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Association of childhood BMI trajectory with post-adolescent and adult lung function is mediated by pre-adolescent DNA methylation. Respir Res 2022; 23:194. [PMID: 35906571 PMCID: PMC9335987 DOI: 10.1186/s12931-022-02089-4] [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: 12/09/2021] [Accepted: 06/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background Body mass index (BMI) has been shown to be associated with lung function. Recent findings showed that DNA methylation (DNAm) variation is likely to be a consequence of changes in BMI. However, whether DNAm mediates the association of BMI with lung function is unknown. We examined the mediating role of DNAm on the association of pre-adolescent BMI trajectories with post-adolescent and adulthood lung function (forced expiratory volume (FEV1), forced vital capacity (FVC), and FEV1/FVC). Methods Analyses were undertaken in the Isle of Wight birth cohort (IOWBC). Group-based trajectory modelling was applied to infer latent BMI trajectories from age 1 to 10 years. An R package, ttscreening, was applied to identify CpGs at 10 years potentially associated with BMI trajectories for each sex. Linear regressions were implemented to further screen CpGs for their association with lung function at 18 years. Path analysis, stratified by sex, was applied to each screened CpG to assess its role of mediation. Internal validation was applied to further examine the mediation consistency of the detected CpGs based on lung function at 26 years. Mendelian randomization (MR-base) was used to test possible causal effects of the identified CpGs. Results Two BMI trajectories (high vs. low) were identified. Of the 442,475 CpG sites, 18 CpGs in males and 33 in females passed screening. Eight CpGs in males and 16 CpGs in females (none overlapping) were identified as mediators. For subjects with high BMI trajectory, high DNAm at all CpGs in males were associated with decreased lung function, while 8 CpGs in females were associated with increased lung function at 18 years. At 26 years, 6 CpGs in males and 14 CpGs in females showed the same direction of indirect effects as those at 18 years. DNAm at CpGs cg19088553 (GRIK2) and cg00612625 (HPSE2) showed a potential causal effect on FEV1. Conclusions The effects of BMI trajectory in early childhood on post-adolescence lung function were likely to be mediated by pre-adolescence DNAm in both males and females, but such mediation effects were likely to diminish over time. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02089-4.
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Abell NS, DeGorter MK, Gloudemans MJ, Greenwald E, Smith KS, He Z, Montgomery SB. Multiple causal variants underlie genetic associations in humans. Science 2022; 375:1247-1254. [PMID: 35298243 DOI: 10.1126/science.abj5117] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Associations between genetic variation and traits are often in noncoding regions with strong linkage disequilibrium (LD), where a single causal variant is assumed to underlie the association. We applied a massively parallel reporter assay (MPRA) to functionally evaluate genetic variants in high, local LD for independent cis-expression quantitative trait loci (eQTL). We found that 17.7% of eQTLs exhibit more than one major allelic effect in tight LD. The detected regulatory variants were highly and specifically enriched for activating chromatin structures and allelic transcription factor binding. Integration of MPRA profiles with eQTL/complex trait colocalizations across 114 human traits and diseases identified causal variant sets demonstrating how genetic association signals can manifest through multiple, tightly linked causal variants.
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Affiliation(s)
- Nathan S Abell
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Marianne K DeGorter
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Emily Greenwald
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kevin S Smith
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA.,Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Stephen B Montgomery
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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Rathod A, Zhang H, Arshad SH, Ewart S, Relton CL, Karmaus W, Holloway JW. DNA Methylation and Asthma Acquisition during Adolescence and Post-Adolescence, an Epigenome-Wide Longitudinal Study. J Pers Med 2022; 12:202. [PMID: 35207690 PMCID: PMC8877984 DOI: 10.3390/jpm12020202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/19/2022] [Indexed: 02/01/2023] Open
Abstract
The role of epigenetics in the pathogenesis of asthma acquisition in adolescence and post-adolescence has been unknown. We carried out a longitudinal epigenome-wide association study, using data from the Isle of Wight Birth Cohort (IOWBC). To improve statistical power, we first screened CpGs based on associations of DNA methylation (DNAm) at an age of 10 years (pre-adolescence) with asthma acquisition at 10-18 years (during adolescence). A logistic regression with repeated measures was applied to CpGs that passed screening to examine the associations of pre-adolescence DNAm with asthma acquisition from 10-18 years and 18-26 years, with an interaction term to evaluate transition period specificity. Findings were further tested in an independent birth cohort, ALSPAC. In total, 205 CpGs (with 150 being females) showed associations with asthma acquisition (main or interaction effects) at FDR = 0.05 in IOWBC, of which 112 (90 being females) showed consistent associations in the ALSPAC. Genes that the identified CpGs were mapped to, e.g., AKAP1 and ENO1, have been shown to be associated with the risk of asthma. Our findings indicated that DNAm at specific CpGs was associated with asthma acquisition. CpGs showing such associations were likely to be different between males and females and, at certain CpGs, were unique to a specific transition period.
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Affiliation(s)
- Aniruddha Rathod
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38111, USA; (A.R.); (W.K.)
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38111, USA; (A.R.); (W.K.)
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight PO30 5TG, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA;
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1QU, UK;
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1QU, UK
- National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust, University of Bristol, Bristol BS8 2BN, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38111, USA; (A.R.); (W.K.)
| | - John W. Holloway
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
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Rathod A, Rathod R, Zhang H, Rahimabad PK, Karmaus W, Arshad H. Association of Asthma and Rhinitis with Epigenetics of Coronavirus Related Genes. Epigenet Insights 2021; 14:25168657211039224. [PMID: 34604700 PMCID: PMC8485269 DOI: 10.1177/25168657211039224] [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: 03/22/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022] Open
Abstract
Introduction: Susceptibility factors for coronavirus disease 2019 (COVID-19) include sex and medical conditions such as asthma and rhinitis. DNA methylation (DNAm) is associated with asthma, rhinitis, and several viruses. We examined associations of asthma/rhinitis with DNAm at CpGs located on coronavirus related genes, and if these associations were sex-specific. Methods: In total, n = 242 subjects aged 26 years from the Isle of Wight Birth Cohort were included in the study. Linear regressions were used to examine sex specific and non-specific associations of DNAm at CpGs on coronavirus related genes with asthma/rhinitis status. Associations of DNAm with gene expression in blood were assessed for functional relevance of identified CpGs. Results: Statistically significant interaction effects of asthma or rhinitis with sex were identified at 40 CpGs for asthma and 27 CpGs for rhinitis. At 21 CpGs, DNAm was associated with asthma, and at 45 CpGs with rhinitis, regardless of sex. Assessment of functional relevance of the identified CpGs indicated a potential of epigenetic regulatory functionality on gene activity at 14 CpGs for asthma and 17 CpGs for rhinitis, and of those 6 CpGs for asthma and 7 CpGs for rhinitis were likely to be sex-specific. Conclusion: Subjects with asthma/rhinitis may have altered susceptibility to COVID-19 due to changes in their DNAm associated with these conditions. Sex specificity on association of asthma/rhinitis with DNAm at certain CpGs, and on the association of DNAm at asthma/rhinitis-linked CpGs with gene expression have the potential to explain the reported sex-specificity in COVID-19 morbidity and mortality.
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Affiliation(s)
- Aniruddha Rathod
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Rutu Rathod
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Parnian Kheirkhah Rahimabad
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,David Hide Asthma and Allergy Research Centre, Isle of Wight, UK.,NIHR Southampton Biomedical Research Center, University Hospital Southampton, Southampton, UK
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Rathod R, Zhang H, Karmaus W, Ewart S, Kadalayil L, Relton C, Ring S, Arshad SH, Holloway JW. BMI trajectory in childhood is associated with asthma incidence at young adulthood mediated by DNA methylation. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2021; 17:77. [PMID: 34301314 PMCID: PMC8299682 DOI: 10.1186/s13223-021-00575-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/02/2021] [Indexed: 11/10/2022]
Abstract
PURPOSE Body mass index (BMI) is associated with asthma but associations of BMI temporal patterns with asthma incidence are unclear. Previous studies suggest that DNA methylation (DNAm) is associated with asthma status and variation in DNAm is a consequence of BMI changes. This study assessed the direct and indirect (via DNAm) effects of BMI trajectories in childhood on asthma incidence at young adulthood. METHODS Data from the Isle of Wight (IoW) birth cohort were included in the analyses. Group-based trajectory modelling was applied to infer latent BMI trajectories from ages 1 to 10 years. An R package, ttscreening, was applied to identify differentially methylated CpGs at age 10 years associated with BMI trajectories, stratified for sex. Logistic regressions were used to further exclude CpGs with DNAm at age 10 years not associated with asthma incidence at 18 years. CpGs discovered via path analyses that mediated the association of BMI trajectories with asthma incidence in the IoW cohort were further tested in an independent cohort, the Avon Longitudinal Study of Children and Parents (ALSPAC). RESULTS Two BMI trajectories (high vs. normal) were identified. Of the 442,474 CpG sites, DNAm at 159 CpGs in males and 212 in females were potentially associated with BMI trajectories. Assessment of their association with asthma incidence identified 9 CpGs in males and 6 CpGs in females. DNAm at 4 of these 15 CpGs showed statistically significant mediation effects (p-value < 0.05). At two of the 4 CpGs (cg23632109 and cg10817500), DNAm completely mediated the association (i.e., only statistically significant indirect effects were identified). In the ALSPAC cohort, at all four CpGs, the same direction of mediating effects were observed as those found in the IoW cohort, although statistically insignificant. CONCLUSION The association of BMI trajectory in childhood with asthma incidence at young adulthood is possibly mediated by DNAm.
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Affiliation(s)
- Rutu Rathod
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA.
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol and University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol and University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - S Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
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Narayanan D, Grayson MH. Comparing respiratory syncytial virus and rhinovirus in development of post-viral airway disease. J Asthma 2020; 59:434-441. [PMID: 33345668 DOI: 10.1080/02770903.2020.1862186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVE Respiratory syncytial virus (RSV) and rhinovirus (RV) are common viral infections that may result in post-viral airway/atopic disease. By understanding the antiviral immune response involved, and the mechanisms that translate/associate with post-viral airway disease, further research can be directed to potential treatments that affect these mechanisms. DATA SOURCES Utilized peer-reviewed manuscripts listed in PubMed that had relevance to RSV/RV and development of atopic/airway disease in both humans and mice. STUDY SELECTIONS Studies that explained the mechanisms behind antiviral response were selected. RESULTS RSV infections have been associated with post-viral airway disease primarily in those without preexisting atopy; however, the mechanistic link connecting the viral infection with atopy is less clear. Mouse models (in particular those using Sendai virus, a virus related to RSV) provide a potential mechanistic pathway that may explain the linkage between RSV and post-viral airway disease. RV infection also can drive post-viral airway disease, but unlike RSV, this seems to occur only in those with preexisting atopy. Studies explore this link by demonstrating an impaired interferon response in atopic individuals, which may make them more susceptible to development of post-viral airway disease with RV infection. CONCLUSION Both RSV and RV are associated with a risk for developing post-viral airway disease and atopy. However, the mechanisms that connect these viruses with post-viral disease appear to be disparate, suggesting that treatments to prevent post-viral airway disease may need to be specific to the viral etiology.
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Affiliation(s)
- Deepika Narayanan
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children's Hospital - The Ohio State University College of Medicine, Columbus, OH, USA
| | - Mitchell H Grayson
- Division of Allergy and Immunology, Department of Pediatrics, Nationwide Children's Hospital - The Ohio State University College of Medicine, Columbus, OH, USA.,The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
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Patel R, Solatikia F, Zhang H, Wolde A, Kadalayil L, Karmaus W, Ewart S, Arathimos R, Relton C, Ring S, Henderson AJ, Arshad SH, Holloway JW. Sex-specific associations of asthma acquisition with changes in DNA methylation during adolescence. Clin Exp Allergy 2020; 51:318-328. [PMID: 33150670 DOI: 10.1111/cea.13776] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/24/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Underlying biological mechanisms involved in sex differences in asthma status changes from pre- to post-adolescence are unclear. DNA methylation (DNAm) has been shown to be associated with the risk of asthma. OBJECTIVE We hypothesized that asthma acquisition from pre- to post-adolescence was associated with changes in DNAm during this period at asthma-associated cytosine-phosphate-guanine (CpG) sites and such an association was sex-specific. METHODS Subjects from the Isle of Wight birth cohort (IOWBC) with DNAm in blood at ages 10 and 18 years (n = 124 females, 151 males) were studied. Using a training-testing approach, epigenome-wide CpGs associated with asthma were identified. Logistic regression was used to examine sex-specific associations of DNAm changes with asthma acquisition between ages 10 and 18 at asthma-associated CpGs. The ALSPAC birth cohort was used for independent replication. To assess functional relevance of identified CpGs, association of DNAm with gene expression in blood was assessed. RESULTS We identified 535 CpGs potentially associated with asthma. Significant interaction effects of DNAm changes and sex on asthma acquisition in adolescence were found at 13 of the 535 CpGs in IOWBC (P-values <1.0 × 10-3 ). In the replication cohort, consistent interaction effects were observed at 10 of the 13 CpGs. At 7 of these 10 CpGs, opposite DNAm changes across adolescence were observed between sexes in both cohorts. In both cohorts, cg20891917, located on IFRD1 linked to asthma, shows strong sex-specific effects on asthma transition (P-values <.01 in both cohorts). CONCLUSION AND CLINICAL RELEVANCE Gender reversal in asthma acquisition is associated with opposite changes in DNAm (males vs females) from pre- to post-adolescence at asthma-associated CpGs. These CpGs are potential biomarkers of sex-specific asthma acquisition in adolescence.
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Affiliation(s)
- Rutu Patel
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Farnaz Solatikia
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA.,Department of Mathematical Sciences, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Alemayehu Wolde
- Department of Mathematical Sciences, University of Memphis, Memphis, TN, USA
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Ryan Arathimos
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK.,Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | | | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,David Hide Asthma and Allergy Research Centre, Isle of Wight, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
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