificity and are not affected by the environment. Because methylation is tissue-specific and, like gene expression, can be modified by environment or disease status, methylation should predict gene expression with more accuracy than SNPs. Therefore, we propose Methyl-TWAS, the first approach that utilizes long-range methylation markers to impute gene expression for in silico TWAS through penalized regression. Methyl-TWAS 1) predicts epigenetically regulated/associated expression (eGReX), which incorporates tissue-specific expression and both genetically- (GReX) and environmentally-regulated expression to identify differentially expressed genes (DEGs) that could not be identified by genotype-based methods; and 2) incorporates both cis- and trans- CpGs, including various regulatory regions to identify DEGs that would be missed using cis- methylation only. Methyl-TWAS outperforms PrediXcan and two other methods in imputing gene expression in the nasal epithelium, particularly for immunity-related genes and DEGs in atopic asthma. Methyl-TWAS identified 3,681 (85.2%) of the 4,316 DEGs identified in a previous TWAS of atopic asthma using measured expression, while PrediXcan could not identify any gene. Methyl-TWAS also outperforms PrediXcan for expression imputation as well as in silico TWAS in white blood cells. Methyl-TWAS is a valuable tool for in silico TWAS, leveraging a growing body of publicly available genome-wide DNA methylation data for a variety of human tissues.
Collapse
Affiliation(s)
- Soyeon Kim
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yidi Qin
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hyun Jung Park
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Molin Yue
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhongli Xu
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juan C. Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
3
|
Kim S, Xu Z, Forno E, Qin Y, Park HJ, Yue M, Yan Q, Manni ML, Acosta-Pérez E, Canino G, Chen W, Celedón JC. Cis- and trans-eQTM analysis reveals novel epigenetic and transcriptomic immune markers of atopic asthma in airway epithelium. J Allergy Clin Immunol 2023; 152:887-898. [PMID: 37271320 PMCID: PMC10592527 DOI: 10.1016/j.jaci.2023.05.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/03/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Expression quantitative trait methylation (eQTM) analyses uncover associations between DNA methylation markers and gene expression. Most eQTM analyses of complex diseases have focused on cis-eQTM pairs (within 1 megabase). OBJECTIVES This study sought to identify cis- and trans-methylation markers associated with gene expression in airway epithelium from youth with and without atopic asthma. METHODS In this study, the investigators conducted both cis- and trans-eQTM analyses in nasal (airway) epithelial samples from 158 Puerto Rican youth with atopic asthma and 100 control subjects without atopy or asthma. The investigators then attempted to replicate their findings in nasal epithelial samples from 2 studies of children, while also examining whether their results in nasal epithelium overlap with those from an eQTM analysis in white blood cells from the Puerto Rican subjects. RESULTS This study identified 9,108 cis-eQTM pairs and 2,131,500 trans-eQTM pairs. Trans-associations were significantly enriched for transcription factor and microRNA target genes. Furthermore, significant cytosine-phosphate-guanine sites (CpGs) were differentially methylated in atopic asthma and significant genes were enriched for genes differentially expressed in atopic asthma. In this study, 50.7% to 62.6% of cis- and trans-eQTM pairs identified in Puerto Rican youth were replicated in 2 smaller cohorts at false discovery rate-adjusted P < .1. Replicated genes in the trans-eQTM analysis included biologically plausible asthma-susceptibility genes (eg, HDC, NLRP3, ITGAE, CDH26, and CST1) and are enriched in immune pathways. CONCLUSIONS Studying both cis- and trans-epigenetic regulation of airway epithelial gene expression can identify potential causal and regulatory pathways or networks for childhood asthma. Trans-eQTM CpGs may regulate gene expression in airway epithelium through effects on transcription factor and microRNA target genes.
Collapse
Affiliation(s)
- Soyeon Kim
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pa
| | - Zhongli Xu
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pa
| | - Yidi Qin
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Hyun Jung Park
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Molin Yue
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Qi Yan
- Department of Obstetrics and Gynecology, Columbia University, New York, NY
| | - Michelle L Manni
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh
| | - Edna Acosta-Pérez
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Wei Chen
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; School of Medicine, Tsinghua University, Beijing, China
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, Pa.
| |
Collapse
|
4
|
Cardenas A, Fadadu RP, Koppelman GH. Epigenome-wide association studies of allergic disease and the environment. J Allergy Clin Immunol 2023; 152:582-590. [PMID: 37295475 PMCID: PMC10564109 DOI: 10.1016/j.jaci.2023.05.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
The epigenome is at the intersection of the environment, genotype, and cellular response. DNA methylation of cytosine nucleotides, the most studied epigenetic modification, has been systematically evaluated in human studies by using untargeted epigenome-wide association studies (EWASs) and shown to be both sensitive to environmental exposures and associated with allergic diseases. In this narrative review, we summarize findings from key EWASs previously conducted on this topic; interpret results from recent studies; and discuss the strengths, challenges, and opportunities regarding epigenetics research on the environment-allergy relationship. The majority of these EWASs have systematically investigated select environmental exposures during the prenatal and early childhood periods and allergy-associated epigenetic changes in leukocyte-isolated DNA and more recently in nasal cells. Overall, many studies have found consistent DNA methylation associations across cohorts for certain exposures, such as smoking (eg, aryl hydrocarbon receptor repressor gene [AHRR] gene), and allergic diseases (eg, EPX gene). We recommend the integration of both environmental exposures and allergy or asthma within long-term prospective designs to strengthen causality as well as biomarker development. Future studies should collect paired target tissues to examine compartment-specific epigenetic responses, incorporate genetic influences in DNA methylation (methylation quantitative trait locus), replicate findings across diverse populations, and carefully interpret epigenetic signatures from bulk, target tissue or isolated cells.
Collapse
Affiliation(s)
- Andres Cardenas
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford University, Stanford, Calif
| | - Raj P Fadadu
- School of Medicine, University of California, San Francisco, Calif
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen, The Netherlands; Groningen Research Institute of Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
5
|
Kalomoiri M, Prakash CR, Lagström S, Hauschulz K, Ewing E, Shchetynsky K, Kular L, Needhamsen M, Jagodic M. Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing. Front Immunol 2023; 14:1251772. [PMID: 37691926 PMCID: PMC10484099 DOI: 10.3389/fimmu.2023.1251772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/02/2023] [Indexed: 09/12/2023] Open
Abstract
The Human Leukocyte Antigen (HLA) locus associates with a variety of complex diseases, particularly autoimmune and inflammatory conditions. The HLA-DR15 haplotype, for example, confers the major risk for developing Multiple Sclerosis in Caucasians, pinpointing an important role in the etiology of this chronic inflammatory disease of the central nervous system. In addition to the protein-coding variants that shape the functional HLA-antigen-T cell interaction, recent studies suggest that the levels of HLA molecule expression, that are epigenetically controlled, also play a role in disease development. However, deciphering the exact molecular mechanisms of the HLA association has been hampered by the tremendous genetic complexity of the locus and a lack of robust approaches to investigate it. Here, we developed a method to specifically enrich the genomic DNA from the HLA class II locus (chr6:32,426,802-34,167,129) and proximal promoters of 2,157 immune-relevant genes, utilizing the Agilent RNA-based SureSelect Methyl-Seq Capture related method, followed by sequencing to detect genetic and epigenetic variation. We demonstrated successful simultaneous detection of the genetic variation and quantification of DNA methylation levels in HLA locus. Moreover, by the detection of differentially methylated positions in promoters of immune-related genes, we identified relevant pathways following stimulation of cells. Taken together, we present a method that can be utilized to study the interplay between genetic variance and epigenetic regulation in the HLA class II region, potentially, in a wide disease context.
Collapse
Affiliation(s)
- Maria Kalomoiri
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chandana Rao Prakash
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sonja Lagström
- Diagnostics and Genomics Group, Agilent Technologies Sweden AB, Sundbyberg, Sweden
| | - Kai Hauschulz
- Diagnostics and Genomics Group, Agilent Technologies Deutschland GmbH, Waldbronn, Germany
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Klementy Shchetynsky
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
6
|
Villicaña S, Castillo-Fernandez J, Hannon E, Christiansen C, Tsai PC, Maddock J, Kuh D, Suderman M, Power C, Relton C, Ploubidis G, Wong A, Hardy R, Goodman A, Ong KK, Bell JT. Genetic impacts on DNA methylation help elucidate regulatory genomic processes. Genome Biol 2023; 24:176. [PMID: 37525248 PMCID: PMC10391992 DOI: 10.1186/s13059-023-03011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/10/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. RESULTS We report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2358 blood samples from three UK cohorts. Methylation levels at 34.2% of CpGs are affected by SNPs, and 98% of effects are cis-acting or within 1 Mbp of the tested CpG. Our results are consistent with meQTL analyses based on the former Illumina Infinium HumanMethylation450 array. Both SNPs and CpGs with meQTLs are overrepresented in enhancers, which have improved coverage on this platform compared to previous approaches. Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identify 1520 co-localisations across 1325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such as USP1 and DOCK7 (total cholesterol levels), and ICOSLG (inflammatory bowel disease). Enrichment analysis of meQTLs and integration with expression QTLs give insights into mechanisms underlying cis-meQTLs (e.g. through disruption of transcription factor binding sites for CTCF and SMC3) and trans-meQTLs (e.g. through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites). CONCLUSIONS Our findings improve the characterisation of the mechanisms underlying DNA methylation variability and are informative for prioritisation of GWAS variants for functional follow-ups. The MeQTL EPIC Database and viewer are available online at https://epicmeqtl.kcl.ac.uk .
Collapse
Affiliation(s)
- Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | | | | | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jane Maddock
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - George Ploubidis
- Centre for Longitudinal Studies, Institute of Education, University College London, London, UK
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Rebecca Hardy
- School of Sport, Exercise & Health Sciences, Loughborough University, Loughborough, UK
- UCL Social Research Institute, University College London, London, UK
| | - Alissa Goodman
- Centre for Longitudinal Studies, Institute of Education, University College London, London, UK
| | - Ken K Ong
- MRC Epidemiology Unit and Department of Paediatrics, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| |
Collapse
|
7
|
Li B, Wang Y, Wang Z, Li X, Kay S, Chupp GL, Zhao H, Gomez JL. Shared genetic architecture of blood eosinophil counts and asthma in UK Biobank. ERJ Open Res 2023; 9:00291-2023. [PMID: 37650091 PMCID: PMC10463033 DOI: 10.1183/23120541.00291-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/07/2023] [Indexed: 09/01/2023] Open
Abstract
Rationale Asthma is a complex, heterogeneous disease strongly associated with type 2 inflammation, and blood eosinophil counts guide therapeutic interventions in moderate and severe asthma. Eosinophils are leukocytes involved in type 2 immune responses. Despite these critical associations between asthma and blood eosinophil counts, the shared genetic architecture of these two traits remains unknown. The objective of the present study was to characterise the genetic architecture of blood eosinophil counts and asthma in the UK Biobank. Methods We performed genome-wide association studies (GWAS) of doctor-diagnosed asthma, blood eosinophil, neutrophil, lymphocyte and monocyte counts in the UK Biobank. Genetic correlation analysis was performed on GWAS results and validated in the Trans-National Asthma Genetic Consortium (TAGC) study of asthma. Results GWAS of doctor-diagnosed asthma and blood eosinophil counts in the UK Biobank identified 585 and 3429 significant variants, respectively. STAT6, a transcription factor involved in interleukin-4 signalling, was a key shared pathway between asthma and blood eosinophil counts. Genetic correlation analysis demonstrated a positive correlation between doctor-diagnosed asthma and blood eosinophil counts (r=0.38±0.10, correlation±se; p=4.7×10-11). As a validation of this association, we found a similar correlation between TAGC and blood eosinophil counts in the UK Biobank (0.37±0.08, correlation±se; p=1.2×10-6). Conclusions These findings define the shared genetic architecture between blood eosinophil counts and asthma risk in subjects of European ancestry and point to a genetic link to the STAT6 signalling pathway in these two traits.
Collapse
Affiliation(s)
- Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- These authors contributed equally to this work
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- These authors contributed equally to this work
| | - Zixiao Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Xinyue Li
- School of Data Science, City University of Hong Kong, Hong Kong SAR, China
| | - Shannon Kay
- Pulmonary, Critical Care and Sleep Medicine Section, Yale University, New Haven, CT, USA
- Center for Precision Pulmonary Medicine (P2MED), Yale University, New Haven, CT, USA
| | - Geoffrey L. Chupp
- Pulmonary, Critical Care and Sleep Medicine Section, Yale University, New Haven, CT, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- These authors share senior authorship
| | - Jose L. Gomez
- Pulmonary, Critical Care and Sleep Medicine Section, Yale University, New Haven, CT, USA
- Center for Precision Pulmonary Medicine (P2MED), Yale University, New Haven, CT, USA
- These authors share senior authorship
| |
Collapse
|
8
|
McEvoy CT, Le Souef PN, Martinez FD. The Role of Lung Function in Determining Which Children Develop Asthma. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:677-683. [PMID: 36706985 PMCID: PMC10329781 DOI: 10.1016/j.jaip.2023.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
Longitudinal studies have demonstrated that altered indices of airway function, assessed shortly after birth, are a risk factor for the subsequent development of wheezing illnesses and asthma, and that these indices predict airway size and airway wall thickness in adult life. Pre- and postnatal factors that directly alter early airway function, such as extreme prematurity and cigarette smoke, may continue to affect airway function and, hence, the risks for wheeze and asthma. Early airway function and an associated asthma risk may also be indirectly influenced by immune system responses, respiratory viruses, the airway microbiome, genetics, and epigenetics, especially if they affect airway epithelial dysfunction. Few if any interventions, apart from smoking avoidance, have been proven to alter the risks of developing asthma, but vitamin C supplementation to pregnant smokers may help decrease the effects of in utero smoke on offspring lung function. We conclude that airway size and the factors influencing this play an important role in determining the risk for asthma across the lifetime. Progress in asthma prevention is long overdue and this may benefit from carefully designed interventions in well-phenotyped longitudinal birth cohorts with early airway function assessments monitored through to adulthood.
Collapse
Affiliation(s)
- Cindy T McEvoy
- Department of Pediatrics, Papé Pediatric Research Institute, Oregon Health & Science University, Portland, Ore.
| | - Peter N Le Souef
- Department of Pediatrics, School of Medical School, University of Western Australia, Crawley, Western Australia, Australia; Department of Respiratory Medicine, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Fernando D Martinez
- Asthma and Airway Disease Research Center and Department of Pediatrics, University of Arizona, Tucson, Ariz
| |
Collapse
|
9
|
de Lima LC, Cruz ÁA, Costa RDS, Silva HDS, Coelho RS, Teixeira HM, Oliveira PR, Barnes KC, Figueiredo CA, Carneiro VL. TSLP and IL25 variants are related to asthma and atopy. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
10
|
Liyanage JSS, Estepp JH, Srivastava K, Li Y, Mori M, Kang G. GMEPS: a fast and efficient likelihood approach for genome-wide mediation analysis under extreme phenotype sequencing. Stat Appl Genet Mol Biol 2022; 21:sagmb-2021-0071. [PMID: 35266368 DOI: 10.1515/sagmb-2021-0071] [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: 09/14/2021] [Accepted: 02/17/2022] [Indexed: 11/15/2022]
Abstract
Due to many advantages such as higher statistical power of detecting the association of genetic variants in human disorders and cost saving, extreme phenotype sequencing (EPS) is a rapidly emerging study design in epidemiological and clinical studies investigating how genetic variations associate with complex phenotypes. However, the investigation of the mediation effect of genetic variants on phenotypes is strictly restrictive under the EPS design because existing methods cannot well accommodate the non-random extreme tails sampling process incurred by the EPS design. In this paper, we propose a likelihood approach for testing the mediation effect of genetic variants through continuous and binary mediators on a continuous phenotype under the EPS design (GMEPS). Besides implementing in EPS design, it can also be utilized as a general mediation analysis procedure. Extensive simulations and two real data applications of a genome-wide association study of benign ethnic neutropenia under EPS design and a candidate-gene study of neurocognitive performance in patients with sickle cell disease under random sampling design demonstrate the superiority of GMEPS under the EPS design over widely used mediation analysis procedures, while demonstrating compatible capabilities under the general random sampling framework.
Collapse
Affiliation(s)
- Janaka S S Liyanage
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
| | - Jeremie H Estepp
- Departments of Global Pediatric Medicine and Hematology, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
| | - Kumar Srivastava
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
| | - Yun Li
- Department of Biostatistics, Department of Genetics, Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill 27599, NC, USA
| | - Motomi Mori
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
| | - Guolian Kang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis 38105, TN, USA
| |
Collapse
|
11
|
Soliai MM, Kato A, Helling BA, Stanhope CT, Norton JE, Naughton KA, Klinger AI, Thompson EE, Clay SM, Kim S, Celedón JC, Gern JE, Jackson DJ, Altman MC, Kern RC, Tan BK, Schleimer RP, Nicolae DL, Pinto JM, Ober C. Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus. Genome Med 2021; 13:157. [PMID: 34629083 PMCID: PMC8504130 DOI: 10.1186/s13073-021-00967-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/10/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified thousands of variants associated with asthma and other complex diseases. However, the functional effects of most of these variants are unknown. Moreover, GWASs do not provide context-specific information on cell types or environmental factors that affect specific disease risks and outcomes. To address these limitations, we used an upper airway epithelial cell (AEC) culture model to assess transcriptional and epigenetic responses to rhinovirus (RV), an asthma-promoting pathogen, and provide context-specific functional annotations to variants discovered in GWASs of asthma. METHODS Genome-wide genetic, gene expression, and DNA methylation data in vehicle- and RV-treated upper AECs were collected from 104 individuals who had a diagnosis of airway disease (n=66) or were healthy participants (n=38). We mapped cis expression and methylation quantitative trait loci (cis-eQTLs and cis-meQTLs, respectively) in each treatment condition (RV and vehicle) in AECs from these individuals. A Bayesian test for colocalization between AEC molecular QTLs and adult onset asthma and childhood onset asthma GWAS SNPs, and a multi-ethnic GWAS of asthma, was used to assign the function to variants associated with asthma. We used Mendelian randomization to demonstrate DNA methylation effects on gene expression at asthma colocalized loci. RESULTS Asthma and allergic disease-associated GWAS SNPs were specifically enriched among molecular QTLs in AECs, but not in GWASs from non-immune diseases, and in AEC eQTLs, but not among eQTLs from other tissues. Colocalization analyses of AEC QTLs with asthma GWAS variants revealed potential molecular mechanisms of asthma, including QTLs at the TSLP locus that were common to both the RV and vehicle treatments and to both childhood onset and adult onset asthma, as well as QTLs at the 17q12-21 asthma locus that were specific to RV exposure and childhood onset asthma, consistent with clinical and epidemiological studies of these loci. CONCLUSIONS This study provides evidence of functional effects for asthma risk variants in AECs and insight into RV-mediated transcriptional and epigenetic response mechanisms that modulate genetic effects in the airway and risk for asthma.
Collapse
Affiliation(s)
- Marcus M Soliai
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
| | - Atsushi Kato
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Britney A Helling
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | - James E Norton
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Aiko I Klinger
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Emma E Thompson
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Selene M Clay
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Soyeon Kim
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, USA
| | - Robert C Kern
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bruce K Tan
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Robert P Schleimer
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dan L Nicolae
- Department of Statistics, University of Chicago, Chicago, IL, USA
| | - Jayant M Pinto
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Carole Ober
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
12
|
Scherer M, Gasparoni G, Rahmouni S, Shashkova T, Arnoux M, Louis E, Nostaeva A, Avalos D, Dermitzakis ET, Aulchenko YS, Lengauer T, Lyons PA, Georges M, Walter J. Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR. Epigenetics Chromatin 2021; 14:44. [PMID: 34530905 PMCID: PMC8444396 DOI: 10.1186/s13072-021-00415-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/02/2021] [Indexed: 12/18/2022] Open
Abstract
Background Understanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for determining methylation quantitative trait loci (methQTL), but also for discriminating general from cell type-specific effects. Results Here, we present a two-step computational framework MAGAR (https://bioconductor.org/packages/MAGAR), which fully supports the identification of methQTLs from matched genotyping and DNA methylation data, and additionally allows for illuminating cell type-specific methQTL effects. In a pilot analysis, we apply MAGAR on data in four tissues (ileum, rectum, T cells, B cells) from healthy individuals and demonstrate the discrimination of common from cell type-specific methQTLs. We experimentally validate both types of methQTLs in an independent data set comprising additional cell types and tissues. Finally, we validate selected methQTLs located in the PON1, ZNF155, and NRG2 genes by ultra-deep local sequencing. In line with previous reports, we find cell type-specific methQTLs to be preferentially located in enhancer elements. Conclusions Our analysis demonstrates that a systematic analysis of methQTLs provides important new insights on the influences of genetic variants to cell type-specific epigenomic variation. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00415-6.
Collapse
Affiliation(s)
- Michael Scherer
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.,Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, Saarbrücken, Germany.,Department of Bioinformatics and Genomics, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Gilles Gasparoni
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Souad Rahmouni
- Unit of Animal Genomics, GIGA-Institute & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Tatiana Shashkova
- Kurchatov Genomics Center of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Research and Training Center on Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Marion Arnoux
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Edouard Louis
- Department of Gastroenterology, Liège University Hospital, CHU Liège, Liège, Belgium
| | | | - Diana Avalos
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics (SIB), University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Yurii S Aulchenko
- Kurchatov Genomics Center of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,Moscow Institute of Physics and Technology (State University), Moscow, Russia.,PolyKnomics BV, 's-Hertogenbosch, The Netherlands
| | - Thomas Lengauer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Paul A Lyons
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - Michel Georges
- Unit of Animal Genomics, GIGA-Institute & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.
| |
Collapse
|
13
|
It's in the (Epi)genetics: Effects of DNA Methylation on Gene Expression in Atopic Asthma? Chest 2021; 158:1799-1801. [PMID: 33160517 DOI: 10.1016/j.chest.2020.07.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/08/2020] [Indexed: 11/22/2022] Open
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
The Airway Epithelium-A Central Player in Asthma Pathogenesis. Int J Mol Sci 2020; 21:ijms21238907. [PMID: 33255348 PMCID: PMC7727704 DOI: 10.3390/ijms21238907] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022] Open
Abstract
Asthma is a chronic inflammatory airway disease characterized by variable airflow obstruction in response to a wide range of exogenous stimuli. The airway epithelium is the first line of defense and plays an important role in initiating host defense and controlling immune responses. Indeed, increasing evidence indicates a range of abnormalities in various aspects of epithelial barrier function in asthma. A central part of this impairment is a disruption of the airway epithelial layer, allowing inhaled substances to pass more easily into the submucosa where they may interact with immune cells. Furthermore, many of the identified susceptibility genes for asthma are expressed in the airway epithelium. This review focuses on the biology of the airway epithelium in health and its pathobiology in asthma. We will specifically discuss external triggers such as allergens, viruses and alarmins and the effect of type 2 inflammatory responses on airway epithelial function in asthma. We will also discuss epigenetic mechanisms responding to external stimuli on the level of transcriptional and posttranscriptional regulation of gene expression, as well the airway epithelium as a potential treatment target in asthma.
Collapse
|
16
|
Heijink IH, Kuchibhotla VNS, Roffel MP, Maes T, Knight DA, Sayers I, Nawijn MC. Epithelial cell dysfunction, a major driver of asthma development. Allergy 2020; 75:1902-1917. [PMID: 32460363 PMCID: PMC7496351 DOI: 10.1111/all.14421] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Airway epithelial barrier dysfunction is frequently observed in asthma and may have important implications. The physical barrier function of the airway epithelium is tightly interwoven with its immunomodulatory actions, while abnormal epithelial repair responses may contribute to remodelling of the airway wall. We propose that abnormalities in the airway epithelial barrier play a crucial role in the sensitization to allergens and pathogenesis of asthma. Many of the identified susceptibility genes for asthma are expressed in the airway epithelium, supporting the notion that events at the airway epithelial surface are critical for the development of the disease. However, the exact mechanisms by which the expression of epithelial susceptibility genes translates into a functionally altered response to environmental risk factors of asthma are still unknown. Interactions between genetic factors and epigenetic regulatory mechanisms may be crucial for asthma susceptibility. Understanding these mechanisms may lead to identification of novel targets for asthma intervention by targeting the airway epithelium. Moreover, exciting new insights have come from recent studies using single‐cell RNA sequencing (scRNA‐Seq) to study the airway epithelium in asthma. This review focuses on the role of airway epithelial barrier function in the susceptibility to develop asthma and novel insights in the modulation of epithelial cell dysfunction in asthma.
Collapse
Affiliation(s)
- Irene H. Heijink
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Pulmonology University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Virinchi N. S. Kuchibhotla
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan NSW Australia
| | - Mirjam P. Roffel
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Respiratory Medicine Laboratory for Translational Research in Obstructive Pulmonary Diseases Ghent University Hospital Ghent University Ghent Belgium
| | - Tania Maes
- Department of Respiratory Medicine Laboratory for Translational Research in Obstructive Pulmonary Diseases Ghent University Hospital Ghent University Ghent Belgium
| | - Darryl A. Knight
- School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan NSW Australia
- UBC Providence Health Care Research Institute Vancouver BC Canada
- Department of Anesthesiology, Pharmacology and Therapeutics University of British Columbia Vancouver BC Canada
| | - Ian Sayers
- Division of Respiratory Medicine National Institute for Health Research Nottingham Biomedical Research Centre University of Nottingham Biodiscovery Institute University of Nottingham Nottingham UK
| | - Martijn C. Nawijn
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
| |
Collapse
|
17
|
Rathod A, Duan J, Zhang H, Holloway JW, Ewart S, Arshad SH, Karmaus W. Interweaving Between Genetic and Epigenetic Studies on Childhood Asthma. Epigenet Insights 2020; 13:2516865720923395. [PMID: 32754683 PMCID: PMC7378715 DOI: 10.1177/2516865720923395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/08/2020] [Indexed: 12/16/2022] Open
Abstract
The cause and underlying mechanisms that contribute to asthma pathogenesis are
not well known. Both genome- and epigenome-wide association studies have
identified genes associated with asthma risk. It is unknown to what extent genes
identified in these two types of studies overlap. Based on existing literature
and the DisGeNET database, we extracted overlapping genes identified in genetic
and epigenetic studies of childhood asthma. Through analyses of variance, we
assessed whether DNA methylation (DNAm) at 5′-C-phosphate-G-3′ (CpGs) on the
overlapping genes was associated with neighboring single-nucleotide
polymorphisms (SNPs) within 1M base pairs (bps) and with low linkage
disequilibrium (r2 < 0.2) in the
childhood asthma-related genes. In total, 285 genes from genetic studies and 226
genes from epigenetic studies were shown to be associated with asthma risk, of
which six overlap. Of the six genes, 79 CpGs and 8229 unique neighboring SNPs
(1M bps) were included in methylation quantitative loci (methQTL) assessment
analyses. We tested the association of DNAm at each of the 79 CpG sites with its
neighboring SNPs. After adjusting for multiple testing by controlling the false
discovery rate to 0.05 when testing methQTL for each CpG site, we found
statistically significant associations in three genes with their neighboring
SNPs and identified 34 unique methQTLs. The rather limited overlap in genes
between genetic and epigenetic studies on asthma and the absence of methQTL in
some of the overlapping genes highlight a need to jointly, rather than
independently, examine genetic and epigenetic effects on asthma risk to improve
our understanding of the underlying mechanisms of asthma.
Collapse
Affiliation(s)
- Aniruddha Rathod
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Jiasong Duan
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - S Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,The David Hide Asthma & Allergy Research Centre, Isle of Wight, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, The University of Memphis, Memphis, TN, USA
| |
Collapse
|
18
|
Kim S, Forno E, Zhang R, Park HJ, Xu Z, Yan Q, Boutaoui N, Acosta-Pérez E, Canino G, Chen W, Celedón JC. Expression Quantitative Trait Methylation Analysis Reveals Methylomic Associations With Gene Expression in Childhood Asthma. Chest 2020; 158:1841-1856. [PMID: 32569636 DOI: 10.1016/j.chest.2020.05.601] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/10/2020] [Accepted: 05/23/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Nasal (airway) epithelial methylation profiles have been associated with asthma, but the effects of such profiles on expression of distant cis-genes are largely unknown. RESEARCH QUESTION To identify genes whose expression is associated with proximal and distal CpG probes (within 1 Mb), and to assess whether and how such genes are differentially expressed in atopic asthma. STUDY DESIGN AND METHODS Genome-wide expression quantitative trait methylation (eQTM) analysis in nasal epithelium from Puerto Rican subjects (aged 9-20 years) with (n = 219) and without (n = 236) asthma. After the eQTM analysis, a Gene Ontology Enrichment analysis was conducted for the top 500 eQTM genes, and mediation analyses were performed to identify paths from DNA methylation to atopic asthma through gene expression. Asthma was defined as physician-diagnosed asthma and wheeze in the previous year, and atopy was defined as at least one positive IgE to allergens. Atopic asthma was defined as the presence of both atopy and asthma. RESULTS We identified 16,867 significant methylation-gene expression pairs (false-discovery rate-adjusted P < .01) in nasal epithelium from study participants. Most eQTM methylation probes were distant (average distance, ∼378 kb) from their target genes, and also more likely to be located in enhancer regions of their target genes in lung tissue than control probes. The top 500 eQTM genes were enriched in pathways for immune processes and epithelial integrity and were more likely to have been previously identified as differentially expressed in atopic asthma. In a mediation analysis, we identified 5,934 paths through which methylation markers could affect atopic asthma through gene expression in nasal epithelium. INTERPRETATION Previous epigenome-wide association studies of asthma have estimated the effects of DNA methylation markers on expression of nearby genes in airway epithelium. Our findings suggest that distant epigenetic regulation of gene expression in airway epithelium plays a role in atopic asthma.
Collapse
Affiliation(s)
- Soyeon Kim
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA
| | - Erick Forno
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA
| | - Rong Zhang
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA
| | - Hyun Jung Park
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA
| | - Zhongli Xu
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA; School of Medicine, Tsinghua University, Beijing, China
| | - Qi Yan
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA
| | - Nadia Boutaoui
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA
| | - Edna Acosta-Pérez
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, PR
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, PR
| | - Wei Chen
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA
| | - Juan C Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA.
| |
Collapse
|
19
|
Solazzo G, Ferrante G, La Grutta S. DNA Methylation in Nasal Epithelium: Strengths and Limitations of an Emergent Biomarker for Childhood Asthma. Front Pediatr 2020; 8:256. [PMID: 32500051 PMCID: PMC7243704 DOI: 10.3389/fped.2020.00256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Asthma is one of the most widespread chronic respiratory conditions. This disease primarily develops in childhood and is influenced by different factors, mainly genetics and environmental factors. DNA methylation is an epigenetic mechanism which may represent a bridge between these two factors, providing a tool to comprehend the interaction between genetics and environment. Most epidemiological studies in this field have been conducted using blood samples, although DNA methylation marks in blood may not be reliable for drawing exhaustive conclusions about DNA methylation in the airways. Because of the role of nasal epithelium in asthma and the tissue specificity of DNA methylation, studying the relationship between DNA methylation and childhood asthma might reveal crucial information about this widespread respiratory disease. The purpose of this review is to describe current findings in this field of research. We will present a viewpoint of selected studies, consider strengths and limitations, and propose future research in this area.
Collapse
Affiliation(s)
- Giulia Solazzo
- Institute for Research and Biomedical Innovation (IRIB), National Research Council (CNR), Palermo, Italy
| | - Giuliana Ferrante
- Department of Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialities, University of Palermo, Palermo, Italy
| | - Stefania La Grutta
- Institute for Research and Biomedical Innovation (IRIB), National Research Council (CNR), Palermo, Italy
| |
Collapse
|