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Liao G, Yan Q, Zhang M, Zhang X, Yang J, Huang H, Liu X, Jiang Y, Gong J, Zhan S, Li D, Huang X. Integrative analysis of network pharmacology and proteomics reveal the protective effect of Xiaoqinglong Decotion on neutrophilic asthma. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118102. [PMID: 38561057 DOI: 10.1016/j.jep.2024.118102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Xiaoqinglong Decotion (XQLD) is a commonly used Chinese herbal formula in clinical practice, especially for allergic diseases such as asthma. However, its intrinsic mechanism for the treatment of neutrophilic asthma (NA) remains unclear. AIM OF THE STUDY The aim of this study was to evaluate the efficacy and potential mechanisms of XQLD on NA using network pharmacology and in vivo experiments. MATERIALS AND METHODS First, the active compounds, potential targets and mechanisms of XQLD against NA were initially elucidated by network pharmacology. Then, OVA/CFA-induced NA mice were treated with XQLD to assess its efficacy. Proteins were then analyzed and quantified using a Tandem Mass Tags approach for differentially expressed proteins (DEPs) to further reveal the mechanisms of NA treatment by XQLD. Finally, the hub genes, critical DEPs and potential pathways were validated. RESULTS 176 active compounds and 180 targets against NA were identified in XQLD. Protein-protein interaction (PPI) network revealed CXCL10, CX3CR1, TLR7, NCF1 and FABP4 as hub genes. In vivo experiments showed that XQLD attenuated inflammatory infiltrates, airway mucus secretion and remodeling in the lungs of NA mice. Moreover, XQLD significantly alleviated airway neutrophil inflammation in NA mice by decreasing the expression of IL-8, MPO and NE. XQLD also reduced the levels of CXCL10, CX3CR1, TLR7, NCF1 and FABP4, which are closely associated with neutrophil inflammation. Proteomics analysis identified 28 overlapping DEPs in the control, NA and XQLD groups, and we found that XQLD inhibited ferroptosis signal pathway (elevated GPX4 and decreased ASCL3) as well as the expression of ARG1, MMP12 and SPP1, while activating the Rap1 signaling pathway. CONCLUSION This study revealed that inhibition of ARG1, MMP12 and SPP1 expression as well as ferroptosis pathways, and activation of the Rap1 signaling pathway contribute to the therapeutic effect of XQLD on NA.
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Affiliation(s)
- Gang Liao
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Qian Yan
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China
| | - Miaofen Zhang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China
| | - Xinxin Zhang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China
| | - Jing Yang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China
| | - Huiting Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaohong Liu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yong Jiang
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Jing Gong
- Guangdong Provincial Second Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Shaofeng Zhan
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Detang Li
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Pharmacy, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Xiufang Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China; Lingnan Medical Research Center of Guangzhou University of Chinese Medicine, Guangzhou, China; Guangdong Provincial Clinical Research Academy of Chinese Medicine, Guangzhou, China.
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Puvvula J, Braun JM, DeFranco EA, Ho SM, Leung YK, Huang S, Zhang X, Vuong AM, Kim SS, Percy Z, Calafat AM, Botelho JC, Chen A. Gestational exposure to environmental chemicals and epigenetic alterations in the placenta and cord blood mononuclear cells. EPIGENETICS COMMUNICATIONS 2024; 4:4. [PMID: 38962689 PMCID: PMC11217138 DOI: 10.1186/s43682-024-00027-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
Background Exposure to environmental chemicals such as phthalates, phenols, and polycyclic aromatic hydrocarbons (PAHs) during pregnancy can increase the risk of adverse newborn outcomes. We explored the associations between maternal exposure to select environmental chemicals and DNA methylation in cord blood mononuclear cells (CBMC) and placental tissue (maternal and fetal sides) to identify potential mechanisms underlying these associations. Method This study included 75 pregnant individuals who planned to give birth at the University of Cincinnati Hospital between 2014 and 2017. Maternal urine samples during the delivery visit were collected and analyzed for 37 biomarkers of phenols (12), phthalates (13), phthalate replacements (4), and PAHs (8). Cord blood and placenta tissue (maternal and fetal sides) were also collected to measure the DNA methylation intensities using the Infinium HumanMethylation450K BeadChip. We used linear regression, adjusting for potential confounders, to assess CpG-specific methylation changes in CBMC (n = 54) and placenta [fetal (n = 67) and maternal (n = 68) sides] associated with gestational chemical exposures (29 of 37 biomarkers measured in this study). To account for multiple testing, we used a false discovery rate q-values < 0.05 and presented results by limiting results with a genomic inflation factor of 1±0.5. Additionally, gene set enrichment analysis was conducted using the Kyoto Encyclopedia of Genes and Genomics pathways. Results Among the 29 chemical biomarkers assessed for differential methylation, maternal concentrations of PAH metabolites (1-hydroxynaphthalene, 2-hydroxyfluorene, 4-hydroxyphenanthrene, 1-hydroxypyrene), monocarboxyisononyl phthalate, mono-3-carboxypropyl phthalate, and bisphenol A were associated with altered methylation in placenta (maternal or fetal side). Among exposure biomarkers associated with epigenetic changes, 1-hydroxynaphthalene, and mono-3-carboxypropyl phthalate were consistently associated with differential CpG methylation in the placenta. Gene enrichment analysis indicated that maternal 1-hydroxynaphthalene was associated with lipid metabolism and cellular processes of the placenta. Additionally, mono-3-carboxypropyl phthalate was associated with organismal systems and genetic information processing of the placenta. Conclusion Among the 29 chemical biomarkers assessed during delivery, 1-hydroxynaphthalene and mono-3-carboxypropyl phthalate were associated with DNA methylation in the placenta. Supplementary Information The online version contains supplementary material available at 10.1186/s43682-024-00027-7.
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Affiliation(s)
- Jagadeesh Puvvula
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Joseph M. Braun
- Department of Epidemiology, Brown University, Providence, RI USA
| | - Emily A. DeFranco
- Department of Obstetrics and Gynecology, College of Medicine, University of Kentucky, Lexington, KY USA
| | - Shuk-Mei Ho
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - Yuet-Kin Leung
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR USA
| | - Shouxiong Huang
- Pathogen-Host Interaction Program, Texas Biomedical Research Institute, San Antonio, TX USA
| | - Xiang Zhang
- Department of Environmental & Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH USA
| | - Ann M. Vuong
- Department of Epidemiology and Biostatistics, School of Public Health, University of Nevada Las Vegas, Las Vegas, NV USA
| | - Stephani S. Kim
- Health Research, Battelle Memorial Institute, Columbus, OH USA
| | - Zana Percy
- Department of Environmental & Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH USA
| | - Antonia M. Calafat
- National Center for Environmental Health, U.S. Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Julianne C. Botelho
- National Center for Environmental Health, U.S. Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Aimin Chen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
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Liao Y, Cavalcante R, Waller J, Deng F, Scruggs A, Huang Y, Atasoy U, Chen Y, Huang S. Differences in the DNA Methylome of T cells in Adults With Asthma of Varying Severity. RESEARCH SQUARE 2024:rs.3.rs-4476948. [PMID: 38946998 PMCID: PMC11213176 DOI: 10.21203/rs.3.rs-4476948/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background DNA methylation plays a critical role in asthma development, but differences in DNA methylation among adults with varying asthma severity or asthma endotypes are less well-defined. Objective To examine how DNA methylomic patterns differ among adults with asthma based on asthma severity and airway inflammation. Methods Peripheral blood T cells from 35 adults with asthma in Beijing, China were serially collected over time (130 samples total) and analyzed for global DNA methylation using the Illumina MethylationEPIC Array. Differential methylation was compared among subjects with varying airway inflammation and severity, as measured by fraction of exhaled nitric oxide, forced expiratory volume in one second (FEV1), and Asthma Control Test (ACT) scores. Results Significant differences in DNA methylation were noted among subjects with different degrees of airway inflammation and asthma severity. These differences in DNA methylation were annotated to genes that were enriched in pathways related to asthma or T cell function and included gene ontology categories related to MHC class II assembly, T cell activation, interleukin (IL)-1, and IL-12. Genes related to P450 drug metabolism, glutathione metabolism, and developmental pathways were also differentially methylated in comparisons between subjects with high vs low FEV1 and ACT. Notable genes that were differentially methylated based on asthma severity included RUNX3, several members of the HLA family, AGT, PTPRC, PTPRJ, and several genes downstream of the JAK2 and TNF signaling pathway. Conclusion These findings demonstrate how adults with asthma of varying severity possess differences in peripheral blood T cell DNA methylation that contribute to the phenotype and severity of their overall disease.
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Kobiela A, Hewelt-Belka W, Frąckowiak JE, Kordulewska N, Hovhannisyan L, Bogucka A, Etherington R, Piróg A, Dapic I, Gabrielsson S, Brown SJ, Ogg GS, Gutowska-Owsiak D. Keratinocyte-derived small extracellular vesicles supply antigens for CD1a-resticted T cells and promote their type 2 bias in the context of filaggrin insufficiency. Front Immunol 2024; 15:1369238. [PMID: 38585273 PMCID: PMC10995404 DOI: 10.3389/fimmu.2024.1369238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/07/2024] [Indexed: 04/09/2024] Open
Abstract
Introduction Exosome-enriched small extracellular vesicles (sEVs) are nanosized organelles known to participate in long distance communication between cells, including in the skin. Atopic dermatitis (AD) is a chronic inflammatory skin disease for which filaggrin (FLG) gene mutations are the strongest genetic risk factor. Filaggrin insufficiency affects multiple cellular function, but it is unclear if sEV-mediated cellular communication originating from the affected keratinocytes is also altered, and if this influences peptide and lipid antigen presentation to T cells in the skin. Methods Available mRNA and protein expression datasets from filaggrin-insufficient keratinocytes (shFLG), organotypic models and AD skin were used for gene ontology analysis with FunRich tool. sEVs secreted by shFLG and control shC cells were isolated from conditioned media by differential centrifugation. Mass spectrometry was carried out for lipidomic and proteomic profiling of the cells and sEVs. T cell responses to protein, peptide, CD1a lipid antigens, as well as phospholipase A2-digested or intact sEVs were measured by ELISpot and ELISA. Results Data analysis revealed extensive remodeling of the sEV compartment in filaggrin insufficient keratinocytes, 3D models and the AD skin. Lipidomic profiles of shFLGsEV showed a reduction in the long chain (LCFAs) and polyunsaturated fatty acids (PUFAs; permissive CD1a ligands) and increased content of the bulky headgroup sphingolipids (non-permissive ligands). This resulted in a reduction of CD1a-mediated interferon-γ T cell responses to the lipids liberated from shFLG-generated sEVs in comparison to those induced by sEVs from control cells, and an increase in interleukin 13 secretion. The altered sEV lipidome reflected a generalized alteration in the cellular lipidome in filaggrin-insufficient cells and the skin of AD patients, resulting from a downregulation of key enzymes implicated in fatty acid elongation and desaturation, i.e., enzymes of the ACSL, ELOVL and FADS family. Discussion We determined that sEVs constitute a source of antigens suitable for CD1a-mediated presentation to T cells. Lipids enclosed within the sEVs secreted on the background of filaggrin insufficiency contribute to allergic inflammation by reducing type 1 responses and inducing a type 2 bias from CD1a-restricted T cells, thus likely perpetuating allergic inflammation in the skin.
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Affiliation(s)
- Adrian Kobiela
- Laboratory of Experimental and Translational Immunology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Gdańsk, Poland
| | - Weronika Hewelt-Belka
- Department of Analytical Chemistry, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Joanna E. Frąckowiak
- Laboratory of Experimental and Translational Immunology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Gdańsk, Poland
| | - Natalia Kordulewska
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, Olsztyn, Poland
| | - Lilit Hovhannisyan
- Laboratory of Experimental and Translational Immunology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Bogucka
- The Mass Spectrometry Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Rachel Etherington
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Artur Piróg
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Susanne Gabrielsson
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Sara J. Brown
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Graham S. Ogg
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Danuta Gutowska-Owsiak
- Laboratory of Experimental and Translational Immunology, Intercollegiate Faculty of Biotechnology of the University of Gdańsk and the Medical University of Gdańsk, Gdańsk, Poland
- MRC Human Immunology Unit, NIHR Biomedical Research Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
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Gore S, Meche B, Shao D, Ginnett B, Zhou K, Azad RK. DiseaseNet: a transfer learning approach to noncommunicable disease classification. BMC Bioinformatics 2024; 25:107. [PMID: 38468193 PMCID: PMC10926612 DOI: 10.1186/s12859-024-05734-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
As noncommunicable diseases (NCDs) pose a significant global health burden, identifying effective diagnostic and predictive markers for these diseases is of paramount importance. Epigenetic modifications, such as DNA methylation, have emerged as potential indicators for NCDs. These have previously been exploited in other contexts within the framework of neural network models that capture complex relationships within the data. Applications of neural networks have led to significant breakthroughs in various biological or biomedical fields but these have not yet been effectively applied to NCD modeling. This is, in part, due to limited datasets that are not amenable to building of robust neural network models. In this work, we leveraged a neural network trained on one class of NCDs, cancer, as the basis for a transfer learning approach to non-cancer NCD modeling. Our results demonstrate promising performance of the model in predicting three NCDs, namely, arthritis, asthma, and schizophrenia, for the respective blood samples, with an overall accuracy (f-measure) of 94.5%. Furthermore, a concept based explanation method called Testing with Concept Activation Vectors (TCAV) was used to investigate the importance of the sample sources and understand how future training datasets for multiple NCD models may be improved. Our findings highlight the effectiveness of transfer learning in developing accurate diagnostic and predictive models for NCDs.
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Affiliation(s)
- Steven Gore
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Bailey Meche
- Department of Mathematics, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Danyang Shao
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Benjamin Ginnett
- Department of Engineering, Eastern Arizona College, Thatcher, AZ, USA
| | - Kelly Zhou
- Department of Computer Science and Engineering, University of North Texas, Denton, TX, USA
| | - Rajeev K Azad
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.
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Powell WT, Reeves SR. From small to big, using microRNA profiling to investigate infant origins of childhood asthma. Eur Respir J 2023; 62:2301052. [PMID: 37536728 DOI: 10.1183/13993003.01052-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Affiliation(s)
- Weston T Powell
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Center for Respiratory Biology and Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA
| | - Stephen R Reeves
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Center for Respiratory Biology and Therapeutics, Seattle Children's Research Institute, Seattle, WA, USA
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Loftus CT, Szpiro AA, Workman T, Wallace ER, Hazlehurst MF, Day DB, Ni Y, Carroll KN, Adgent MA, Moore PE, Barrett ES, Nguyen RHN, Kannan K, Robinson M, Masterson EE, Tylavsky FA, Bush NR, LeWinn KZ, Sathyanarayana S, Karr CJ. Maternal exposure to urinary polycyclic aromatic hydrocarbons (PAH) in pregnancy and childhood asthma in a pooled multi-cohort study. ENVIRONMENT INTERNATIONAL 2022; 170:107494. [PMID: 36279735 PMCID: PMC9810359 DOI: 10.1016/j.envint.2022.107494] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/06/2022] [Accepted: 08/29/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Prenatal exposure to polycyclic aromatic hydrocarbons (PAH) may increase risk of pediatric asthma, but existing human studies are limited. OBJECTIVES We estimated associations between gestational PAHs and pediatric asthma in a diverse US sample and evaluated effect modification by child sex, maternal asthma, and prenatal vitamin D status. METHODS We pooled two prospective pregnancy cohorts in the ECHO PATHWAYS Consortium, CANDLE and TIDES, for an analytic sample of N = 1296 mother-child dyads. Mono-hydroxylated PAH metabolites (OH-PAHs) were measured in mid-pregnancy urine. Mothers completed the International Study on Allergies and Asthma in Childhood survey at child age 4-6 years. Poisson regression with robust standard errors was used to estimate relative risk of current wheeze, current asthma, ever asthma, and strict asthma associated with each metabolite, adjusted for potential confounders. We used interaction models to assess effect modification. We explored associations between OH-PAH mixtures and outcomes using logistic weighted quantile sum regression augmented by a permutation test to control Type 1 errors. RESULTS The sociodemographically diverse sample spanned five cities. Mean (SD) child age at assessment was 4.4 (0.4) years. While there was little evidence that either individual OH-PAHs or mixtures were associated with outcomes, we observed effect modification by child sex for most pairs of OH-PAHs and outcomes, with adverse associations specific to females. For example, a 2-fold increase in 2-hydroxy-phenanthrene was associated with current asthma in females but not males (RRfemale = 1.29 [95 % CI: 1.09, 1.52], RRmale = 0.95 [95 % CI: 0.79, 1.13]; pinteraction = 0.004). There was no consistent evidence of modification by vitamin D status or maternal asthma. DISCUSSION This analysis, the largest cohort study of gestational PAH exposure and childhood asthma to date, suggests adverse associations for females only. These preliminary findings are consistent with hypothesized endocrine disruption properties of PAHs, which may lead to sexually dimorphic effects.
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Affiliation(s)
- Christine T Loftus
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA.
| | - Adam A Szpiro
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Tomomi Workman
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Erin R Wallace
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Marnie F Hazlehurst
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Drew B Day
- Department of Child Health, Behavior, and Development, Seattle Children's Research Institute, Seattle, WA, USA
| | - Yu Ni
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Kecia N Carroll
- Department of Pediatrics, Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Margaret A Adgent
- Department of Pediatrics, College of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paul E Moore
- Division of Allergy, Immunology, and Pulmonology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emily S Barrett
- Department of Epidemiology, Environmental and Occupational Health Sciences Institute, Rutgers School of Public Health, Piscataway, NJ, USA
| | - Ruby H N Nguyen
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Kurunthachalam Kannan
- Department of Pediatrics, Department of Environmental Medicine, New York University School of Medicine, New York City, NY, USA
| | - Morgan Robinson
- Department of Pediatrics, Department of Environmental Medicine, New York University School of Medicine, New York City, NY, USA
| | - Erin E Masterson
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Frances A Tylavsky
- Department of Preventive Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Nicole R Bush
- Department of Psychiatry and Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kaja Z LeWinn
- Department of Psychiatry and Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sheela Sathyanarayana
- Department of Child Health, Behavior, and Development, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, School of Medicine, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Catherine J Karr
- Department of Pediatrics, School of Medicine, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
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Starling AP, Wood C, Liu C, Kechris K, Yang IV, Friedman C, Thomas DSK, Peel JL, Adgate JL, Magzamen S, Martenies SE, Allshouse WB, Dabelea D. Ambient air pollution during pregnancy and DNA methylation in umbilical cord blood, with potential mediation of associations with infant adiposity: The Healthy Start study. ENVIRONMENTAL RESEARCH 2022; 214:113881. [PMID: 35835166 PMCID: PMC10402394 DOI: 10.1016/j.envres.2022.113881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 06/11/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Prenatal exposure to ambient air pollution has been associated with adverse offspring health outcomes. Childhood health effects of prenatal exposures may be mediated through changes to DNA methylation detectable at birth. METHODS Among 429 non-smoking women in a cohort study of mother-infant pairs in Colorado, USA, we estimated associations between prenatal exposure to ambient fine particulate matter (PM2.5) and ozone (O3), and epigenome-wide DNA methylation of umbilical cord blood cells at delivery (2010-2014). We calculated average PM2.5 and O3 in each trimester of pregnancy and the full pregnancy using inverse-distance-weighted interpolation. We fit linear regression models adjusted for potential confounders and cell proportions to estimate associations between air pollutants and methylation at each of 432,943 CpGs. Differentially methylated regions (DMRs) were identified using comb-p. Previously in this cohort, we reported positive associations between 3rd trimester O3 exposure and infant adiposity at 5 months of age. Here, we quantified the potential for mediation of that association by changes in DNA methylation in cord blood. RESULTS We identified several DMRs for each pollutant and period of pregnancy. The greatest number of significant DMRs were associated with third trimester PM2.5 (21 DMRs). No single CpGs were associated with air pollutants at a false discovery rate <0.05. We found that up to 8% of the effect of 3rd trimester O3 on 5-month adiposity may be mediated by locus-specific methylation changes, but mediation estimates were not statistically significant. CONCLUSIONS Differentially methylated regions in cord blood were identified in association with maternal exposure to PM2.5 and O3. Genes annotated to the significant sites played roles in cardiometabolic disease, immune function and inflammation, and neurologic disorders. We found limited evidence of mediation by DNA methylation of associations between third trimester O3 exposure and 5-month infant adiposity.
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Affiliation(s)
- Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Cheyret Wood
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Cuining Liu
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ivana V Yang
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Chloe Friedman
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Deborah S K Thomas
- Department of Geography and Earth Sciences, University of North Carolina Charlotte, NC, USA
| | - Jennifer L Peel
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - John L Adgate
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sheryl Magzamen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Department of Epidemiology, Colorado School of Public Health, Colorado State University, Fort Collins, CO, USA
| | - Sheena E Martenies
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - William B Allshouse
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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9
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Das DN, Ravi N. Influences of polycyclic aromatic hydrocarbon on the epigenome toxicity and its applicability in human health risk assessment. ENVIRONMENTAL RESEARCH 2022; 213:113677. [PMID: 35714684 DOI: 10.1016/j.envres.2022.113677] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The existence of polycyclic aromatic hydrocarbons (PAHs) in ambient air is an escalating concern worldwide because of their ability to cause cancer and induce permanent changes in the genetic material. Growing evidence implies that during early life-sensitive stages, the risk of progression of acute and chronic diseases depends on epigenetic changes initiated by the influence of environmental cues. Several reports deciphered the relationship between exposure to environmental chemicals and epigenetics, and have known toxicants that alter the epigenetic states. Amongst PAHs, benzo[a]pyrene (B[a]P) is accepted as a group 1 cancer-causing agent by the International Agency for the Research on Cancer (IARC). B[a]P is a well-studied pro-carcinogen that is metabolically activated by the aryl hydrocarbon receptor (AhR)/cytochrome P450 pathway. Cytochrome P450 plays a pivotal role in the stimulation step, which is essential for DNA adduct formation. Accruing evidence suggests that epigenetic alterations assume a fundamental part in PAH-promoted carcinogenesis. This interaction between PAHs and epigenetic factors results in an altered profile of these marks, globally and locus-specific. Some of the epigenetic changes due to exposure to PAHs lead to increased disease susceptibility and progression. It is well understood that exposure to environmental carcinogens, such as PAH triggers disease pathways through changes in the genome. Several evidence reported due to the epigenome-wide association studies, that early life adverse environmental events may trigger widespread and persistent variations in transcriptional profiling. Moreover, these variations respond to DNA damage and/or a consequence of epigenetic modifications that need further investigation. Growing evidence has associated PAHs with epigenetic variations involving alterations in DNA methylation, histone modification, and micro RNA (miRNA) regulation. Epigenetic alterations to PAH exposure were related to chronic diseases, such as pulmonary disease, cardiovascular disease, endocrine disruptor, nervous system disorder, and cancer. This hormetic response gives a novel perception concerning the toxicity of PAHs and the biological reaction that may be a distinct reliance on exposure. This review sheds light on understanding the latest evidence about how PAHs can alter epigenetic patterns and human health. In conclusion, as several epigenetic change mechanisms remain unclear yet, further analyses derived from PAHs exposure must be performed to find new targets and disease biomarkers. In spite of the current limitations, numerous evidence supports the perception that epigenetics grips substantial potential for advancing our knowledge about the molecular mechanisms of environmental toxicants, also for predicting health-associated risks due to environmental circumstances exposure and individual susceptibility.
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Affiliation(s)
- Durgesh Nandini Das
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Nathan Ravi
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, 63110, USA; Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA; Institute for Public Health, Washington University in St. Louis, St. Louis, MO, 63110, USA; Veterans Affairs St. Louis Hospital, St. Louis, MO, 63106, USA.
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10
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Govender P, Ghai M, Okpeku M. Sex-specific DNA methylation: impact on human health and development. Mol Genet Genomics 2022; 297:1451-1466. [PMID: 35969270 DOI: 10.1007/s00438-022-01935-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
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11
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Sharma S, Yang IV, Schwartz DA. Epigenetic regulation of immune function in asthma. J Allergy Clin Immunol 2022; 150:259-265. [PMID: 35717251 PMCID: PMC9378596 DOI: 10.1016/j.jaci.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 12/13/2022]
Abstract
Asthma is a common complex respiratory disease characterized by chronic airway inflammation and partially reversible airflow obstruction resulting from genetic and environmental determinants. Because epigenetic marks influence gene expression and can be modified by both environmental exposures and genetic variation, they are increasingly recognized as relevant to the pathogenesis of asthma and may be a key link between environmental exposures and asthma susceptibility. Unlike changes to DNA sequence, epigenetic signatures are dynamic and reversible, creating an opportunity for not only therapeutic targets but may serve as biomarkers to follow disease course and identify molecular subtypes in heterogeneous diseases such as asthma. In this review, we will examine the relationship between asthma and 3 key epigenetic processes that modify gene expression: DNA methylation, modification of histone tails, and noncoding RNAs. In addition to presenting a comprehensive assessment of the existing epigenetic studies focusing on immune regulation in asthma, we will discuss future directions for epigenetic investigation in allergic airway disease.
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Affiliation(s)
- Sunita Sharma
- Divisions of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo.
| | - Ivana V Yang
- Divisions of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo; Divisions of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - David A Schwartz
- Divisions of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colo
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12
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DNA methylation signatures in airway cells from adult children of asthmatic mothers reflect subtypes of severe asthma. Proc Natl Acad Sci U S A 2022; 119:e2116467119. [PMID: 35666868 PMCID: PMC9214527 DOI: 10.1073/pnas.2116467119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Maternal asthma is one of the most replicated risk factors for childhood-onset asthma. However, the underlying mechanisms are unknown. We identified DNA methylation signatures in bronchial epithelial cells from adults with asthma that were specific to those with a mother with asthma. These maternal asthma-associated methylation signatures were correlated with distinct gene regulatory pathways and clinical features. Genes in 16 pathways discriminated cases with and without maternal asthma and suggested impaired T cell signaling and responses to viral and bacterial pathogens in asthmatic children of an asthmatic mother. Our findings suggest that the prenatal environment in pregnancies of mothers with asthma alters epigenetically mediated developmental programs that may lead to severe asthma in their children through diverse gene regulatory pathways. Maternal asthma (MA) is among the most consistent risk factors for asthma in children. Possible mechanisms for this observation are epigenetic modifications in utero that have lasting effects on developmental programs in children of mothers with asthma. To test this hypothesis, we performed differential DNA methylation analyses of 398,186 individual CpG sites in primary bronchial epithelial cells (BECs) from 42 nonasthma controls and 88 asthma cases, including 56 without MA (NMA) and 32 with MA. We used weighted gene coexpression network analysis (WGCNA) of 69 and 554 differentially methylated CpGs (DMCs) that were specific to NMA and MA cases, respectively, compared with controls. WGCNA grouped 66 NMA-DMCs and 203 MA-DMCs into two and five comethylation modules, respectively. The eigenvector of one MA-associated module (turquoise) was uniquely correlated with 85 genes expressed in BECs and enriched for 36 pathways, 16 of which discriminated between NMA and MA using machine learning. Genes in all 16 pathways were decreased in MA compared with NMA cases (P = 7.1 × 10−3), a finding that replicated in nasal epithelial cells from an independent cohort (P = 0.02). Functional interpretation of these pathways suggested impaired T cell signaling and responses to viral and bacterial pathogens. The MA-associated turquoise module eigenvector was additionally correlated with clinical features of severe asthma and reflective of type 2 (T2)-low asthma (i.e., low total serum immunoglobulin E, fractional exhaled nitric oxide, and eosinophilia). Overall, these data suggest that MA alters diverse epigenetically mediated pathways that lead to distinct subtypes of severe asthma in adults, including hard-to-treat T2-low asthma.
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13
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Hamzai L, Lopez Galvez N, Hoh E, Dodder NG, Matt GE, Quintana PJ. A systematic review of the use of silicone wristbands for environmental exposure assessment, with a focus on polycyclic aromatic hydrocarbons (PAHs). JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2022; 32:244-258. [PMID: 34302044 DOI: 10.1038/s41370-021-00359-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Exposure assessment is critical for connecting environmental pollutants to health outcomes and evaluating impacts of interventions or environmental policies. Silicone wristbands (SWBs) show promise for multi-pollutant exposure assessment, including polycyclic aromatic hydrocarbons (PAHs), a ubiquitous class of toxic environmental pollutants. OBJECTIVE To review published studies where SWBs were worn on the wrist for human environmental exposure assessments and evaluate the ability of SWBs to capture personal exposures, identify gaps which need to be addressed to implement this tool, and make recommendations for future studies to advance the field of exposure science through utilization of SWBs. METHODS We performed a systematic search and a cited reference search in Scopus and extracted key study descriptions. RESULTS Thirty-nine unique studies were identified, with analytes including PAHs, pesticides, flame retardants, and tobacco products. SWBs were shipped under ambient conditions without apparent analyte loss, indicating utility for global exposure and health studies. Nineteen articles detected a total of 60 PAHs in at least one SWB. Correlations with other concurrent biological and air measurements indicate the SWB captures exposure to flame retardants, tobacco products, and PAHs. SIGNIFICANCE SWBs show promise as a simple-to-deploy tool to estimate environmental and occupational exposures to chemical mixtures, including PAHs.
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Affiliation(s)
- Laila Hamzai
- School of Public Health, San Diego State University, San Diego, CA, USA
| | | | - Eunha Hoh
- School of Public Health, San Diego State University, San Diego, CA, USA
| | - Nathan G Dodder
- San Diego State University Research Foundation, San Diego, CA, USA
| | - Georg E Matt
- Department of Psychology, San Diego State University, San Diego, CA, USA
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14
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Bolte EE, Moorshead D, Aagaard KM. Maternal and early life exposures and their potential to influence development of the microbiome. Genome Med 2022; 14:4. [PMID: 35016706 PMCID: PMC8751292 DOI: 10.1186/s13073-021-01005-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/16/2021] [Indexed: 02/07/2023] Open
Abstract
At the dawn of the twentieth century, the medical care of mothers and children was largely relegated to family members and informally trained birth attendants. As the industrial era progressed, early and key public health observations among women and children linked the persistence of adverse health outcomes to poverty and poor nutrition. In the time hence, numerous studies connecting genetics ("nature") to public health and epidemiologic data on the role of the environment ("nurture") have yielded insights into the importance of early life exposures in relation to the occurrence of common diseases, such as diabetes, allergic and atopic disease, cardiovascular disease, and obesity. As a result of these parallel efforts in science, medicine, and public health, the developing brain, immune system, and metabolic physiology are now recognized as being particularly vulnerable to poor nutrition and stressful environments from the start of pregnancy to 3 years of age. In particular, compelling evidence arising from a diverse array of studies across mammalian lineages suggest that modifications to our metagenome and/or microbiome occur following certain environmental exposures during pregnancy and lactation, which in turn render risk of childhood and adult diseases. In this review, we will consider the evidence suggesting that development of the offspring microbiome may be vulnerable to maternal exposures, including an analysis of the data regarding the presence or absence of a low-biomass intrauterine microbiome.
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Affiliation(s)
- Erin E Bolte
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, USA
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, USA
| | - David Moorshead
- Immunology & Microbiology Graduate Program, Baylor College of Medicine, Houston, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, USA
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, USA
| | - Kjersti M Aagaard
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
- Immunology & Microbiology Graduate Program, Baylor College of Medicine, Houston, USA.
- Medical Scientist Training Program, Baylor College of Medicine, Houston, USA.
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, USA.
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, USA.
- Department of Molecular & Cell Biology, Baylor College of Medicine, Houston, USA.
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, USA.
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15
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Abstract
The prevalence of allergic diseases such as asthma is globally increasing, posing threat to the life quality of the affected population. Genome-wide association studies (GWAS) suggest that genetic variations only account for a small proportion of immunoglobulin E (IgE)-mediated type I hypersensitivity. Recently, epigenetics has gained attention as an approach to further understand the missing heritability and underpinning mechanisms of allergic diseases. Furthermore, epigenetic regulation allows the evaluation of the interaction between an individual's genetic predisposition and their environmental exposures. This chapter summarizes several large-scale epigenome-wide association studies (EWAS) on asthma and other allergic diseases and draws a blueprint for future analysis and research direction.
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Affiliation(s)
- Yale Jiang
- 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.
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16
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Tan H, Liu X, Yin S, Zhao C, Su L, Li X, Khalid M, Setälä H, Hui N. Immune-mediated disease associated microbial community responded to PAH stress in phyllosphere of roadside greenspaces in Shanghai. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118379. [PMID: 34662594 DOI: 10.1016/j.envpol.2021.118379] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms in urban greenspaces play key roles in ecosystem service provision and potentially influence human health. Increasing evidence suggests that anthropogenic disturbance poses constant stress on urban microbial communities, yet, as previous studies have focused on non-contaminated greenspaces, it has remained largely unknown how microorganisms respond to anthropogenic stress in roadside greenspaces with contamination. Our previous effort determined phyllosphere PAHs of camphor trees in 84 sites of roadside greenspaces along the urban-rural gradient in Shanghai. Here, we further investigated the phyllosphere microbial communities (PMCs) of the same sites across the same urban categories, including urban, suburban, and rural areas using high-throughput DNA sequencing. We aimed to explore how PMCs, especially those associated with immune-mediated diseases (IMDs), were affected by PAHs and the surrounding land-use types. We found that several microorganisms associated with increasing IMD risk were stimulated by PAHs. The composition of PMCs differed between the three urban categories which can be largely explained by the variation of phyllosphere PAH concentration and the surrounding land-use types. Similar to our previous study, suburban areas were linked with the most potential adverse health effects, where we observed the lowest bacterial diversity, the highest relative abundance of IMD-associated bacteria, and the highest relative abundance of Pathotroph. Urban green-blue infrastructure (GBI) was positively correlated with the diversity of PMCs, whereas urban grey infrastructure tended to homogenize PMCs. Notably, GBI also reduced the relative abundance of IMD-associated and pathogenic microbes, indicating the potential health benefits of GBI in land-use planning. Taken together, our study emphasizes the need to further investigate environmental communities in contaminated traffic environments, as human microbiomes are directly exposed to risky microorganisms.
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Affiliation(s)
- Haoxin Tan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, 200240, Shanghai, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Xinxin Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Instrumental Analysis Center, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Shan Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, 200240, Shanghai, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Chang Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, 200240, Shanghai, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Lantian Su
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, 200240, Shanghai, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Xiaoxiao Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, 200240, Shanghai, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Muhammad Khalid
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, 200240, Shanghai, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China.
| | - Heikki Setälä
- Department of Environmental Sciences, University of Helsinki, FIN-15140, Lahti, Finland.
| | - Nan Hui
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China; Department of Environmental Sciences, University of Helsinki, FIN-15140, Lahti, Finland.
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17
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Bermick J, Schaller M. Epigenetic regulation of pediatric and neonatal immune responses. Pediatr Res 2022; 91:297-327. [PMID: 34239066 DOI: 10.1038/s41390-021-01630-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Epigenetic regulation of transcription is a collective term that refers to mechanisms known to regulate gene transcription without changing the underlying DNA sequence. These mechanisms include DNA methylation and histone tail modifications which influence chromatin accessibility, and microRNAs that act through post-transcriptional gene silencing. Epigenetics is known to regulate a variety of biological processes, and the role of epigtenetics in immunity and immune-mediated diseases is becoming increasingly recognized. While DNA methylation is the most widely studied, each of these systems play an important role in the development and maintenance of appropriate immune responses. There is clear evidence that epigenetic mechanisms contribute to developmental stage-specific immune responses in a cell-specific manner. There is also mounting evidence that prenatal exposures alter epigenetic profiles and subsequent immune function in exposed offspring. Early life exposures that are associated with poor long-term health outcomes also appear to impact immune specific epigenetic patterning. Finally, each of these epigenetic mechanisms contribute to the pathogenesis of a wide variety of diseases that manifest during childhood. This review will discuss each of these areas in detail. IMPACT: Epigenetics, including DNA methylation, histone tail modifications, and microRNA expression, dictate immune cell phenotypes. Epigenetics influence immune development and subsequent immune health. Prenatal, perinatal, and postnatal exposures alter immune cell epigenetic profiles and subsequent immune function. Numerous pediatric-onset diseases have an epigenetic component. Several successful strategies for childhood diseases target epigenetic mechanisms.
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Affiliation(s)
- Jennifer Bermick
- Department of Pediatrics, Division of Neonatology, University of Iowa, Iowa City, IA, USA. .,Iowa Inflammation Program, University of Iowa, Iowa City, IA, USA.
| | - Matthew Schaller
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Florida, Gainesville, FL, USA
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18
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Hu J, Bao Y, Huang H, Zhang Z, Chen F, Li L, Wu Q. The preliminary investigation of potential response biomarkers to PAHs exposure on childhood asthma. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2022; 32:82-93. [PMID: 33972693 DOI: 10.1038/s41370-021-00334-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Exposure to polycyclic aromatic hydrocarbons (PAHs) is a potential risk factor for asthma prevalence. This study aims to explore whether PAHs exposure is associated with childhood asthma by altering microbial diversity and metabolic profiles. METHODS Thirty children with asthma and 30 children as control in Nanjing, China were recruited. Urinary 1-hydroxypyrene (1-OHPyr) level was determined by UPLC-Orbitrap-MS as a PAHs exposure biomarker. Logistic regression was conducted to investigate the association between 1-OHPyr and childhood asthma. Microbial diversity was analyzed by 16S rRNA gene sequencing. Metabolic profiles were obtained by UPLC-Orbitrap-MS methods. Differential microbiota and metabolites were screened and selected as response biomarkers or intermediates. Mediation analysis was conducted to assess the association between PAHs and asthma mediated by intermediates. RESULTS Participating children with and without asthma aged 6.43 ± 2.23 years. The urinary 1-OHPyr level ranged from 0.10 to 1.51 μmol/mol (creatinine corrected) in the participants. The urinary 1-OHPyr level was associated with childhood asthma (OR = 7.21, 95% CI: 1.03-50.42 per 1 μmol/mol unit). Microbial diversity was decreased in the group with asthma and there was a significant shift in the abundance of Proteobacteria (at the phylum level), Veillonella and Prevotella (at the genus level). The enrichment pathway analysis showed that differentially expressed metabolites were involved in purine metabolism, amino acid metabolism, and lipid and fatty acid metabolism. The urinary 1-OHPyr level was associated with the abundance of Actinomyces sp. oral clone IO076 and 7-methylguanine that showed a mediation effect on the association between urinary 1-OHPyr levels and childhood asthma by mediation analysis. CONCLUSIONS Urinary 1-OHPyr exposure was associated with childhood asthma, microbial diversity, and metabolic profiles. Microbial diversity and metabolic profiles may be intermediates as response biomarkers to PAHs exposure in childhood asthma. Further research is needed to confirm these study results and determine the underlying mechanism.
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Affiliation(s)
- Jinye Hu
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, Nanjing Medical University, Nanjing, China
| | - Yuling Bao
- Department of Respiratory, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Huang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhan Zhang
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, Nanjing Medical University, Nanjing, China
| | - Feng Chen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lei Li
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, Nanjing Medical University, Nanjing, China.
| | - Qian Wu
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, Nanjing Medical University, Nanjing, China.
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19
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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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20
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Role of Epigenetics in the Pathogenesis, Treatment, Prediction, and Cellular Transformation of Asthma. Mediators Inflamm 2021; 2021:9412929. [PMID: 34566492 PMCID: PMC8457970 DOI: 10.1155/2021/9412929] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
Asthma is a mysterious disease with heterogeneity in etiology, pathogenesis, and clinical phenotypes. Although ongoing studies have provided a better understanding of asthma, its natural history, progression, pathogenesis, diversified phenotypes, and even the exact epigenetic linkage between childhood asthma and adult-onset/old age asthma remain elusive in many aspects. Asthma heritability has been established through genetic studies, but genetics is not the only influencing factor in asthma. The increasing incidence and some unsolved queries suggest that there may be other elements related to asthma heredity. Epigenetic mechanisms link genetic and environmental factors with developmental trajectories in asthma. This review provides an overview of asthma epigenetics and its components, including several epigenetic studies on asthma, and discusses the epigenetic linkage between childhood asthma and adult-onset/old age asthma. Studies involving asthma epigenetics present valuable novel approaches to solve issues related to asthma. Asthma epigenetic research guides us towards gene therapy and personalized T cell therapy, directs the discovery of new therapeutic agents, predicts long-term outcomes in severe cases, and is also involved in the cellular transformation of childhood asthma to adult-onset/old age asthma.
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Wang C, Wang D, Zhao H, Wang J, Liu N, Shi H, Tian J, Wang X, Zhang Z. Traffic-related PM 2.5 and diverse constituents disturb the balance of Th17/Treg cells by STAT3/RORγt-STAT5/Foxp3 signaling pathway in a rat model of asthma. Int Immunopharmacol 2021; 96:107788. [PMID: 34162152 DOI: 10.1016/j.intimp.2021.107788] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/08/2023]
Abstract
Water-soluble ions (WSI) and organic extract (OE) in traffic-related particulate matter with aerodynamic diameters ≤ 2.5 μm (TRPM2.5) are potential risk factors for asthma exacerbation. Although CD4+ T lymphocytes mediated immune response is involved in the pathogenesis of asthma, the effect of WSI-TRPM2.5 and OE-TRPM2.5 on the balance of Th17/Treg cells in asthma remains poorly understood. In this study, the ovalbumin (OVA)-sensitized rats were repeatedly exposure to TRPM2.5 (3 mg/kg·bw), WSI-TRPM2.5 (1.8 mg/kg·bw, 7.2 mg/kg·bw) and OE-TRPM2.5 (0.6 mg/kg·bw, 2.4 mg/kg·bw) every three days for five times. The inflammation response and hyperemia edema were observed in the lung and trachea tissues. DNA methylation levels of STAT3 and RORγt genes in rats with WSI-TRPM2.5 and OE-TRPM2.5 treatment were decreased. DNA methylation level in STAT5 gene tended to decrease, with no change observed on Foxp3 expression. WSI-TRPM2.5 and OE-TRPM2.5 enhanced the mRNA and protein expression of STAT3 and RORγt while inhibited the expression of STAT5 and Foxp3, which may contribute to the imbalance of Th17/Treg cells (P < 0.05). More importantly, recovered balance of Th17/Treg cell subsets, upregulated p-STAT5 and Foxp3 expression and reduced p-STAT3 and RORγt levels were observed after 5-Aza treatment. Our results demonstrate that the STAT3/RORγt-STAT5/Foxp3 signaling pathway is involved in asthma exacerbation induced by WSI-TRPM2.5 and OE-TRPM2.5 through disrupting the balance of Th17/Treg cells. The alteration of DNA methylation of STAT3, STAT5, and RORγt genes may be involved in asthma exacerbation as well.
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Affiliation(s)
- Caihong Wang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Dan Wang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Huichao Zhao
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China; Department of Nutrition and Food Hygiene, School of Public Health, Qingdao University, Qingdao 266000, Shandong, China
| | - Jing Wang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Nannan Liu
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Hao Shi
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Jiayu Tian
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Xin Wang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Zhihong Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China.
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22
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Wang W, Li Q, Zhang L, Cui J, Yu H, Wang X, Ouyang X, Tao F, Xu P, Tang H. Genetic mapping of highly versatile and solvent-tolerant Pseudomonas putida B6-2 (ATCC BAA-2545) as a 'superstar' for mineralization of PAHs and dioxin-like compounds. Environ Microbiol 2021; 23:4309-4325. [PMID: 34056829 DOI: 10.1111/1462-2920.15613] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and dioxin-like compounds, including sulfur, nitrogen and oxygen heterocycles, are widespread and toxic environmental pollutants. A wide variety of microorganisms capable of growing with aromatic polycyclic compounds are essential for bioremediation of the contaminated sites and the Earth's carbon cycle. Here, cells of Pseudomonas putida B6-2 (ATCC BAA-2545) grown in the presence of biphenyl (BP) are able to simultaneously degrade PAHs and their derivatives, even when they are present as mixtures, and tolerate high concentrations of extremely toxic solvents. Genetic analysis of the 6.37 Mb genome of strain B6-2 reveals coexistence of gene clusters responsible for central catabolic systems of aromatic compounds and for solvent tolerance. We used functional transcriptomics and proteomics to identify the candidate genes associated with catabolism of BP and a mixture of BP, dibenzofuran, dibenzothiophene and carbazole. Moreover, we observed dynamic changes in transcriptional levels with BP, including in metabolic pathways of aromatic compounds, chemotaxis, efflux pumps and transporters potentially involved in adaptation to PAHs. This study on the highly versatile activities of strain B6-2 suggests it to be a potentially useful model for bioremediation of polluted sites and for investigation of biochemical, genetic and evolutionary aspects of Pseudomonas.
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Affiliation(s)
- Weiwei Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qinggang Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Lige Zhang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Cui
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hao Yu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyu Wang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Pulczinski JC, Shang Y, Dao T, Limjunyawong N, Sun Q, Mitzner W, Cheng RYS, Tang WY. Multigenerational Epigenetic Regulation of Allergic Diseases: Utilizing an Experimental Dust Mite-Induced Asthma Model. Front Genet 2021; 12:624561. [PMID: 33868365 PMCID: PMC8047068 DOI: 10.3389/fgene.2021.624561] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022] Open
Abstract
Environmental exposures have been linked to increased asthma risk, particularly during pregnancy and in early life. Here we use a mouse model of allergic lung disease to examine the effects of pre- and perinatal house dust mite (HDM) allergen exposure on offspring phenotypic and transcriptional outcomes in three generations. We show that maternal HDM exposure (F0) acts synergistically with adult HDM exposure, leading to enhanced airway hyperresponsiveness (AHR) and lung inflammation when compared to mice exposed solely in adulthood. Additionally, a subset of F1 males were not challenged in adulthood, and used to generate F2 progeny, which was then used to generate F3 progeny. Upon adult challenge to HDM, F2, and F3 males generated from the maternal HDM (F0) exposure lineage displayed increased airway reactivity and inflammation when compared to mice exposed solely in adulthood. These findings indicate that maternal allergen exposure is capable of enhancing either susceptibly to or severity of allergic airway disease. To examine the role of epigenetic inheritance of asthma susceptibility induced by maternal HDM exposure, we utilized a genome-wide MeDIP-seq and hMeDIP-seq analysis to identify genes differentially methylated (DMG) and hydroxymethylated (DHG), and their association with the enhanced AHR. In addition, we validated the relationship between DNA methylation and mRNA expression of the DMGs and DHGs in the male sub-generations (F1-F3). We found the expression of Kchn1, Nron, and Spag17 to be differentially hydroxymethylated and upregulated in the F1 exposed to HDM both in early life and in adulthood when compared to F1 mice exposed solely in adulthood. Kcnh1 remained upregulated in the F2 and F3 from the maternal HDM (F0) exposure lineage, when compared to F1 mice exposed solely in adulthood. In summary, we demonstrated that maternal HDM exposure in early life can alter the gene expression and phenotype of offspring upon adult HDM exposure, resulting in more severe disease. These effects persist at least two generations past the initial insult, transmitted along the paternal line.
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Affiliation(s)
- Jairus C. Pulczinski
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Yan Shang
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Tyna Dao
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Nathachit Limjunyawong
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Qinying Sun
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Wayne Mitzner
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Robert YS Cheng
- Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Wan-yee Tang
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States
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Sheikhpour M, Maleki M, Ebrahimi Vargoorani M, Amiri V. A review of epigenetic changes in asthma: methylation and acetylation. Clin Epigenetics 2021; 13:65. [PMID: 33781317 PMCID: PMC8008616 DOI: 10.1186/s13148-021-01049-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/04/2021] [Indexed: 12/30/2022] Open
Abstract
Several studies show that childhood and adulthood asthma and its symptoms can be modulated through epigenetic modifications. Epigenetic changes are inheritable modifications that can modify the gene expression without changing the DNA sequence. The most common epigenetic alternations consist of DNA methylation and histone modifications. How these changes lead to asthmatic phenotype or promote the asthma features, in particular by immune pathways regulation, is an understudied topic. Since external effects, like exposure to tobacco smoke, air pollution, and drugs, influence both asthma development and the epigenome, elucidating the role of epigenetic changes in asthma is of great importance. This review presents available evidence on the epigenetic process that drives asthma genes and pathways, with a particular focus on DNA methylation, histone methylation, and acetylation. We gathered and assessed studies conducted in this field over the past two decades. Our study examined asthma in different aspects and also shed light on the limitations and the important factors involved in the outcomes of the studies. To date, most of the studies in this area have been carried out on DNA methylation. Therefore, the need for diagnostic and therapeutic applications through this molecular process calls for more research on the histone modifications in this disease.
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Affiliation(s)
- Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Mobina Maleki
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Ebrahimi Vargoorani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, College of Basic Sciences, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Vahid Amiri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
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Isaevska E, Moccia C, Asta F, Cibella F, Gagliardi L, Ronfani L, Rusconi F, Stazi MA, Richiardi L. Exposure to ambient air pollution in the first 1000 days of life and alterations in the DNA methylome and telomere length in children: A systematic review. ENVIRONMENTAL RESEARCH 2021; 193:110504. [PMID: 33221306 DOI: 10.1016/j.envres.2020.110504] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Exposure to air pollution during the first 1000 days of life (from conception to the 2nd year of life) might be of particular relevance for long-term child health. Changes in molecular markers such as DNA methylation and telomere length could underlie the association between air pollution exposure and pollution-related diseases as well as serve as biomarkers for past exposure. The objective of this systematic review was to assess the association between air pollution exposure during pregnancy and the first two years of life and changes in DNA methylation or telomere length in children. METHODS PubMed was searched in October 2020 by using terms relative to ambient air pollution exposure, DNA methylation, telomere length and the population of interest: mother/child dyads and children. Screening and selection of the articles was completed independently by two reviewers. Thirty-two articles matched our criteria. The majority of the articles focused on gestational air pollution exposure and measured DNA methylation/telomere length in newborn cord blood or placental tissue, to study global, candidate-gene or epigenome-wide methylation patterns and/or telomere length. The number of studies in children was limited. RESULTS Ambient air pollution exposure during pregnancy was associated with global loss of methylation in newborn cord blood and placenta, indicating the beginning of the pregnancy as a potential period of susceptibility. Candidate gene and epigenome-wide association studies provided evidence that gestational exposure to air pollutants can lead to locus-specific changes in methylation, in newborn cord blood and placenta, particularly in genes involved in cellular responses to oxidative stress, mitochondrial function, inflammation, growth and early life development. Telomere length shortening in newborns and children was seen in relation to gestational pollutant exposure. CONCLUSIONS Ambient air pollution during pregnancy is associated with changes in both global and locus-specific DNA methylation and with telomere length shortening. Future studies need to test the robustness of the association across different populations, to explore potential windows of vulnerability and assess the role of the methylation and telomere length as mediators in the association between early exposure to ambient air pollutants and specific childhood health outcomes.
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Affiliation(s)
- Elena Isaevska
- Department of Medical Sciences, University of Turin, CPO Piemonte, Turin, Italy.
| | - Chiara Moccia
- Department of Medical Sciences, University of Turin, CPO Piemonte, Turin, Italy.
| | - Federica Asta
- Department of Epidemiology, Lazio Regional Health Service, ASL Roma 1, Rome, Italy.
| | - Fabio Cibella
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), Palermo, Italy.
| | - Luigi Gagliardi
- Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy.
| | - Luca Ronfani
- Clinical Epidemiology and Public Health Research Unit, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy.
| | - Franca Rusconi
- Unit of Epidemiology, Meyer Children's University Hospital, Florence, Italy.
| | - Maria Antonietta Stazi
- Center "Behavioral Sciences and Mental Health", Istituto Superiore di Sanità, Rome, Italy.
| | - Lorenzo Richiardi
- Department of Medical Sciences, University of Turin, CPO Piemonte, Turin, Italy.
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Analysis of Single Nucleotide Variants (SNVs) Induced by Exposure to PM 10 in Lung Epithelial Cells Using Whole Genome Sequencing. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18031046. [PMID: 33503946 PMCID: PMC7908261 DOI: 10.3390/ijerph18031046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/23/2022]
Abstract
There are many epidemiological studies asserting that fine dust causes lung cancer, but the biological mechanism is not clear. This study was conducted to investigate the effect of PM10 (particulate matter less than 10 μm) on single nucleotide variants through whole genome sequencing in lung epithelial cancer cell lines (HCC-827, NCI-H358) that have been exposed to PM10. The two cell lines were exposed to PM10 for 15 days. We performed experimental and next generation sequencing analyses on experimental group that had been exposed to PM10 as well as an unexposed control group. After exposure to PM10, 3005 single nucleotide variants were newly identified in the NCI-H358 group, and 4402 mutations were identified in the HCC-827 group. We analyzed these single nucleotide variants with the Mutalisk program. We observed kataegis in chromosome 1 in NCI-H358 and chromosome 7 in HCC-827. In mutational signatures analysis, the COSMIC mutational signature 5 was highest in both HCC-827 and NCI-H358 groups, and each cosine similarity was 0.964 in HCC-827 and 0.979 in the NCI-H358 group. The etiology of COSMIC mutational signature 5 is unknown at present. Well-designed studies are needed to determine whether environmental factors, such as PM10, cause COSMIC mutational signature 5.
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Mechanistic Implications of Biomass-Derived Particulate Matter for Immunity and Immune Disorders. TOXICS 2021; 9:toxics9020018. [PMID: 33498426 PMCID: PMC7909393 DOI: 10.3390/toxics9020018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/04/2021] [Accepted: 01/15/2021] [Indexed: 12/29/2022]
Abstract
Particulate matter (PM) is a major and the most harmful component of urban air pollution, which may adversely affect human health. PM exposure has been associated with several human diseases, notably respiratory and cardiovascular diseases. In particular, recent evidence suggests that exposure to biomass-derived PM associates with airway inflammation and can aggravate asthma and other allergic diseases. Defective or excess responsiveness in the immune system regulates distinct pathologies, such as infections, hypersensitivity, and malignancies. Therefore, PM-induced modulation of the immune system is crucial for understanding how it causes these diseases and highlighting key molecular mechanisms that can mitigate the underlying pathologies. Emerging evidence has revealed that immune responses to biomass-derived PM exposure are closely associated with the risk of diverse hypersensitivity disorders, including asthma, allergic rhinitis, atopic dermatitis, and allergen sensitization. Moreover, immunological alteration by PM accounts for increased susceptibility to infectious diseases, such as tuberculosis and coronavirus disease-2019 (COVID-19). Evidence-based understanding of the immunological effects of PM and the molecular machinery would provide novel insights into clinical interventions or prevention against acute and chronic environmental disorders induced by biomass-derived PM.
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28
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Kim SS, Vuong AM, Dietrich KN, Chen A. Proximity to traffic and exposure to polycyclic aromatic hydrocarbons in relation to Attention Deficit Hyperactivity Disorder and conduct disorder in U.S. children. Int J Hyg Environ Health 2021; 232:113686. [PMID: 33429141 DOI: 10.1016/j.ijheh.2020.113686] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND Traffic related air pollution (TRAP) and its component polycyclic aromatic hydrocarbons (PAHs) may be neurotoxic in children. There is limited research on postnatal exposure to TRAP and PAHs and child neurodevelopment. METHODS We linked data from the U.S. NHANES 2001-2004 with the National Highway Planning Network 2005 to examine the proximity to major roads (highway or urban/rural principal arterials), urinary PAH metabolites, and diagnosis of Attention Deficit Hyperactivity Disorder (ADHD) and Conduct Disorder (CD) based on Diagnostic Interview Schedule for Children (C-DISC) in 1253 children aged 8-15 years. We calculated odds ratios (ORs) and 95% Confidence Intervals (CIs) for ADHD and CD by traffic proximity and PAH exposures using logistic regression adjusted for confounders. RESULTS Higher ADHD prevalence was observed among children living <500 m (9.86%) compared to those ≥500 m (3.84%) from a major road. Prevalence of children with CD was comparable (<500 m: 2.51% and ≥500 m: 2.43%). We found little difference in urinary PAH metabolite levels between children living near major roads and those who did not. Children living <500 m from a major road had a non-significant OR of 2.06 (95% CI 0.85-5.03) for ADHD diagnosis. Children living on ≥2 major roads within 500 m of a highway had a non-significant OR of 2.27 (95% CI 0.71-7.26) for ADHD diagnosis. There was no association between proximity to major roads and CD diagnosis. CONCLUSION We found living close to a major road was not associated with increased PAH levels. We did not find statistically significant relation between proximity to a major road or urinary PAH metabolite levels and ADHD or CD diagnosis in this cross-sectional analysis. Prospective studies are needed for the investigation of postnatal TRAP exposure and ADHD and CD diagnosis.
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Affiliation(s)
- Stephani S Kim
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Currently at Department of Anesthesiology & Pain Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ann M Vuong
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Currently at Department of Environmental and Occupational Health, School of Public Health, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Kim N Dietrich
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Aimin Chen
- Division of Epidemiology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Currently at Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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29
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Ambade B, Sethi SS, Kumar A, Sankar TK, Kurwadkar S. Health Risk Assessment, Composition, and Distribution of Polycyclic Aromatic Hydrocarbons (PAHs) in Drinking Water of Southern Jharkhand, East India. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 80:120-133. [PMID: 33211120 DOI: 10.1007/s00244-020-00779-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/30/2020] [Indexed: 05/27/2023]
Abstract
The studies on polycyclic aromatic hydrocarbons (PAHs) occurrence, distribution, health risk, and composition in drinking water are limited in India and worldwide. The main objective of this study was to find the contaminant sources, composition, health risk, and distribution of USEPA's 16 priority pollutant PAHs in the drinking water samples collected between July 2019 to September 2019 from six districts of Southern Jharkhand. The Σ16PAHs mean ± standard deviation [SD] concentration values were ordered as East Singhbhum (ES) (21.5 ± 14.8 ng L-1) > West Singhbhum (WS) (16.57 ± 13.21 ng L-1) > Saraikela Kharsawan (SK) (11.48 ± 9.92 ng L-1) > Khunti (KH) (10.32 ± 9.09 ng L-1) > Simdega (SM) (9.96 ± 7.85 ng L-1) > Gumla (GU) (9.41 ± 8.63 ng L-1). The results show that ES and WS districts' groundwater samples were more contaminated by the PAHs, which may be attributed to the presence of many small-, medium-, and large-scale industries and high vehicular density in these districts. The concentrations of lower molecular weight ring (3-rings) and middle molecular weight ring (4-rings) PAHs were dominant throughout all drinking samples. The concentration of the 3-ring PAH Anthracene and 4-ring PAH Fluoranthene were dominant in all districts. The molecular ratios suggested that the potential sources of PAHs are fuel combustion and coal, grass, and wood burning. Risk assessment shows that the incremental lifetime cancer risk and risk index (RI) were ranged from 0.02 × 10-10 to 4.93 × 10-10 for children and 0.01 × 10-10 to 2.98 × 10-10 for adults. The RI values for seven carcinogenic PAHs were 8.83 × 10-10 for children and 7.38 × 10-10 for adults. Although the carcinogenic risks were within the permissible values, chronic exposure to PAHs through the ingestion of drinking water could still be a human health concern.
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Affiliation(s)
- Balram Ambade
- Department of Chemistry, National Institute of Technology, Jamshedpur, 831014, Jharkhand, India.
| | - Shrikanta Shankar Sethi
- Department of Chemistry, National Institute of Technology, Jamshedpur, 831014, Jharkhand, India
| | - Amit Kumar
- Department of Chemistry, National Institute of Technology, Jamshedpur, 831014, Jharkhand, India
| | - Tapan Kumar Sankar
- Department of Chemistry, National Institute of Technology, Jamshedpur, 831014, Jharkhand, India
| | - Sudarshan Kurwadkar
- Department of Civil and Environmental Engineering, California State University, Fullerton, CA, USA
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30
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Rahman MA, Rahman MS, Uddin MJ, Mamum-Or-Rashid ANM, Pang MG, Rhim H. Emerging risk of environmental factors: insight mechanisms of Alzheimer's diseases. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:44659-44672. [PMID: 32201908 DOI: 10.1007/s11356-020-08243-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/25/2020] [Indexed: 06/10/2023]
Abstract
Neurodegenerative disorders are typically sporadic in nature in addition to usually influenced through an extensive range of environmental factors, lifestyle, and genetic elements. Latest observations have hypothesized that exposure of environmental factors may increase the prospective risk of Alzheimer's diseases (AD). However, the role of environmental factors as a possible dangerous issue has extended importance concerned in AD pathology, although actual etiology of the disorder is still not yet clear. Thus, the aim of this review is to highlight the possible correlation between environmental factors and AD, based on the present literature view. Environmental risk factors might play an important role in decelerating or accelerating AD progression. Among well-known environmental risk factors, prolonged exposure to several heavy metals, for example, aluminum, arsenic, cadmium, lead, and mercury; particulate air, and some pesticides as well as metal-containing nanoparticles have been participated to cause AD. These heavy metals have the capacity to enhance amyloid β (Aβ) peptide along with tau phosphorylation, initiating amyloid/senile plaques, as well as neurofibrillary tangle formation; therefore, neuronal cell death has been observed. Furthermore, particulate air, pesticides, and heavy metal exposure have been recommended to lead AD susceptibility and phenotypic diversity though epigenetic mechanisms. Therefore, this review deliberates recent findings detailing the mechanisms for a better understanding the relationship between AD and environmental risk factors along with their mechanisms of action on the brain functions.
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Affiliation(s)
- Md Ataur Rahman
- Center for Neuroscience, Korea Institute of Science and Technology (KIST), 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea.
- Department of Biotechnology and Genetic Engineering, Global Biotechnology & Biomedical Research Network (GBBRN), Faculty of Biological Sciences, Islamic University, Kushtia, 7003, Bangladesh.
| | - Md Saidur Rahman
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, 456-756, Republic of Korea
| | - Md Jamal Uddin
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Republic of Korea
- ABEx Bio-Research Center, East Azampur, Dhaka, 1230, Bangladesh
| | - A N M Mamum-Or-Rashid
- Anti-Aging Medical Research Center and Glycation Stress Research Center, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Myung-Geol Pang
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, 456-756, Republic of Korea
| | - Hyewhon Rhim
- Center for Neuroscience, Korea Institute of Science and Technology (KIST), 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea.
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea.
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Noth EM, Lurmann F, Perrino C, Vaughn D, Minor HA, Hammond SK. Decrease in Ambient Polycyclic Aromatic Hydrocarbon Concentrations in California's San Joaquin Valley 2000-2019. ATMOSPHERIC ENVIRONMENT (OXFORD, ENGLAND : 1994) 2020; 242:117818. [PMID: 32982565 PMCID: PMC7518520 DOI: 10.1016/j.atmosenv.2020.117818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
As part of our ongoing research to understand the impact of polycyclic aromatic hydrocarbon (PAH) exposures on health in the San Joaquin Valley, we evaluated airborne PAH concentration data collected over 19 years (2000-2019) at the central air monitoring site in Fresno, California. We found a dramatic decline in outdoor airborne PAH concentrations between 2000 and 2004 that has been maintained through 2019. This decline was present in both the continuous particle-bound PAHs and the filter-based individual PAHs. The decline was more extreme when restricted to winter concentrations. Annual mean PAHs concentrations in 2017- 2018 of particle-bound PAHs were 6.8 ng/m3 or 62% lower than 2000 - 2001. The decline for winter concentrations of continuous particle-bound PAHs between winter 2019 and winter 2001 was 17.2 ng/m3, a drop of 70%. The 2001 to 2018 decline in average wintertime concentrations for filter-based individual PAHs was 82%. We examined industrial emissions, on-road vehicle emissions, residential wood burning, and agricultural and biomass waste burning as possible explanations. The major decline in PAHs from 2000-2004 was coincident with and most likely due to a similar decline in the amount of agricultural and biomass waste burned in Fresno and Madera Counties. On-road vehicle emissions and residential wood burning did not decline until after 2005. Industrial emissions were too low (2% of total) to explain such large decreases in PAH concentrations.
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Affiliation(s)
- Elizabeth M. Noth
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, 2121 Berkeley Way #5302, Berkeley, CA 94720-7360
| | - Fred Lurmann
- Sonoma Technology, Inc., 1450 N. McDowell Blvd., Petaluma, CA 94954
| | - Charles Perrino
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, 2121 Berkeley Way #5302, Berkeley, CA 94720-7360
| | - David Vaughn
- Sonoma Technology, Inc., 1450 N. McDowell Blvd., Petaluma, CA 94954
| | - Hilary A. Minor
- Sonoma Technology, Inc., 1450 N. McDowell Blvd., Petaluma, CA 94954
| | - S. Katharine Hammond
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, 2121 Berkeley Way #5302, Berkeley, CA 94720-7360
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Jo YJ, Yoon SB, Park BJ, Lee SI, Kim KJ, Kim SY, Kim M, Lee JK, Lee SY, Lee DH, Kwon T, Son Y, Lee JR, Kwon J, Kim JS. Particulate Matter Exposure During Oocyte Maturation: Cell Cycle Arrest, ROS Generation, and Early Apoptosis in Mice. Front Cell Dev Biol 2020; 8:602097. [PMID: 33324650 PMCID: PMC7726243 DOI: 10.3389/fcell.2020.602097] [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: 09/02/2020] [Accepted: 11/02/2020] [Indexed: 11/13/2022] Open
Abstract
Particulate matter (PM) is a general atmospheric pollutant released into the air by an anthropogenic and naturally derived mixture of substances. Current studies indicate that fine dust can result in different health defects, including endothelial dysfunction, asthma, lung cancer, cardiovascular diseases, uterine leiomyoma, deterioration in sperm quality, and overall birth impairment. However, the most prominent effects of PM10 (diameter < 10 μM) exposure on the female reproductive system, especially with respect to oocyte maturation, remain unclear. In the present study, maturing mouse oocytes were treated with PM10 and the phenotypes of the resulting toxic effects were investigated. Exposure to PM10 led to impairment of maturation capacity by inducing cell cycle arrest and blocking normal polar body extrusion during in vitro maturation and activation of fertilization of mouse oocytes. Additionally, defects in tubulin formation and DNA alignment were observed in PM10-treated oocytes during metaphase I to anaphase/telophase I transition. Moreover, PM10 induced reactive oxygen species generation, mitochondrial dysfunction, DNA damage, and early apoptosis. Taken together, these results indicate that PM10 exposure leads to a decline in oocyte quality and affects the subsequent embryonic development potential of mammalian oocytes.
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Affiliation(s)
- Yu-Jin Jo
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Seung-Bin Yoon
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Byoung-Jin Park
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Sang Il Lee
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Ki Jin Kim
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Se-Yong Kim
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Minseong Kim
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Jun-Ki Lee
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Sang-Yong Lee
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Dong-Ho Lee
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Taeho Kwon
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Yeonghoon Son
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Ja-Rang Lee
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Jeongwoo Kwon
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
| | - Ji-Su Kim
- Primate Resources Center (PRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, South Korea
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Laine JE, Bodinier B, Robinson O, Plusquin M, Scalbert A, Keski-Rahkonen P, Robinot N, Vermeulen R, Pizzi C, Asta F, Nawrot T, Gulliver J, Chatzi L, Kogevinas M, Nieuwenhuijsen M, Sunyer J, Vrijheid M, Chadeau-Hyam M, Vineis P. Prenatal Exposure to Multiple Air Pollutants, Mediating Molecular Mechanisms, and Shifts in Birthweight. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14502-14513. [PMID: 33124810 DOI: 10.1021/acs.est.0c02657] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Mechanisms underlying adverse birth and later in life health effects from exposure to air pollution during the prenatal period have not been not fully elucidated, especially in the context of mixtures. We assessed the effects of prenatal exposure to mixtures of air pollutants of particulate matter (PM), PM2.5, PM10, nitrogen oxides, NO2, NOx, ultrafine particles (UFP), and oxidative potential (OP) of PM2.5 on infant birthweight in four European birth cohorts and the mechanistic underpinnings through cross-omics of metabolites and inflammatory proteins. The association between mixtures of air pollutants and birthweight z-scores (standardized for gestational age) was assessed for three different mixture models, using Bayesian machine kernel regression (BKMR). We determined the direct effect for PM2.5, PM10, NO2, and mediation by cross-omic signatures (identified using sparse partial least-squares regression) using causal mediation BKMR models. There was a negative association with birthweight z-scores and exposure to mixtures of air pollutants, where up to -0.21 or approximately a 96 g decrease in birthweight, comparing the 75th percentile to the median level of exposure to the air pollutant mixture could occur. Shifts in birthweight z-scores from prenatal exposure to PM2.5, PM10, and NO2 were mediated by molecular mechanisms, represented by cross-omics scores. Interleukin-17 and epidermal growth factor were identified as important inflammatory responses underlyingair pollution-associated shifts in birthweight. Our results signify that by identifying mechanisms through which mixtures of air pollutants operate, the causality of air pollution-associated shifts in birthweight is better supported, substantiating the need for reducing exposure in vulnerable populations.
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Affiliation(s)
- Jessica E Laine
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, Imperial College London, London SW7 2BU, United Kingdom
| | - Barbara Bodinier
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, Imperial College London, London SW7 2BU, United Kingdom
| | - Oliver Robinson
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, Imperial College London, London SW7 2BU, United Kingdom
| | - Michelle Plusquin
- Center for Environmental Sciences, Hasselt University, Hasselt 3500, Belgium
| | - Augustin Scalbert
- Nutrition and Metabolism Section, Biomarkers Group, International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Pekka Keski-Rahkonen
- Nutrition and Metabolism Section, Biomarkers Group, International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Nivonirina Robinot
- Nutrition and Metabolism Section, Biomarkers Group, International Agency for Research on Cancer (IARC), Lyon 69372, France
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Environmental Epidemiology Division, Utrecht University, Utrecht 3584 CS, Netherlands
| | - Costanza Pizzi
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin 10126, Italy
| | - Federica Asta
- Department of Epidemiology, Lazio Regional Health Service, ASL Roma 1, Rome 00147, Italy
| | - Tim Nawrot
- Center for Environmental Sciences, Hasselt University, Hasselt 3500, Belgium
- Department of Public Health, Environment and Health Unit, Leuven University (KU Leuven), Leuven 3000, Belgium
| | - John Gulliver
- Centre for Environmental Health and Sustainability & School of Geography, Geology and the Environment, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Leda Chatzi
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion 700 13, Crete, Greece
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona 08003, Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP), Madrid 28029, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona 08003, Spain
| | | | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona 08003, Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP), Madrid 28029, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona 08003, Spain
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona 08003, Spain
- CIBER Epidemiologia y Salud Pública (CIBERESP), Madrid 28029, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, Imperial College London, London SW7 2BU, United Kingdom
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, MRC Centre for Environment and Health, Imperial College London, London SW7 2BU, United Kingdom
- Italian Institute of Technology, Genova 16163, Italy
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Potential role of polycyclic aromatic hydrocarbons in air pollution-induced non-malignant respiratory diseases. Respir Res 2020; 21:299. [PMID: 33187512 PMCID: PMC7666487 DOI: 10.1186/s12931-020-01563-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/01/2020] [Indexed: 12/12/2022] Open
Abstract
Epidemiological studies have found strong associations between air pollution and respiratory effects including development and/or exacerbation of asthma and chronic obstructive pulmonary disease (COPD) as well as increased occurrence of respiratory infections and lung cancer. It has become increasingly clear that also polycyclic aromatic hydrocarbons (PAHs) may affect processes linked to non-malignant diseases in the airways. The aim of the present paper was to review epidemiological studies on associations between gas phase and particle-bound PAHs in ambient air and non-malignant respiratory diseases or closely related physiological processes, to assess whether PAH-exposure may explain some of the effects associated with air pollution. Based on experimental in vivo and in vitro studies, we also explore possible mechanisms for how different PAHs may contribute to such events. Epidemiological studies show strongest evidence for an association between PAHs and asthma development and respiratory function in children. This is supported by studies on prenatal and postnatal exposure. Exposure to PAHs in adults seems to be linked to respiratory functions, exacerbation of asthma and increased morbidity/mortality of obstructive lung diseases. However, available studies are few and weak. Notably, the PAHs measured in plasma/urine also represent other exposure routes than inhalation. Furthermore, the role of PAHs measured in air is difficult to disentangle from that of other air pollution components originating from combustion processes. Experimental studies show that PAHs may trigger various processes linked to non-malignant respiratory diseases. Physiological- and pathological responses include redox imbalance, oxidative stress, inflammation both from the innate and adaptive immune systems, smooth muscle constriction, epithelial- and endothelial dysfunction and dysregulated lung development. Such biological responses may at the molecular level be initiated by PAH-binding to the aryl hydrocarbon receptor (AhR), but possibly also through interactions with beta-adrenergic receptors. In addition, reactive PAH metabolites or reactive oxygen species (ROS) may interfere directly with ion transporters and enzymes involved in signal transduction. Overall, the reviewed literature shows that respiratory effects of PAH-exposure in ambient air may extend beyond lung cancer. The relative importance of the specific PAHs ability to induce disease may differ between the biological endpoint in question.
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Men S, Yu Y. Prospects for Use of Single-Cell Sequencing to Assess DNA Methylation in Asthma. Med Sci Monit 2020; 26:e925514. [PMID: 33009362 PMCID: PMC7539641 DOI: 10.12659/msm.925514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022] Open
Abstract
Asthma is a complex disease with an increasing prevalence rate caused by the interaction of multiple genetically inherited and environmental factors. Epigenetics link genetic susceptibility and environmental factors. DNA methylation is an epigenetic modification that plays a crucial role in the regulation of growth and development, gene expression, and disease. Relatively little is known about DNA methylation in asthma, with few studies to date using single-cell sequencing to analyze the molecular mechanism by which DNA methylation regulates asthma. Cells with similar phenotypes may be heterogeneous in function and transcription, as may their genetic information. Although multi-omics methods, such as studies of the genome, transcriptome, and epigenome, can be used to evaluate biological processes, these methods are applicable only to groups of cells or tissues and provide averages that may obscure direct correlations among multiple layers of data. Single-cell sequencing technology can clarify the methylation and expression of genes in different populations of cells, in contrast to traditional multi-omics sequencing, which can determine only average values of cell populations. Single-cell sequence can therefore better reflect the pathogenesis of asthma, as it can clarify the function and regulatory mechanism of DNA methylation in asthma, and detect new genes and molecular markers that may become therapeutic targets in this disease.
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36
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Hu J, Bao Y, Zhu Y, Osman R, Shen M, Zhang Z, Wang L, Cao S, Li L, Wu Q. The Preliminary Study on the Association Between PAHs and Air Pollutants and Microbiota Diversity. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 79:321-332. [PMID: 32897393 DOI: 10.1007/s00244-020-00757-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
The purpose of this study was to investigate the association among polycyclic aromatic hydrocarbons (PAHs) exposure and air pollutants and the diversity of microbiota. Daily average concentrations of six common air pollutants were obtained from China National Environmental Monitoring Centre. The PAHs exposure levels were evaluated by external and internal exposure detection methods, including monitoring atmospheric PAHs and urinary hydroxyl-polycyclic aromatic hydrocarbon (OH-PAH) metabolite levels. We analyzed the diversity of environmental and commensal bacterial communities with 16S rRNA gene sequencing and performed functional enrichment with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Correlation analysis and logistic regression modeling were conducted to evaluate the relationship of PAHs levels with air pollutants and microbial diversity. Correlation analysis found that the concentrations of atmospheric PAHs were significantly positively correlated with those of PM10, NO2, and SO2. There also was a positive correlation between the abundance of the genus Micrococcus (Actinobacteria) and high molecular weight PAHs, and Bacillus, such as genera and low molecular weight PAHs in the atmosphere. Logistic regression showed that the level of urinary 1-OHPyrene was associated with childhood asthma after sex and age adjustment. The level of urinary 1-OHPyrene was significantly positively correlated with that of PM2.5 and PM10. In addition, the level of 1-OHPyrene was positively correlated with oral Prevotella-7 abundance. Functional enrichment analysis demonstrated that PAHs exposure may disturb signaling pathways by the imbalance of commensal microbiota, such as purine metabolism, pyrimidine metabolites, lipid metabolism, and one carbon pool by folate, which may contribute to public health issues. Our results confirmed that atmospheric PAHs and urinary 1-OHPyrene were correlated with part of six common air pollutants and indicated that PAHs pollution may alter both environmental and commensal microbiota communities associated with health-related problems. The potential health and environmental impacts of PAHs should be further explored.
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Affiliation(s)
- Jinye Hu
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yuling Bao
- Department of Respiratory, Nanjing Children's Hospital Affiliated to Nanjing Medical University, Nanjing, 210008, China
| | - Yuqi Zhu
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Ranagul Osman
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Mengfan Shen
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhan Zhang
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Li Wang
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Shuyuan Cao
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Lei Li
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Qian Wu
- The Key Laboratory of Modern Toxicology of Ministry of Education and Department of Health Inspection and Quarantine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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Poutasse CM, Poston WSC, Jahnke SA, Haddock CK, Tidwell LG, Hoffman PD, Anderson KA. Discovery of firefighter chemical exposures using military-style silicone dog tags. ENVIRONMENT INTERNATIONAL 2020; 142:105818. [PMID: 32521346 PMCID: PMC9985454 DOI: 10.1016/j.envint.2020.105818] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 05/07/2023]
Abstract
Occupational chemical hazards in the fire service are hypothesized to play a role in increased cancer risk, and reliable sampling technologies are necessary for conducting firefighter chemical exposure assessments. This study presents the military-style dog tag as a new configuration of silicone passive sampling device to sample individual firefighters' exposures at one high and one low fire call volume department in the Kansas City, Missouri metropolitan area. The recruited firefighters (n = 56) wore separate dog tags to assess on- and off-duty exposures (ndogtags = 110), for a total of 30 24 h shifts. Using a 63 PAH method (GC-MS/MS), the tags detected 45 unique PAHs, of which 18 have not been previously reported as firefighting exposures. PAH concentrations were higher for on- compared to off-duty tags (0.25 < Cohen's d ≤ 0.80) and for the high compared to the low fire call volume department (0.25 ≤ d < 0.70). Using a 1530 analyte screening method (GC-MS), di-n-butyl phthalate, diisobutyl phthalate, guaiacol, and DEET were commonly detected analytes. The number of fire attacks a firefighter participated in was more strongly correlated with PAH concentrations than firefighter rank or years in the fire service. This suggested that quantitative data should be employed for firefighter exposure assessments, rather than surrogate measures. Because several detected analytes are listed as possible carcinogens, future firefighter exposure studies should consider evaluating complex mixtures to assess individual health risks.
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Affiliation(s)
- Carolyn M Poutasse
- Department of Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Walker S C Poston
- Center for Fire, Rescue, and EMS Health Research, NDRI-USA, Leawood, KS 66224, USA
| | - Sara A Jahnke
- Center for Fire, Rescue, and EMS Health Research, NDRI-USA, Leawood, KS 66224, USA
| | | | - Lane G Tidwell
- Department of Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Peter D Hoffman
- Department of Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Kim A Anderson
- Department of Toxicology, Oregon State University, Corvallis, OR 97331, USA.
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Banerjee S, Suter MA, Aagaard KM. Interactions between Environmental Exposures and the Microbiome: Implications for Fetal Programming. CURRENT OPINION IN ENDOCRINE AND METABOLIC RESEARCH 2020; 13:39-48. [PMID: 33283070 PMCID: PMC7716732 DOI: 10.1016/j.coemr.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Decades of population-based health outcomes data highlight the importance of understanding how environmental exposures in pregnancy affect maternal and neonatal outcomes. Animal model research and epidemiological studies have revealed that such exposures are able to alter fetal programming through stable changes in the epigenome, including altered DNA methylation patterns and histone modifications in the developing fetus and infant. It is similarly known that while microbes can biotransform environmental chemicals via conjugation and de-conjugation, specific exposures can also alter the community profile and function of the human microbiome. In this review, we consider how alterations to the maternal and or fetal/infant microbiome through environmental exposures could directly and indirectly alter fetal programming. We highlight two specific environmental exposures, cadmium (Cd) and polycyclic aromatic hydrocarbons (PAHs), and outline their effects on the developing fetus and the perinatal (maternal and fetal/infant) microbiome. We further consider how chemical exposures in the setting of natural disasters may be of particular importance to environmental health.
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Affiliation(s)
- Sohini Banerjee
- Baylor College of Medicine, Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine and Departments of Molecular & Human Genetics, Molecular & Cell Biology, and Molecular Physiology & Biophysics, 1 Baylor Plaza, Houston, TX 77030
| | - Melissa A. Suter
- Baylor College of Medicine, Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine and Departments of Molecular & Human Genetics, Molecular & Cell Biology, and Molecular Physiology & Biophysics, 1 Baylor Plaza, Houston, TX 77030
| | - Kjersti M. Aagaard
- Baylor College of Medicine, Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine and Departments of Molecular & Human Genetics, Molecular & Cell Biology, and Molecular Physiology & Biophysics, 1 Baylor Plaza, Houston, TX 77030
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39
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Mu Z, Zhang J. The Role of Genetics, the Environment, and Epigenetics in Atopic Dermatitis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1253:107-140. [PMID: 32445093 DOI: 10.1007/978-981-15-3449-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Atopic Dermatitis (AD) is a common inflammatory disease with a genetic background. The prevalence of AD has been increasing in many countries. AD patients often have manifestations of pruritus, generalized skin dryness, and eczematous lesions. The pathogenesis of AD is complicated. The impaired skin barrier and immune imbalance play significant roles in the development of AD. Environmental factors such as allergens and pollutants are associated with the increasing prevalence. Many genetic and environmental factors induce a skin barrier deficiency, and this can lead to immune imbalance, which exacerbates the impaired skin barrier to form a vicious cycle (outside-inside-outside view). Genetic studies find many gene mutations and genetic variants, such as filaggrin mutations, which may directly induce the deficiency of the skin barrier and immune system. Epigenetic studies provide a connection between the relationship of an impaired skin barrier and immune and environmental factors, such as tobacco exposure, pollutants, microbes, and diet and nutrients. AD is a multigene disease, and thus there are many targets for regulation of expression of these genes which may contribute to the pathogenesis of AD. However, the epigenetic regulation of environmental factors in AD pathogenesis still needs to be further researched.
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Affiliation(s)
- Zhanglei Mu
- Department of Dermatology, Peking University People's Hospital, Beijing, China
| | - Jianzhong Zhang
- Department of Dermatology, Peking University People's Hospital, Beijing, China.
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40
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Long A, Bunning B, Sampath V, DeKruyff RH, Nadeau KC. Epigenetics and the Environment in Airway Disease: Asthma and Allergic Rhinitis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1253:153-181. [PMID: 32445095 DOI: 10.1007/978-981-15-3449-2_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Asthma and rhinitis are complex, heterogeneous diseases characterized by chronic inflammation of the upper and lower airways. While genome-wide association studies (GWAS) have identified a number of susceptible loci and candidate genes associated with the pathogenesis of asthma and allergic rhinitis (AR), the risk-associated alleles account for only a very small percent of the genetic risk. In allergic airway and other complex diseases, it is thought that epigenetic modifications, including DNA methylation, histone modifications, and non-coding microRNAs, caused by complex interactions between the underlying genome and the environment may account for some of this "missing heritability" and may explain the high degree of plasticity in immune responses. In this chapter, we will focus on the current knowledge of classical epigenetic modifications, DNA methylation and histone modifications, and their potential role in asthma and AR. In particular, we will review epigenetic variations associated with maternal airway disease, demographics, environment, and non-specific associations. The role of specific genetic haplotypes in environmentally induced epigenetic changes are also discussed. A major limitation of many of the current studies of asthma epigenetics is that they evaluate epigenetic modifications in both allergic and non-allergic asthma, making it difficult to distinguish those epigenetic modifications that mediate allergic asthma from those that mediate non-allergic asthma. Additionally, most DNA methylation studies in asthma use peripheral or cord blood due to poor accessibility of airway cells or tissue. Unlike DNA sequences, epigenetic alterations are quite cell- and tissue-specific, and epigenetic changes found in airway tissue or cells may be discordant from that of circulating blood. These two confounding factors should be considered when reviewing epigenetic studies in allergic airway disease.
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Affiliation(s)
- Andrew Long
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.,Department of Pharmacy, Lucile Packard Children's Hospital, Stanford, CA, 94304, USA
| | - Bryan Bunning
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Vanitha Sampath
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Rosemarie H DeKruyff
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Kari C Nadeau
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.
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41
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Wang Y, Qian M, Tang D, Herbstman J, Perera F, Wang S. A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes. Bioinformatics 2020; 36:653-659. [PMID: 31504174 DOI: 10.1093/bioinformatics/btz630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/18/2019] [Accepted: 08/19/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Deoxyribonucleic acid (DNA) methylation plays a crucial role in human health. Studies have demonstrated associations between DNA methylation and environmental factors with evidence also supporting the idea that DNA methylation may modify the risk of environmental factors on health outcomes. However, due to high dimensionality and low study power, current studies usually focus on finding differential methylation on health outcomes at CpG level or gene level combining multiple CpGs and/or finding environmental effects on health outcomes but ignoring their interactions on health outcomes. Here we introduce the idea of a pseudo-data matrix constructed with cross-product terms between CpGs and environmental factors that are able to capture their interactions. We then develop a powerful and flexible weighted distance-based method with the pseudo-data matrix where association strength was used as weights on CpGs, environmental factors and their interactions to up-weight signals and down-weight noises in distance calculations. RESULTS We compared the power of this novel approach and several comparison methods in simulated datasets and the Mothers and Newborns birth cohort of the Columbia Center for Children's Environmental Health to determine whether prenatal polycyclic aromatic hydrocarbons interacts with DNA methylation in association with Attention Deficit Hyperactivity Disorder and Mental Development Index at age 3. AVAILABILITY AND IMPLEMENTATION An R code for the proposed method Dw-M-E-int together with a tutorial and a sample dataset is available for downloading from http://www.columbia.edu/∼sw2206/softwares.htm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ya Wang
- Department of Biostatistics, New York, NY 10032, USA
| | - Min Qian
- Department of Biostatistics, New York, NY 10032, USA
| | - Deliang Tang
- Columbia Center for Children's Environmental Health, Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Julie Herbstman
- Columbia Center for Children's Environmental Health, Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Frederica Perera
- Columbia Center for Children's Environmental Health, Department of Environmental Health Science, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Shuang Wang
- Department of Biostatistics, New York, NY 10032, USA
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42
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Lin PI, Shu H, Mersha TB. Comparing DNA methylation profiles across different tissues associated with the diagnosis of pediatric asthma. Sci Rep 2020; 10:151. [PMID: 31932625 PMCID: PMC6957523 DOI: 10.1038/s41598-019-56310-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 12/02/2019] [Indexed: 12/30/2022] Open
Abstract
DNA methylation (DNAm) profiles in central airway epithelial cells (AECs) may play a key role in pathological processes in asthma. The goal of the current study is to compare the diagnostic performance of DNAm markers across three tissues: AECs, nasal epithelial cells (NECs), and peripheral blood mononuclear cells (PBMCs). Additionally, we focused on the results using the machine learning algorithm in the context of multi-locus effects to evaluate the diagnostic performance of the optimal subset of CpG sites. We obtained 74 subjects with asthma and 41 controls from AECs, 15 subjects with asthma and 14 controls from NECs, 697 subjects with asthma and 97 controls from PBMCs. Epigenome-wide DNA methylation levels in AECs, NECs and PBMCs were measured using the Infinium Human Methylation 450 K BeadChip. Overlap analysis across the three different sample sources at the locus and pathway levels were studied to investigate shared or unique pathophysiological processes of asthma across tissues. Using the top 100 asthma-associated methylation markers as classifiers from each dataset, we found that both AEC- and NEC-based DNAm signatures exerted a lower classification error than the PBMC-based DNAm markers (p-value = 0.0002). The area-under-the-curve (AUC) analysis based on out-of-bag errors using the random forest classification algorithm revealed that PBMC-, NEC-, and AEC-based methylation data yielded 31 loci (AUC: 0.87), 8 loci (AUC: 0.99), and 4 loci (AUC: 0.97) from each optimal subset of tissue-specific markers, respectively. We also discovered the locus-locus interaction of DNAm levels of the CDH6 gene and RAPGEF3 gene might interact with each other to jointly predict the risk of asthma – which suggests the pivotal role of cell-cell junction in the pathological changes of asthma. Both AECs and NECs might provide better diagnostic accuracy and efficacy levels than PBMCs. Further research is warranted to evaluate how these tissue-specific DNAm markers classify and predict asthma risk.
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Affiliation(s)
- Ping-I Lin
- Department of Health Sciences, Karlstad University, Karlstad, Sweden
| | - Huan Shu
- Department of Health Sciences, Karlstad University, Karlstad, Sweden.,Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA.
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43
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Huang Y, Zhang H, Wang C, Zhou J, Li Y, Hu C. DNA methylation suppresses liver Hamp expression in response to iron deficiency after bariatric surgery. Surg Obes Relat Dis 2020; 16:109-118. [DOI: 10.1016/j.soard.2019.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/25/2019] [Accepted: 10/05/2019] [Indexed: 01/06/2023]
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44
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Bae DJ, Jun JA, Chang HS, Park JS, Park CS. Epigenetic Changes in Asthma: Role of DNA CpG Methylation. Tuberc Respir Dis (Seoul) 2020; 83:1-13. [PMID: 31905427 PMCID: PMC6953489 DOI: 10.4046/trd.2018.0088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/19/2019] [Accepted: 08/30/2019] [Indexed: 12/21/2022] Open
Abstract
For the past three decades, more than a thousand of genetic studies have been performed to find out the genetic variants responsible for the risk of asthma. Until now, all of the discovered single nucleotide polymorphisms have explained genetic effects less than initially expected. Thus, clarification of environmental factors has been brought up to overcome the 'missing' heritability. The most exciting solution is epigenesis because it intervenes at the junction between the genome and the environment. Epigenesis is an alteration of genetic expression without changes of DNA sequence caused by environmental factors such as nutrients, allergens, cigarette smoke, air pollutants, use of drugs and infectious agents during pre- and post-natal periods and even in adulthood. Three major forms of epigenesis are composed of DNA methylation, histone modifications, and specific microRNA. Recently, several studies have been published on epigenesis in asthma and allergy as a powerful tool for research of genetic heritability in asthma albeit epigenetic changes are at the starting point to obtain the data on specific phenotypes of asthma. In this presentation, we mainly review the potential role of DNA CpG methylation in the risk of asthma and its sub-phenotypes including nonsteroidal anti-inflammatory exacerbated respiratory diseases.
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Affiliation(s)
- Da Jeong Bae
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Ji Ae Jun
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang Graduate School, Bucheon, Korea
| | - Hun Soo Chang
- Department of Environmental Health Sciences, Soonchunhyang University, Asan, Korea
| | - Jong Sook Park
- Division of Allergy and Respiratory Medicine, Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Choon Sik Park
- Division of Allergy and Respiratory Medicine, Genome Research Center, Soonchunhyang University Bucheon Hospital, Bucheon, Korea.
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45
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Zhang L, Morisaki H, Wei Y, Li Z, Yang L, Zhou Q, Zhang X, Xing W, Hu M, Shima M, Toriba A, Hayakawa K, Tang N. Characteristics of air pollutants inside and outside a primary school classroom in Beijing and respiratory health impact on children. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113147. [PMID: 31522002 DOI: 10.1016/j.envpol.2019.113147] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/28/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
This study investigated the spatial and temporal distributions of particulate and gaseous air pollutants in a primary school in Beijing and assessed their health impact on the children. The results show that air quality inside the classroom was greatly affected by the input of outdoor pollutants; high levels of pollution were observed during both the heating and nonheating periods and indicate that indoor and outdoor air pollution posed a threat to the children's health. Traffic sources near the primary school were the main contributors to indoor and outdoor pollutants during both periods. Moreover, air quality in this primary school was affected by coal combustion and atmospheric reactions during the heating and nonheating periods, respectively. Based on the estimation by exposure-response functions and the weighting of indoor and outdoor pollutants during different periods, the levels of PM2.5, PM 10 and O3 at school had adverse respiratory health effects on children. Longer exposures during the nonheating period contributed to higher health risks. These results emphasized that emission sources nearby had a direct impact on air quality in school and children's respiratory health. Therefore, measures should be taken for double control on air pollution inside and outside the classroom to protect children from it.
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Affiliation(s)
- Lulu Zhang
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Hiroshi Morisaki
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Yongjie Wei
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Zhigang Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Lu Yang
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Quanyu Zhou
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Xuan Zhang
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Wanli Xing
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Min Hu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Science and Engineering, Peking University, Beijing, 100871, China
| | - Masayuki Shima
- Department of Public Health, Hyogo College of Medicine, Nishinomiya, Hyogo, 663-8501, Japan
| | - Akira Toriba
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Kazuichi Hayakawa
- Institute of Nature and Environmental Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Ning Tang
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan; Institute of Nature and Environmental Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
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46
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Abstract
PURPOSE OF REVIEW Asthma is one of the most common chronic respiratory diseases linked with increased morbidity and healthcare utilization. The underlying pathophysiological processes and causal relationships of asthma with epigenetic mechanisms are partially understood. Here we review human studies of epigenetic mechanisms in asthma, with a special focus on DNA methylation. RECENT FINDINGS Epigenetic studies of childhood asthma have identified specific methylation signatures associated with allergic inflammation in the airway and immune cells, demonstrating a regulatory role for methylation in asthma pathogenesis. Despite these novel findings, additional research in the role of epigenetic mechanisms underlying asthma endotypes is needed. Similarly, studies of histone modifications are also lacking in asthma. Future studies of epigenetic mechanisms in asthma will benefit from data integration in well phenotyped cohorts. This review provides an overview of the current literature on epigenetic studies in human asthma, with special emphasis on methylation and childhood asthma.
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Affiliation(s)
- Jose L Gomez
- Pulmonary, Critical Care and Sleep, Yale University School of Medicine, 300 Cedar Street, New Haven, CT, 06520, USA.
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47
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The role of epigenetics in respiratory health in urban populations in low and middle-income countries. GLOBAL HEALTH EPIDEMIOLOGY AND GENOMICS 2019; 4:e8. [PMID: 32047643 PMCID: PMC6983949 DOI: 10.1017/gheg.2019.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
As urbanization increases in low- and middle-income countries (LMICs), urban populations will be increasingly exposed to a range of environmental risk factors for non-communicable diseases. Inadequate living conditions in urban settings may influence mechanisms that regulate gene expression, leading to the development of non-communicable respiratory diseases. We conducted a systematic review of the literature to assess the relationship between respiratory health and epigenetic factors to urban environmental exposures observed in LMICs using MEDLINE, PubMed, EMBASE, and Google Scholar searching a combination of the terms: epigenetics, chronic respiratory diseases (CRDs), lung development, chronic obstructive airway disease, and asthma. A total of 2835 articles were obtained, and 48 articles were included in this review. We found that environmental factors during early development are related to epigenetic effects that may be associated with a higher risk of CRDs. Epigenetic dysregulation of gene expression of the histone deacetylase (HDAC) and histone acetyltransferase gene families was likely involved in lung health of slum dwellers. Respiratory-related environmental exposures influence HDAC function and deoxyribonucleic acid methylation and are important risk factors in the development of CRD. Additional epigenetic research is needed to improve our understanding of associations between environmental exposures and non-communicable respiratory diseases.
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48
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Understanding Root Causes of Asthma. Perinatal Environmental Exposures and Epigenetic Regulation. Ann Am Thorac Soc 2019; 15:S103-S108. [PMID: 29676631 DOI: 10.1513/annalsats.201706-514mg] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A common explanation for the origins and rising prevalence of asthma is that they involve complex interactions between hereditary predispositions and environmental exposures that are incompletely understood. Yet, emerging evidence substantiates the paradigm that environmental exposures prenatally and during very early childhood induce epigenetic alterations that affect the expression of asthma genes and, thereby, asthma itself. Here, we review much of the key evidence supporting this paradigm. First, we describe evidence that the prenatal and early postnatal periods are key time windows of susceptibility to environmental exposures that may trigger asthma. Second, we explain how environmental epigenetic regulation may explain the immunopathology underlying asthma. Third, we outline specific evidence that environmental exposures induce epigenetic regulation, both from animal models and robust human epidemiological research. Finally, we review some emerging topics, including the importance of coexposures, population divergence, and how epigenetic regulation may change over time. Despite all the inherent complexity, great progress has been made toward understanding what we still consider reversible asthma risk factors. These, in time, may impact patient care.
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49
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Franzago M, La Rovere M, Guanciali Franchi P, Vitacolonna E, Stuppia L. Epigenetics and human reproduction: the primary prevention of the noncommunicable diseases. Epigenomics 2019; 11:1441-1460. [PMID: 31596147 DOI: 10.2217/epi-2019-0163] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Epigenetic regulation of gene expression plays a key role in affecting human health and diseases with particular regard to human reproduction. The major concern in this field is represented by the epigenetic modifications in the embryo and the increased risk of long-life disorders induced by the use of assisted reproduction techniques, able to affect the epigenetic assessment in the first steps of embryo development. In this review, we analyze the correlation between epigenetic modifications and human reproduction, suggesting that the reversibility of the epigenetic processes could represent a novel resource for the treatment of the couple's infertility and that parental lifestyle in periconceptional period could be considered as an important issue of primary prevention.
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Affiliation(s)
- Marica Franzago
- Department of Medicine & Aging, School of Medicine & Health Sciences, 'G. d'Annunzio' University, Chieti-Pescara, Chieti, Italy.,Center for Aging Studies & Translational Medicine (CESI-MET), 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Marina La Rovere
- Department of Psychological, Health & Territorial Sciences, School of Medicine & Health Sciences, 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Paolo Guanciali Franchi
- Department of Medical, Oral & Biotechnological Sciences, School of Medicine & Health Sciences, 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
| | - Ester Vitacolonna
- Department of Medicine & Aging, School of Medicine & Health Sciences, 'G. d'Annunzio' University, Chieti-Pescara, Chieti, Italy
| | - Liborio Stuppia
- Center for Aging Studies & Translational Medicine (CESI-MET), 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy.,Department of Psychological, Health & Territorial Sciences, School of Medicine & Health Sciences, 'G. d'Annunzio' University of Chieti-Pescara, Chieti, Italy
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50
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Clifford RL, Patel J, MacIsaac JL, McEwen LM, Johnson SR, Shaw D, Knox AJ, Hackett TL, Kobor MS. Airway epithelial cell isolation techniques affect DNA methylation profiles with consequences for analysis of asthma related perturbations to DNA methylation. Sci Rep 2019; 9:14409. [PMID: 31595000 PMCID: PMC6783553 DOI: 10.1038/s41598-019-50873-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/15/2019] [Indexed: 12/14/2022] Open
Abstract
The airway epithelium forms the interface between the inhaled environment and the lung. The airway epithelium is dysfunctional in asthma and epigenetic mechanisms are considered a contributory factor. We hypothesised that the DNA methylation profiles of cultured primary airway epithelial cells (AECs) would differ between cells isolated from individuals with asthma (n = 17) versus those without asthma (n = 16). AECs were isolated from patients by two different isolation techniques; pronase digestion (9 non-asthmatic, 8 asthmatic) and bronchial brushings (7 non-asthmatic and 9 asthmatic). DNA methylation was assessed using an Illumina Infinium HumanMethylation450 BeadChip array. DNA methylation of AECs clustered by isolation technique and linear regression identified 111 CpG sites differentially methylated between isolation techniques in healthy individuals. As a consequence, the effect of asthmatic status on DNA methylation was assessed within AEC samples isolated using the same technique. In pronase isolated AECs, 15 DNA regions were differentially methylated between asthmatics and non-asthmatics. In bronchial brush isolated AECs, 849 differentially methylated DNA regions were identified with no overlap to pronase regions. In conclusion, regardless of cell isolation technique, differential DNA methylation was associated with asthmatic status in AECs, providing further evidence for aberrant DNA methylation as a signature of epithelial dysfunction in asthma.
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Affiliation(s)
- Rachel L Clifford
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK. .,Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Jamie Patel
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa M McEwen
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simon R Johnson
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Dominick Shaw
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Alan J Knox
- Nottingham NIHR Biomedical Research Centre, Nottingham MRC Molecular Pathology Node, Division of Respiratory Medicine, University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Tillie-Louise Hackett
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada.,Department of Anaesthesiology, Pharmacology & Therapeutics, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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