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Lukyanchuk A, Muraki N, Kawai T, Sato T, Hata K, Ito T, Tajima A. Long-term exposure to diesel exhaust particles induces concordant changes in DNA methylation and transcriptome in human adenocarcinoma alveolar basal epithelial cells. Epigenetics Chromatin 2024; 17:24. [PMID: 39103936 DOI: 10.1186/s13072-024-00549-3] [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: 03/08/2024] [Accepted: 07/19/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND Diesel exhaust particles (DEP), which contain hazardous compounds, are emitted during the combustion of diesel. As approximately one-third of the vehicles worldwide use diesel, there are growing concerns about the risks posed by DEP to human health. Long-term exposure to DEP is associated with airway hyperresponsiveness, pulmonary fibrosis, and inflammation; however, the molecular mechanisms behind the effects of DEP on the respiratory tract are poorly understood. Such mechanisms can be addressed by examining transcriptional and DNA methylation changes. Although several studies have focused on the effects of short-term DEP exposure on gene expression, research on the transcriptional effects and genome-wide DNA methylation changes caused by long-term DEP exposure is lacking. Hence, in this study, we investigated transcriptional and DNA methylation changes in human adenocarcinoma alveolar basal epithelial A549 cells caused by prolonged exposure to DEP and determined whether these changes are concordant. RESULTS DNA methylation analysis using the Illumina Infinium MethylationEPIC BeadChips showed that the methylation levels of DEP-affected CpG sites in A549 cells changed in a dose-dependent manner; the extent of change increased with increasing dose reaching the statistical significance only in samples exposed to 30 µg/ml DEP. Four-week exposure to 30 µg/ml of DEP significantly induced DNA hypomethylation at 24,464 CpG sites, which were significantly enriched for DNase hypersensitive sites, genomic regions marked by H3K4me1 and H3K27ac, and several transcription factor binding sites. In contrast, 9,436 CpG sites with increased DNA methylation levels were significantly overrepresented in genomic regions marked by H3K27me3 as well as H3K4me1 and H3K27ac. In parallel, gene expression profiling by RNA sequencing demonstrated that long-term exposure to DEP altered the expression levels of 2,410 genes, enriching 16 gene sets including Xenobiotic metabolism, Inflammatory response, and Senescence. In silico analysis revealed that the expression levels of 854 genes correlated with the methylation levels of the DEP-affected cis-CpG sites. CONCLUSIONS To our knowledge, this is the first report of genome-wide transcriptional and DNA methylation changes and their associations in A549 cells following long-term exposure to DEP.
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Affiliation(s)
- Alexandra Lukyanchuk
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan
- Krasnoyarsk State Medical University Named After Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
| | - Naomi Muraki
- Health Effects Research Group, Environment Research Division, Japan Automobile Research Institute, Tsukuba, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Human Molecular Genetics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tsuyoshi Ito
- Health Effects Research Group, Environment Research Division, Japan Automobile Research Institute, Tsukuba, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-8640, Japan.
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Lee S, Sbihi H, MacIsaac JL, Balshaw R, Ambalavanan A, Subbarao P, Mandhane PJ, Moraes TJ, Turvey SE, Duan Q, Brauer M, Brook JR, Kobor MS, Jones MJ. Persistent DNA Methylation Changes across the First Year of Life and Prenatal NO2 Exposure in a Canadian Prospective Birth Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:47004. [PMID: 38573328 DOI: 10.1289/ehp13034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
BACKGROUND Evidence suggests that prenatal air pollution exposure alters DNA methylation (DNAm), which could go on to affect long-term health. It remains unclear whether DNAm alterations present at birth persist through early life. Identifying persistent DNAm changes would provide greater insight into the molecular mechanisms contributing to the association of prenatal air pollution exposure with atopic diseases. OBJECTIVES This study investigated DNAm differences associated with prenatal nitrogen dioxide (NO 2 ) exposure (a surrogate measure of traffic-related air pollution) at birth and 1 y of age and examined their role in atopic disease. We focused on regions showing persistent DNAm differences from birth to 1 y of age and regions uniquely associated with postnatal NO 2 exposure. METHODS Microarrays measured DNAm at birth and at 1 y of age for an atopy-enriched subset of Canadian Health Infant Longitudinal Development (CHILD) study participants. Individual and regional DNAm differences associated with prenatal NO 2 (n = 128 ) were identified, and their persistence at age 1 y were investigated using linear mixed effects models (n = 124 ). Postnatal-specific DNAm differences (n = 125 ) were isolated, and their association with NO 2 in the first year of life was examined. Causal mediation investigated whether DNAm differences mediated associations between NO 2 and age 1 y atopy or wheeze. Analyses were repeated using biological sex-stratified data. RESULTS At birth (n = 128 ), 18 regions of DNAm were associated with NO 2 , with several annotated to HOX genes. Some of these regions were specifically identified in males (n = 73 ), but not females (n = 55 ). The effect of prenatal NO 2 across CpGs within altered regions persisted at 1 y of age. No significant mediation effects were identified. Sex-stratified analyses identified postnatal-specific DNAm alterations. DISCUSSION Regional cord blood DNAm differences associated with prenatal NO 2 persisted through at least the first year of life in CHILD participants. Some differences may represent sex-specific alterations, but replication in larger cohorts is needed. The early postnatal period remained a sensitive window to DNAm perturbations. https://doi.org/10.1289/EHP13034.
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Affiliation(s)
- Samantha Lee
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Hind Sbihi
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Padmaja Subbarao
- Department of Pediatrics & Translational Medicine, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Piushkumar J Mandhane
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Medicine, USCI University, Kuala Lumpur, Malaysia
| | - Theo J Moraes
- Department of Pediatrics & Translational Medicine, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Stuart E Turvey
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Qingling Duan
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
- School of Computing, Queen's University, Kingston, Ontario, Canada
| | - Michael Brauer
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey R Brook
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Biology of Breathing Theme, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
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Cardenas A, Fadadu R, Bunyavanich S. Climate change and epigenetic biomarkers in allergic and airway diseases. J Allergy Clin Immunol 2023; 152:1060-1072. [PMID: 37741554 PMCID: PMC10843253 DOI: 10.1016/j.jaci.2023.09.011] [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: 08/25/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
Human epigenetic variation is associated with both environmental exposures and allergic diseases and can potentially serve as a biomarker connecting climate change with allergy and airway diseases. In this narrative review, we summarize recent human epigenetic studies examining exposure to temperature, precipitation, extreme weather events, and malnutrition to discuss findings as they relate to allergic and airway diseases. Temperature has been the most widely studied exposure, with the studies implicating both short-term and long-term exposures with epigenetic alterations and epigenetic aging. Few studies have examined natural disasters or extreme weather events. The studies available have reported differential DNA methylation of multiple genes and pathways, some of which were previously associated with asthma or allergy. Few studies have integrated climate-related events, epigenetic biomarkers, and allergic disease together. Prospective longitudinal studies are needed along with the collection of target tissues beyond blood samples, such as nasal and skin cells. Finally, global collaboration to increase diverse representation of study participants, particularly those most affected by climate injustice, as well as strengthen replication, validation, and harmonization of measurements will be needed to elucidate the impacts of climate change on the human epigenome.
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Affiliation(s)
- Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, Calif.
| | - Raj Fadadu
- School of Medicine, University of California, San Francisco, Calif
| | - Supinda Bunyavanich
- Division of Allergy and Immunology, Department of Pediatrics, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
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Cardenas A, Fadadu RP, Koppelman GH. Epigenome-wide association studies of allergic disease and the environment. J Allergy Clin Immunol 2023; 152:582-590. [PMID: 37295475 PMCID: PMC10564109 DOI: 10.1016/j.jaci.2023.05.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
The epigenome is at the intersection of the environment, genotype, and cellular response. DNA methylation of cytosine nucleotides, the most studied epigenetic modification, has been systematically evaluated in human studies by using untargeted epigenome-wide association studies (EWASs) and shown to be both sensitive to environmental exposures and associated with allergic diseases. In this narrative review, we summarize findings from key EWASs previously conducted on this topic; interpret results from recent studies; and discuss the strengths, challenges, and opportunities regarding epigenetics research on the environment-allergy relationship. The majority of these EWASs have systematically investigated select environmental exposures during the prenatal and early childhood periods and allergy-associated epigenetic changes in leukocyte-isolated DNA and more recently in nasal cells. Overall, many studies have found consistent DNA methylation associations across cohorts for certain exposures, such as smoking (eg, aryl hydrocarbon receptor repressor gene [AHRR] gene), and allergic diseases (eg, EPX gene). We recommend the integration of both environmental exposures and allergy or asthma within long-term prospective designs to strengthen causality as well as biomarker development. Future studies should collect paired target tissues to examine compartment-specific epigenetic responses, incorporate genetic influences in DNA methylation (methylation quantitative trait locus), replicate findings across diverse populations, and carefully interpret epigenetic signatures from bulk, target tissue or isolated cells.
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Affiliation(s)
- Andres Cardenas
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford University, Stanford, Calif
| | - Raj P Fadadu
- School of Medicine, University of California, San Francisco, Calif
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen, The Netherlands; Groningen Research Institute of Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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Morin A, Thompson EE, Helling BA, Shorey-Kendrick LE, Faber P, Gebretsadik T, Bacharier LB, Kattan M, O'Connor GT, Rivera-Spoljaric K, Wood RA, Barnes KC, Mathias RA, Altman MC, Hansen K, McEvoy CT, Spindel ER, Hartert T, Jackson DJ, Gern JE, McKennan CG, Ober C. A functional genomics pipeline to identify high-value asthma and allergy CpGs in the human methylome. J Allergy Clin Immunol 2023; 151:1609-1621. [PMID: 36754293 PMCID: PMC10859971 DOI: 10.1016/j.jaci.2022.12.828] [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: 08/16/2022] [Revised: 11/24/2022] [Accepted: 12/20/2022] [Indexed: 02/09/2023]
Abstract
BACKGROUND DNA methylation of cytosines at cytosine-phosphate-guanine (CpG) dinucleotides (CpGs) is a widespread epigenetic mark, but genome-wide variation has been relatively unexplored due to the limited representation of variable CpGs on commercial high-throughput arrays. OBJECTIVES To explore this hidden portion of the epigenome, this study combined whole-genome bisulfite sequencing with in silico evidence of gene regulatory regions to design a custom array of high-value CpGs. This study focused on airway epithelial cells from children with and without allergic asthma because these cells mediate the effects of inhaled microbes, pollution, and allergens on asthma and allergic disease risk. METHODS This study identified differentially methylated regions from whole-genome bisulfite sequencing in nasal epithelial cell DNA from a total of 39 children with and without allergic asthma of both European and African ancestries. This study selected CpGs from differentially methylated regions, previous allergy or asthma epigenome-wide association studies (EWAS), or genome-wide association study loci, and overlapped them with functional annotations for inclusion on a custom Asthma&Allergy array. This study used both the custom and EPIC arrays to perform EWAS of allergic sensitization (AS) in nasal epithelial cell DNA from children in the URECA (Urban Environment and Childhood Asthma) birth cohort and using the custom array in the INSPIRE [Infant Susceptibility to Pulmonary Infections and Asthma Following RSV Exposure] birth cohort. Each CpG on the arrays was assigned to its nearest gene and its promotor capture Hi-C interacting gene and performed expression quantitative trait methylation (eQTM) studies for both sets of genes. RESULTS Custom array CpGs were enriched for intermediate methylation levels compared to EPIC CpGs. Intermediate methylation CpGs were further enriched among those associated with AS and for eQTMs on both arrays. CONCLUSIONS This study revealed signature features of high-value CpGs and evidence for epigenetic regulation of genes at AS EWAS loci that are robust to race/ethnicity, ascertainment, age, and geography.
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Affiliation(s)
- Andréanne Morin
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Emma E Thompson
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | | | - Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Ore
| | - Pieter Faber
- Genomics Core, University of Chicago, Chicago, Ill
| | - Tebeb Gebretsadik
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tenn
| | - Leonard B Bacharier
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt University Medical Center, Nashville, Tenn
| | - Meyer Kattan
- Department of Pediatrics, Columbia University Medical Center, New York, NY
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Mass
| | | | - Robert A Wood
- Department of Pediatrics, Johns Hopkins University, Baltimore, Md
| | | | | | - Matthew C Altman
- Systems Immunology Division, Benaroya Research Institute Systems, Seattle, Wash; Department of Medicine, University of Washington, Seattle, Wash
| | - Kasper Hansen
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Md
| | - Cindy T McEvoy
- Department of Pediatrics, Oregon Health and Science University, Portland, Ore
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, Ore
| | - Tina Hartert
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tenn
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Chris G McKennan
- Department of Statistics, University of Pittsburgh, Pittsburgh, Pa.
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill.
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Du X, Jiang Y, Zhang Q, Zhu X, Zhang Y, Liu C, Niu Y, Cai J, Kan H, Chen R. Genome-Wide Profiling of Exosomal Long Noncoding RNAs Following Air Pollution Exposure: A Randomized, Crossover Trial. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2856-2863. [PMID: 36757895 DOI: 10.1021/acs.est.2c05956] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Changes in human genome-wide long noncoding RNAs (lncRNAs) associated with air pollution are unknown. This study aimed to investigate the effect of air pollution on human exosomal lncRNAs. A randomized, crossover trial was conducted among 35 healthy adults. Participants were allocated to 4 h exposure in road (high air pollution) and park (low air pollution) sessions in random order with a 2 week washout period. RNA sequencing was performed to measure lncRNAs. Differential lncRNAs were identified using a linear mixed-effect model. Mean concentrations of air pollutants such as ultrafine particles (UFP), black carbon (BC), carbon monoxide (CO), and nitrogen dioxide (NO2) were 2-3 times higher in the road than those in the park. Fifty-five lncRNAs [false discovery rate (FDR) < 0.05] including lncRNA NORAD, MALAT1, and H19 were changed in response to air pollution exposure. We found that 54 lncRNAs were associated with CO, 49 lncRNAs with UFP, 49 lncRNAs with BC, 48 lncRNAs with NO2, and 4 lncRNAs with PM2.5 (FDR < 0.05). These differential lncRNAs participated in dozens of pathways including cardiovascular signaling, epithelial cell proliferation, inflammation, and transforming growth factor. This trial for the first time profiled changes of human exosomal lncRNAs following air pollution. Our findings revealed multiple biological processes moderated by lncRNAs and provided epigenetic insights into cardiovascular effects of air pollution.
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Affiliation(s)
- Xihao Du
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Yixuan Jiang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Qingli Zhang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Xinlei Zhu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Yang Zhang
- Department of Systems Biology for Medicine, Shanghai Medical College, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Cong Liu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Yue Niu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Jing Cai
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
- National Center for Children's Health, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Renjie Chen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
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Du X, Jiang Y, Li H, Zhang Q, Zhu X, Zhou L, Wang W, Zhang Y, Liu C, Niu Y, Chu C, Cai J, Chen R, Kan H. Traffic-related air pollution and genome-wide DNA methylation: A randomized, crossover trial. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:157968. [PMID: 35963411 DOI: 10.1016/j.scitotenv.2022.157968] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/03/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Traffic-related air pollution (TRAP) has been associated with changes in gene-specific DNA methylation. However, few studies have investigated impact of TRAP exposure on genome-wide DNA methylation in circulating blood of human. OBJECTIVE To explore the association between TRAP exposure and genome-wide DNA methylation. METHODS We conducted a randomized, crossover exposure trial among 35 healthy adults in Shanghai, China. All subjects were randomly allocated to a traffic-free park or a main road for consecutive 4 h, respectively. Blood genome-wide DNA methylation after each exposure session was measured by the Infinium Methylation EPIC BeadChip (850K). The differentially methylated CpGs loci associated with TRAP exposure were identified using linear mixed-effect model. RESULTS The average concentrations of traffic-related air pollutants including black carbon, ultrafine particles, carbon dioxide, and nitrogen dioxide were 2-3 times higher in the road compared to those in the park. Methylation levels of 68 CpG loci were significantly changed (false discovery rate < 0.05) following TRAP exposure, among which 49 were hypermethylated and 19 were hypomethylated. The annotated genes based on the differential CpGs loci were related to pathways in cardiovascular signaling, cytokine signaling, immune response, nervous system signaling, and metabolism. CONCLUSIONS We found that TRAP exposure was associated with DNA methylation in dozens of genes concerning cardiometabolic health. This trial for the first-time profiled genome-wide methylation changes induced by TRAP exposure using the 850K assay, providing epigenetic insights in understanding the cardiometabolic effects of TRAP exposure.
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Affiliation(s)
- Xihao Du
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Yixuan Jiang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Huichu Li
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Qingli Zhang
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Xinlei Zhu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Lu Zhou
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Weidong Wang
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Yang Zhang
- Department of Systems Biology for Medicine and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cong Liu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Yue Niu
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Chen Chu
- Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | - Jing Cai
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China
| | - Renjie Chen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China.
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and NHC Key Lab of Health Technology Assessment, Fudan University, Shanghai 200032, China; Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
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8
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Noureddine N, Chalubinski M, Wawrzyniak P. The Role of Defective Epithelial Barriers in Allergic Lung Disease and Asthma Development. J Asthma Allergy 2022; 15:487-504. [PMID: 35463205 PMCID: PMC9030405 DOI: 10.2147/jaa.s324080] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/06/2022] [Indexed: 12/15/2022] Open
Abstract
The respiratory epithelium constitutes the physical barrier between the human body and the environment, thus providing functional and immunological protection. It is often exposed to allergens, microbial substances, pathogens, pollutants, and environmental toxins, which lead to dysregulation of the epithelial barrier and result in the chronic inflammation seen in allergic diseases and asthma. This epithelial barrier dysfunction results from the disturbed tight junction formation, which are multi-protein subunits that promote cell-cell adhesion and barrier integrity. The increasing interest and evidence of the role of impaired epithelial barrier function in allergy and asthma highlight the need for innovative approaches that can provide new knowledge in this area. Here, we review and discuss the current role and mechanism of epithelial barrier dysfunction in developing allergic diseases and the effect of current allergy therapies on epithelial barrier restoration.
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Affiliation(s)
- Nazek Noureddine
- Division of Clinical Chemistry and Biochemistry, University Children’s Hospital Zurich, Zurich, Switzerland
- Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland
- Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Maciej Chalubinski
- Department of Immunology and Allergy, Medical University of Lodz, Lodz, Poland
| | - Paulina Wawrzyniak
- Division of Clinical Chemistry and Biochemistry, University Children’s Hospital Zurich, Zurich, Switzerland
- Children’s Research Center, University Children’s Hospital Zurich, Zurich, Switzerland
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Mukherjee S, Dasgupta S, Mishra PK, Chaudhury K. Air pollution-induced epigenetic changes: disease development and a possible link with hypersensitivity pneumonitis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:55981-56002. [PMID: 34498177 PMCID: PMC8425320 DOI: 10.1007/s11356-021-16056-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/16/2021] [Indexed: 05/16/2023]
Abstract
Air pollution is a serious threat to our health and has become one of the major causes of many diseases including cardiovascular disease, respiratory disease, and cancer. The association between air pollution and various diseases has long been a topic of research interest. However, it remains unclear how air pollution actually impacts health by modulating several important cellular functions. Recently, some evidence has emerged about air pollution-induced epigenetic changes, which are linked with the etiology of various human diseases. Among several epigenetic modifications, DNA methylation represents the most prominent epigenetic alteration underlying the air pollution-induced pathogenic mechanism. Several other types of epigenetic changes, such as histone modifications, miRNA, and non-coding RNA expression, have also been found to have been linked with air pollution. Hypersensitivity pneumonitis (HP), one of the most prevalent forms of interstitial lung diseases (ILDs), is triggered by the inhalation of certain organic and inorganic substances. HP is characterized by inflammation in the tissues around the lungs' airways and may lead to irreversible lung scarring over time. This review, in addition to other diseases, attempts to understand whether certain pollutants influence HP development through such epigenetic modifications.
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Affiliation(s)
- Suranjana Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
| | - Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Pradyumna K Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, 462030, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
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