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Gallazzi M, Pizzolante M, Biganzoli EM, Bollati V. Wonder symphony: epigenetics and the enchantment of the arts. ENVIRONMENTAL EPIGENETICS 2024; 10:dvae001. [PMID: 38496252 PMCID: PMC10944288 DOI: 10.1093/eep/dvae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/11/2023] [Accepted: 01/30/2024] [Indexed: 03/19/2024]
Abstract
Epigenetics, the study of heritable changes in gene expression without altering the DNA sequence, has gained significant attention due to its implications for gene regulation and chromatin stability. Epigenetic mechanisms play a fundamental role in gene-environment interactions, shaping individual development and adaptation. DNA methylation, histone modifications, and non-coding RNAs are key epigenetic regulators. Epigenetic changes can be triggered by environmental factors, including stress, toxins, and social interactions, influencing health and well-being. Positive experiences, such as engagement with the arts, have been linked to emotional responses and neurotransmitter release. While the impacts of detrimental factors on epigenetics have been widely studied, the effects of positive influences are less explored. Specifically, visual art and music have profound effects on emotions, cognition, and mood regulation. Exposure to arts enhances memory, reduces stress, and fosters social inclusion. Recent research has begun to explore the links between positive experiences and epigenetic modifications, suggesting that aesthetic experiences, including visual art and music fruition, might induce dynamic and/or stable changes in gene expression profiles. However, this field is in its infancy, and more research is needed to establish clear connections. Collaborative efforts among genetics, epigenetics, neuroscience, psychology, and the arts are essential for a comprehensive understanding. Longitudinal studies tracking sustained exposure to positive experiences and examining the influence of childhood artistic education on the biological bases of therapeutic effects of art and music are promising avenues for future research. Ultimately, understanding how positive experiences influence epigenetics could provide insights into the long-term enhancement of human well-being.
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Affiliation(s)
- Marta Gallazzi
- Catholic University of Milan, Milan 20123, Italy
- EPIGET LAB, Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, Milan 20122, Italy
| | - Marta Pizzolante
- Research Center in Communication Psychology (PSICOM), Department of Psychology, Catholic University of Milan, Milan 20123, Italy
| | - Elia Mario Biganzoli
- Unit of Medical Statistics, Bioinformatics and Epidemiology, Department of Biomedical and Clinical Sciences (DIBIC), University of Milan, Via Giovanni Battista Grassi, 74, Milan 20157, Italy
- Unit of Clinical Research and Medical Statistics, Ospedale “L. Sacco” LITA Campus, Via Giovanni Battista Grassi, 74 Milan 20157, Italy
| | - Valentina Bollati
- EPIGET LAB, Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, Milan 20122, Italy
- Occupational Health Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via San Barnaba 8, Milan 20122, Italy
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2
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Fang F, Quach B, Lawrence KG, van Dongen J, Marks JA, Lundgren S, Lin M, Odintsova VV, Costeira R, Xu Z, Zhou L, Mandal M, Xia Y, Vink JM, Bierut LJ, Ollikainen M, Taylor JA, Bell JT, Kaprio J, Boomsma DI, Xu K, Sandler DP, Hancock DB, Johnson EO. Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use. Mol Psychiatry 2024; 29:124-133. [PMID: 37935791 PMCID: PMC11078760 DOI: 10.1038/s41380-023-02310-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023]
Abstract
Cannabis is widely used worldwide, yet its links to health outcomes are not fully understood. DNA methylation can serve as a mediator to link environmental exposures to health outcomes. We conducted an epigenome-wide association study (EWAS) of peripheral blood-based DNA methylation and lifetime cannabis use (ever vs. never) in a meta-analysis including 9436 participants (7795 European and 1641 African ancestry) from seven cohorts. Accounting for effects of cigarette smoking, our trans-ancestry EWAS meta-analysis revealed four CpG sites significantly associated with lifetime cannabis use at a false discovery rate of 0.05 ( p < 5.85 × 10 - 7 ) : cg22572071 near gene ADGRF1, cg15280358 in ADAM12, cg00813162 in ACTN1, and cg01101459 near LINC01132. Additionally, our EWAS analysis in participants who never smoked cigarettes identified another epigenome-wide significant CpG site, cg14237301 annotated to APOBR. We used a leave-one-out approach to evaluate methylation scores constructed as a weighted sum of the significant CpGs. The best model can explain 3.79% of the variance in lifetime cannabis use. These findings unravel the DNA methylation changes associated with lifetime cannabis use that are independent of cigarette smoking and may serve as a starting point for further research on the mechanisms through which cannabis exposure impacts health outcomes.
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Affiliation(s)
- Fang Fang
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA.
| | - Bryan Quach
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Kaitlyn G Lawrence
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jesse A Marks
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Sara Lundgren
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Mingkuan Lin
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
| | - Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ricardo Costeira
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Linran Zhou
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Meisha Mandal
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Yujing Xia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jacqueline M Vink
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Laura J Bierut
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO, USA
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, West Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Dana B Hancock
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
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3
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Chen Y, Zhao M, Ji K, Li J, Wang S, Lu L, Chen Z, Zeng J. Association of nicotine dependence and gut microbiota: a bidirectional two-sample Mendelian randomization study. Front Immunol 2023; 14:1244272. [PMID: 38022531 PMCID: PMC10664251 DOI: 10.3389/fimmu.2023.1244272] [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: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background Nicotine dependence is a key factor influencing the diversity of gut microbiota, and targeting gut microbiota may become a new approach for the prevention and treatment of nicotine dependence. However, the causal relationship between the two is still unclear. This study aims to investigate the causal relationship between nicotine dependence and gut microbiota. Methods A two-sample bidirectional Mendelian randomization (MR) study was conducted using the largest existing gut microbiota and nicotine dependence genome-wide association studies (GWAS). Causal relationships between genetically predicted nicotine dependence and gut microbiota abundance were examined using inverse variance weighted, MR-Egger, weighted median, simple mode, weighted mode, and MR-PRESSO approaches. Cochrane's Q test, MR-Egger intercept test, and leave-one-out analysis were performed as sensitivity analyses to assess the robustness of the results. Multivariable Mendelian randomization analysis was also conducted to eliminate the interference of smoking-related phenotypes. Reverse Mendelian randomization analysis was then performed to determine the causal relationship between genetically predicted gut microbiota abundance and nicotine dependence. Results Genetically predicted nicotine dependence had a causal effect on Christensenellaceae (β: -0.52, 95% CI: -0.934-0.106, P = 0.014). The Eubacterium xylanophilum group (OR: 1.106, 95% CI: 1.004-1.218), Lachnoclostridium (OR: 1.118, 95% CI: 1.001-1.249) and Holdemania (OR: 1.08, 95% CI: 1.001-1.167) were risk factors for nicotine dependence. Peptostreptococcaceae (OR: 0.905, 95% CI: 0.837-0.977), Desulfovibrio (OR: 0.014, 95% CI: 0.819-0.977), Dorea (OR: 0.841, 95% CI. 0.731-0.968), Faecalibacterium (OR: 0.831, 95% CI: 0.735-0.939) and Sutterella (OR: 0.838, 95% CI: 0.739-0.951) were protective factor for nicotine dependence. The sensitivity analysis showed consistent results. Conclusion The Mendelian randomization study confirmed the causal link between genetically predicted risk of nicotine dependence and genetically predicted abundance of gut microbiota. Gut microbiota may serve as a biomarker and offer insights for addressing nicotine dependence.
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Affiliation(s)
- Yuexuan Chen
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Mengjiao Zhao
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kaisong Ji
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jingjing Li
- Department of Acupuncture, Baoan District Hospital of Traditional Chinese Medicine, Shenzhen, China
| | - Shuxin Wang
- Department of Acupuncture, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liming Lu
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhenhu Chen
- Department of Acupuncture, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jingchun Zeng
- Department of Acupuncture, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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5
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Sato A, Ishigami A. Effects of heated tobacco product aerosol extracts on DNA methylation and gene transcription in lung epithelial cells. Toxicol Appl Pharmacol 2023; 475:116637. [PMID: 37499768 DOI: 10.1016/j.taap.2023.116637] [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: 07/01/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
AIMS Smoking causes DNA methylation (DNAm) alterations that lead to lung cancer development. Although the use of heated tobacco products (HTPs) has recently increased, their impact on health remains unclear. This study aimed to evaluate the effects of HTPs on DNAm and gene transcription in human lung epithelial cells in vitro. MAIN METHODS Human lung adenocarcinoma (A549) cells with type II alveolar epithelial characteristics were treated with aerosol extracts of two HTPs or a smoke extract of combustible reference cigarette (RC). Global 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) levels were quantified using dot blot analysis. Furthermore, reduced representation of bisulfite sequencing, DNA microarray, and quantitative PCR analyses were performed to determine CpG methylation and gene transcription changes induced by HTP and RC. KEY FINDINGS Global 5-mC and 5-hmC levels were decreased by the RC extract but not the HTP extracts. However, an HTP extract altered the CpG methylation pattern, and Gene Ontology enrichment analysis of the differentially methylated regions of the RC and HTP groups showed a similar pattern. The HTP extract affected gene expression, albeit to a lesser extent than the RC extract. In particular, the HTP extract markedly affected the mRNA expression and promoter methylation of cytochrome P450 family 1 subfamily A member 1 (CYP1A1), which is associated with carcinogenic risk. SIGNIFICANCE The study results suggest that HTPs as well as conventional combustible cigarettes can alter CpG methylation and gene transcription in lung epithelial cells.
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Affiliation(s)
- Ayami Sato
- Molecular Regulation of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo 173-0015, Japan
| | - Akihito Ishigami
- Molecular Regulation of Aging, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo 173-0015, Japan.
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Tanino R, Tsubata Y, Hotta T, Okimoto T, Amano Y, Takechi M, Tanaka T, Akita T, Nagase M, Yamashita C, Wada K, Isobe T. Characterization of a spontaneous mouse model of mild, accelerated aging via ECM degradation in emphysematous lungs. Sci Rep 2023; 13:10740. [PMID: 37400563 DOI: 10.1038/s41598-023-37638-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023] Open
Abstract
Emphysema limits airflow and causes irreversible progression of chronic obstructive pulmonary disease (COPD). Strain differences must be considered when selecting mouse models of COPD, owing to disease complexity. We previously reported that a novel C57BL/6JJcl substrain, the Mayumi-Emphysema (ME) mouse, exhibits spontaneous emphysema; however, the other characteristics remain unknown. We aimed to characterize the lungs of ME mice and determine their experimental availability as a model. ME mice had a lower body weight than the control C57BL/6JJcl mice, with a median survival time of ~80 weeks. ME mice developed diffused emphysema with respiratory dysfunction from 8 to 26 weeks of age, but did not develop bronchial wall thickening. Proteomic analyses revealed five extracellular matrix-related clusters in downregulated lung proteins in ME mice. Moreover, EFEMP2/fibulin-4, an essential extracellular matrix protein, was the most downregulated protein in the lungs of ME mice. Murine and human EFEMP2 were detected in the pulmonary artery. Furthermore, patients with mild COPD showed decreased EFEMP2 levels in the pulmonary artery when compared to those without COPD. The ME mouse is a model of mild, accelerated aging with low-inflammatory emphysema and respiratory dysfunction that progresses with age and pulmonary EFEMP2 decrease, similar to that observed in patients with mild COPD.
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Affiliation(s)
- Ryosuke Tanino
- Department of Internal Medicine, Division of Respiratory Medicine and Medical Oncology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan
| | - Yukari Tsubata
- Department of Internal Medicine, Division of Respiratory Medicine and Medical Oncology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan.
| | - Takamasa Hotta
- Department of Internal Medicine, Division of Respiratory Medicine and Medical Oncology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan
| | - Tamio Okimoto
- Department of Internal Medicine, Division of Respiratory Medicine and Medical Oncology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan
| | - Yoshihiro Amano
- Department of Internal Medicine, Division of Respiratory Medicine and Medical Oncology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan
| | - Mayumi Takechi
- Department of Experimental Animals, Interdisciplinary Center for Science Research, Organization for Research and Academic Information, Shimane University, Izumo, Japan
| | - Tetsuya Tanaka
- Department of Human Nutrition, Faculty of Contemporary Life Science, Chugoku Gakuen University, Okayama, Japan
| | - Tomomi Akita
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Mamiko Nagase
- Department of Organ Pathology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Chikamasa Yamashita
- Department of Pharmaceutics and Drug Delivery, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan
| | - Koichiro Wada
- Department of Pharmacology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Takeshi Isobe
- Department of Internal Medicine, Division of Respiratory Medicine and Medical Oncology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo, Shimane, 693-8501, Japan
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Fang F, Andersen AM, Philibert R, Hancock DB. Epigenetic biomarkers for smoking cessation. ADDICTION NEUROSCIENCE 2023; 6:100079. [PMID: 37123087 PMCID: PMC10136056 DOI: 10.1016/j.addicn.2023.100079] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cigarette smoking has been associated with epigenetic alterations that may be reversible upon cessation. As the most-studied epigenetic modification, DNA methylation is strongly associated with smoking exposure, providing a potential mechanism that links smoking to adverse health outcomes. Here, we reviewed the reversibility of DNA methylation in accessible peripheral tissues, mainly blood, in relation to cigarette smoking cessation and the utility of DNA methylation as a biomarker signature to differentiate current, former, and never smokers and to quantify time since cessation. We summarized thousands of differentially methylated Cytosine-Guanine (CpG) dinucleotides and regions associated with smoking cessation from candidate gene and epigenome-wide association studies, as well as the prediction accuracy of the multi-CpG predictors for smoking status. Overall, there is robust evidence for DNA methylation signature of cigarette smoking cessation. However, there are still gaps to fill, including (1) cell-type heterogeneity in measuring blood DNA methylation; (2) underrepresentation of non-European ancestry populations; (3) limited longitudinal data to quantitatively measure DNA methylation after smoking cessation over time; and (4) limited data to study the impact of smoking cessation on other epigenetic features, noncoding RNAs, and histone modifications. Epigenetic machinery provides promising biomarkers that can improve success in smoking cessation in the clinical setting. To achieve this goal, larger and more-diverse samples with longitudinal measures of a broader spectrum of epigenetic marks will be essential to developing a robust DNA methylation biomarker assay, followed by meeting validation requirements for the assay before being implemented as a clinically useful tool.
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Affiliation(s)
- Fang Fang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
| | - Allan M. Andersen
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, USA
- Behavioral Diagnostics LLC, 2500 Crosspark Rd, Coralville, IA 52241, USA
- Department of Biomedical Engineering, 5601 Seamans Center for the Engineering Arts and Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Dana B. Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, 3040 East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA
- Corresponding author. (D.B. Hancock)
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Mishra PP, Mishra BH, Raitoharju E, Mononen N, Viikari J, Juonala M, Hutri-Kähönen N, Kähönen M, Raitakari OT, Lehtimäki T. Gene Set Based Integrated Methylome and Transcriptome Analysis Reveals Potential Molecular Mechanisms Linking Cigarette Smoking and Related Diseases. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:193-204. [PMID: 37145884 DOI: 10.1089/omi.2023.0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Advanced integrative analysis of DNA methylation and transcriptomics data may provide deeper insights into smoke-induced epigenetic alterations, their effects on gene expression and related biological processes, linking cigarette smoking and related diseases. We hypothesize that accumulation of DNA methylation changes in CpG sites across genomic locations of different genes might have biological significance. We tested the hypothesis by performing gene set based integrative analysis of blood DNA methylation and transcriptomics data to identify potential transcriptomic consequences of smoking via changes in DNA methylation in the Young Finns Study (YFS) participants (n = 1114, aged 34-49 years, women: 54%, men: 46%). First, we performed epigenome-wide association study (EWAS) of smoking. We then defined sets of genes based on DNA methylation status within their genomic regions, for example, sets of genes containing hyper- or hypomethylated CpG sites in their body or promoter regions. Gene set analysis was performed using transcriptomics data from the same participants. Two sets of genes, one containing 49 genes with hypomethylated CpG sites in their body region and the other containing 33 genes with hypomethylated CpG sites in their promoter region, were differentially expressed among the smokers. Genes in the two gene sets are involved in bone formation, metal ion transport, cell death, peptidyl-serine phosphorylation, and cerebral cortex development process, revealing epigenetic-transcriptomic pathways to smoking-related diseases such as osteoporosis, atherosclerosis, and cognitive impairment. These findings contribute to a deeper understanding of the pathophysiology of smoking-related diseases and may provide potential therapeutic targets.
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Affiliation(s)
- Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Binisha H Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere University Hospital, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Jorma Viikari
- Department of Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
| | - Markus Juonala
- Department of Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
| | - Nina Hutri-Kähönen
- Department of Paediatrics, Tampere University Hospital, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
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Castagné R, Ménard S, Delpierre C. The epigenome as a biological candidate to incorporate the social environment over the life course and generations. Epigenomics 2023; 15:5-10. [PMID: 36916280 DOI: 10.2217/epi-2022-0457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Affiliation(s)
- Raphaële Castagné
- Center for Epidemiology & Research in POPulation Health (CERPOP), UMR 1295, Université Toulouse III Paul Sabatier, INSERM, 31000, Toulouse, France
| | - Sandrine Ménard
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, Toulouse, 31024, France
| | - Cyrille Delpierre
- Center for Epidemiology & Research in POPulation Health (CERPOP), UMR 1295, Université Toulouse III Paul Sabatier, INSERM, 31000, Toulouse, France
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10
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Tran JH, Stuart KV, de Vries V, Vergroesen JE, Cousins CC, Hysi PG, Do R, Rocheleau G, Kang JH, Wiggs JL, MacGregor S, Khawaja AP, Mackey DA, Klaver CCW, Ramdas WD, Pasquale LR. Genetic Associations Between Smoking- and Glaucoma-Related Traits. Transl Vis Sci Technol 2023; 12:20. [PMID: 36786746 PMCID: PMC9932549 DOI: 10.1167/tvst.12.2.20] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Purpose The purpose of this study was to describe the genetic relationship between smoking and glaucoma. Methods We used summary-level genetic data for smoking initiation, smoking intensity (cigarettes per day [CPD]), intraocular pressure (IOP), vertical cup-disc ratio, and open-angle glaucoma (OAG) to estimate global genetic correlations (rg) and perform two-sample Mendelian randomization (MR) experiments that explored relations between traits. Finally, we examined associations between smoking genetic risk scores (GRS) and smoking traits with measured IOP and OAG in Rotterdam Study participants. Results We identified weak inverse rg between smoking- and glaucoma-related traits that were insignificant after Bonferroni correction. However, MR analysis revealed that genetically predicted smoking initiation was associated with lower IOP (-0.18 mm Hg per SD, 95% confidence interval [CI] = -0.30 to -0.06, P = 0.003). Furthermore, genetically predicted smoking intensity was associated with decreased OAG risk (odds ratio [OR] = 0.74 per SD, 95% CI = 0.61 to 0.90, P = 0.002). In the Rotterdam Study, the smoking initiation GRS was associated with lower IOP (-0.09 mm Hg per SD, 95% CI = -0.17 to -0.01, P = 0.04) and lower odds of OAG (OR = 0.84 per SD, 95% CI = 0.73 to 0.98, P = 0.02) in multivariable-adjusted analyses. In contrast, neither smoking history nor CPD was associated with IOP (P ≥ 0.38) or OAG (P ≥ 0.54). Associations between the smoking intensity GRS and glaucoma traits were null (P ≥ 0.13). Conclusions MR experiments and GRS generated from Rotterdam Study participants support an inverse relationship between smoking and glaucoma. Translational Relevance Understanding the genetic drivers of the inverse relationship between smoking and glaucoma could yield new insights into glaucoma pathophysiology.
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Affiliation(s)
- Jessica H. Tran
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelsey V. Stuart
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, UK
| | - Victor de Vries
- Departments of Ophthalmology and Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joëlle E. Vergroesen
- Departments of Ophthalmology and Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Clara C. Cousins
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Pirro G. Hysi
- Department of Ophthalmology, King's College London, St. Thomas’ Hospital, London, UK
- Department of Twin Research & Genetic Epidemiology, King's College London, St. Thomas’ Hospital, London, UK
| | - Ron Do
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ghislain Rocheleau
- Charles Bronfman Institute for Personalized Medicine, Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jae H. Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Janey L. Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Stuart MacGregor
- Department of Statistical Genetics, QIMR Bergohofer Medical Research Institute, Brisbane, Australia
| | - Anthony P. Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, UK
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Western Australia, Australia
| | - Caroline C. W. Klaver
- Departments of Ophthalmology and Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboudumc, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Molecular and Clinical Ophthalmology, University of Basel, Basel, Switzerland
| | - Wishal D. Ramdas
- Departments of Ophthalmology and Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Louis R. Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Sekovanić A, Dorotić A, Pašalić D, Orct T, Kljaković-Gašpić Z, Grgec AS, Stasenko S, Mioč T, Piasek M, Jurasović J. The effects of maternal cigarette smoking on cadmium and lead levels, miRNA expression and biochemical parameters across the feto-placental unit. Heliyon 2022; 8:e12568. [PMID: 36636214 PMCID: PMC9830161 DOI: 10.1016/j.heliyon.2022.e12568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/12/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Several miRNAs have been previously identified to be associated with cigarette smoke and/or the toxic metals cadmium (Cd) and lead (Pb). The aim of this study was to investigate the associations of maternal cigarette smoking with cadmium (Cd) and lead (Pb) levels, candidate miRNA expression and biochemical parameters across the feto-placental unit. miRNAs were isolated according to protocols provided by manufacturer from 72 healthy postpartum women using Qiagens' kits based on phenol/guanidine samples lysis and silica-membrane purification of total RNA. Candidate miRNAs (miR-1537, miR-190b, miR-16, miR-21, and miR-146a) were quantified by real-time PCR. Biochemical parameters were analyzed in plasma samples by standardized and harmonized enzymatic methods using appropriate calibrators, while CRP was determined by immunoturbidimetric method. Concentration of Cd and Pb in whole blood and placenta samples were measured by inductively coupled plasma mass spectroscopy. Cd levels in smokers were higher in all of the analyzed compartments of the feto-placental unit, Pb in maternal blood and placenta than non-smokers. Smokers also had a higher expression of miR-16 in maternal and miR-146a in cord plasma, and lower expression of miR-21 in the placenta in comparison to non-smokers. Urate concentrations in the maternal plasma of smokers were lower than this value in non-smokers. The study has demonstrated that maternal smoking was associated with toxic metals (Cd and Pb) levels, urate concentration and alteration of miRNA expression. Given that the effects of maternal smoking on miRNA expression are inadequate, all compartments of the feto-placental unit should be analyzed to obtain a complete picture. This paper is the first to report on the results of expression of cellular and circulating miRNAs simultaneously in maternal and fetal compartments and in the placenta.
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Affiliation(s)
- Ankica Sekovanić
- Analytical Toxicology and Mineral Metabolism Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia
| | - Adrijana Dorotić
- Department of Medical Laboratory Diagnostics, University Hospital Sveti Duh, 10000 Zagreb, Croatia
| | - Daria Pašalić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, University of Zagreb, School of Medicine, 10000 Zagreb, Croatia
- Corresponding author.
| | - Tatjana Orct
- Analytical Toxicology and Mineral Metabolism Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia
| | - Zorana Kljaković-Gašpić
- Analytical Toxicology and Mineral Metabolism Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia
| | - Antonija Sulimanec Grgec
- Analytical Toxicology and Mineral Metabolism Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia
| | - Sandra Stasenko
- Clinical Department of Obstetrics and Gynecology, Merkur University Hospital, 10000 Zagreb, Croatia
| | - Tatjana Mioč
- Clinical Department of Obstetrics and Gynecology, Merkur University Hospital, 10000 Zagreb, Croatia
| | - Martina Piasek
- Analytical Toxicology and Mineral Metabolism Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia
| | - Jasna Jurasović
- Analytical Toxicology and Mineral Metabolism Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia
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12
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Lussier AA, Zhu Y, Smith BJ, Simpkin AJ, Smith AD, Suderman MJ, Walton E, Ressler KJ, Dunn EC. Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies. Epigenetics 2022; 17:1373-1388. [PMID: 35156895 PMCID: PMC9601563 DOI: 10.1080/15592294.2022.2028072] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 12/02/2021] [Accepted: 01/04/2022] [Indexed: 11/03/2022] Open
Abstract
Biomedical research has grown increasingly cooperative through the sharing of consortia-level epigenetic data. Since consortia preprocess data prior to distribution, new processing pipelines can lead to different versions of the same dataset. Similarly, analytic frameworks evolve to incorporate cutting-edge methods and best practices. However, it remains unknown how different data and analytic versions alter the results of epigenome-wide analyses, which could influence the replicability of epigenetic associations. Thus, we assessed the impact of these changes using data from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. We analysed DNA methylation from two data versions, processed using separate preprocessing and analytic pipelines, examining associations between seven childhood adversities or prenatal smoking exposure and DNA methylation at age 7. We performed two sets of analyses: (1) epigenome-wide association studies (EWAS); (2) Structured Life Course Modelling Approach (SLCMA), a two-stage method that models time-dependent effects. SLCMA results were also compared across two analytic versions. Data version changes impacted both EWAS and SLCMA analyses, yielding different associations at conventional p-value thresholds. However, the magnitude and direction of associations was generally consistent between data versions, regardless of p-values. Differences were especially apparent in analyses of childhood adversity, while smoking associations were more consistent using significance thresholds. SLCMA analytic versions similarly altered top associations, but time-dependent effects remained concordant. Alterations to data and analytic versions influenced the results of epigenome-wide analyses. Our findings highlight that magnitude and direction are better measures for replication and stability than p-value thresholds.
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Affiliation(s)
- Alexandre A. Lussier
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yiwen Zhu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brooke J. Smith
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Andrew J. Simpkin
- School of Mathematics,Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Andrew D.A.C. Smith
- Mathematics and Statistics Research Group, University of the West of England, Bristol, UK
| | - Matthew J. Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Esther Walton
- Department of Psychology, University of Bath, Bath, UK
| | - Kerry J. Ressler
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- McLean Hospital, Belmont, MA, USA
| | - Erin C. Dunn
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center on the Developing Child, Harvard University, Cambridge, MA, USA
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Alfredsson L, Klareskog L, Hedström AK. Influence of Smoking on Disease Activity and Quality of Life in Patients With Rheumatoid Arthritis: Results From a Swedish Case-Control Study With Longitudinal Follow-Up. Arthritis Care Res (Hoboken) 2022; 75:1269-1277. [PMID: 36149365 DOI: 10.1002/acr.25026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/18/2022] [Accepted: 09/20/2022] [Indexed: 01/20/2023]
Abstract
OBJECTIVE Inconclusive findings have been reported regarding the influence of smoking on disease outcomes in established rheumatoid arthritis (RA). This study was undertaken to investigate the influence of smoking habits on disease activity and health-related quality of life (HRQoL) in RA patients. METHODS Patients with newly diagnosed RA (n = 1,531) from the population-based case-control Epidemiological Investigation of Rheumatoid Arthritis study were followed up for up to 3 years after recruitment. Using logistic regression models, the risks of unfavorable outcomes in patients with different smoking habits were compared using self-reported swollen and tender joint counts, the Short Form 36 health survey, the Health Assessment Questionnaire, and the Hospital Anxiety and Depression Scale by calculating odds ratios with 95% confidence intervals. RESULTS At 1-year and 3-year follow-up, current smokers reported higher disease activity and lower HRQoL life compared to non-smokers, regarding both physical and mental aspects. Patients who stopped smoking within 1-year post-baseline had less disease activity measured as swollen joint counts at 1-year follow-up compared to those who continued smoking. Patients who stopped smoking after the 1-year follow-up had higher disease activity and lower HRQoL at baseline than smokers who did not quit, and late smoking cessation was not associated with more favorable outcomes compared to continued smoking. CONCLUSION Current smoking is associated with increased disease activity and lower HRQoL among RA patients. Smoking cessation within the first year after baseline appears to have a favorable effect on disease activity.
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Affiliation(s)
| | - Lars Klareskog
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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14
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Hung RJ, Khodayari Moez E, Kim SJ, Budhathoki S, Brooks JD. Considerations of Biomarker Application for Cancer Continuum in the Era of Precision Medicine. CURR EPIDEMIOL REP 2022; 9:200-211. [DOI: 10.1007/s40471-022-00295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Vieujean S, Caron B, Haghnejad V, Jouzeau JY, Netter P, Heba AC, Ndiaye NC, Moulin D, Barreto G, Danese S, Peyrin-Biroulet L. Impact of the Exposome on the Epigenome in Inflammatory Bowel Disease Patients and Animal Models. Int J Mol Sci 2022; 23:7611. [PMID: 35886959 PMCID: PMC9321337 DOI: 10.3390/ijms23147611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic inflammatory disorders of the gastrointestinal tract that encompass two main phenotypes, namely Crohn's disease and ulcerative colitis. These conditions occur in genetically predisposed individuals in response to environmental factors. Epigenetics, acting by DNA methylation, post-translational histones modifications or by non-coding RNAs, could explain how the exposome (or all environmental influences over the life course, from conception to death) could influence the gene expression to contribute to intestinal inflammation. We performed a scoping search using Medline to identify all the elements of the exposome that may play a role in intestinal inflammation through epigenetic modifications, as well as the underlying mechanisms. The environmental factors epigenetically influencing the occurrence of intestinal inflammation are the maternal lifestyle (mainly diet, the occurrence of infection during pregnancy and smoking); breastfeeding; microbiota; diet (including a low-fiber diet, high-fat diet and deficiency in micronutrients); smoking habits, vitamin D and drugs (e.g., IBD treatments, antibiotics and probiotics). Influenced by both microbiota and diet, short-chain fatty acids are gut microbiota-derived metabolites resulting from the anaerobic fermentation of non-digestible dietary fibers, playing an epigenetically mediated role in the integrity of the epithelial barrier and in the defense against invading microorganisms. Although the impact of some environmental factors has been identified, the exposome-induced epimutations in IBD remain a largely underexplored field. How these environmental exposures induce epigenetic modifications (in terms of duration, frequency and the timing at which they occur) and how other environmental factors associated with IBD modulate epigenetics deserve to be further investigated.
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Affiliation(s)
- Sophie Vieujean
- Hepato-Gastroenterology and Digestive Oncology, University Hospital CHU of Liège, 4000 Liege, Belgium;
| | - Bénédicte Caron
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Vincent Haghnejad
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
| | - Jean-Yves Jouzeau
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Patrick Netter
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Anne-Charlotte Heba
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - Ndeye Coumba Ndiaye
- NGERE (Nutrition-Genetics and Exposure to Environmental Risks), National Institute of Health and Medical Research, University of Lorraine, F-54000 Nancy, France; (A.-C.H.); (N.C.N.)
| | - David Moulin
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
| | - Guillermo Barreto
- CNRS (French National Centre for Scientific Research), Laboratoire IMoPA, Université de Lorraine, UMR 7365, F-54000 Nancy, France; (J.-Y.J.); (P.N.); (D.M.); (G.B.)
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Universidad de la Salud del Estado de Puebla, Puebla 72000, Mexico
| | - Silvio Danese
- Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and University Vita-Salute San Raffaele, 20132 Milan, Italy;
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology NGERE (INSERM U1256), Nancy University Hospital, University of Lorraine, Vandœuvre-lès-Nancy, F-54052 Nancy, France; (B.C.); (V.H.)
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16
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Davies KJM, Richmond S, Medeiros-Mirra RJ, Abbas HH, Wilson-Nagrani CE, Davis MG, Zhurov A. The effect of maternal smoking and alcohol consumption on lip morphology. J Orthod 2022; 49:403-411. [PMID: 35723071 DOI: 10.1177/14653125221094337] [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] [Indexed: 10/18/2022]
Abstract
OBJECTIVE To determine whether maternal smoking and/or alcohol consumption has an influence on lip morphology. Maternal smoking is a known risk factor for orofacial clefts; however, its influence on normal lip variation is unknown. Recent research regarding normal lip morphology has been contradictory. DESIGN Retrospective cohort study. SETTING AND PARTICIPANTS A total of 4747 children from the Avon Longitudinal Study of Parents and Children (ALSPAC) who each had 3D facial scans carried out at 15 years of age were included in the study. METHODS Each of the participants was automatically categorised regarding predetermined lip morphological traits. Questionnaires completed by their mothers identified smoking and alcohol habits during pregnancy. Logistic regression analyses were applied to determine the effect of maternal smoking and alcohol consumption on lip morphology. RESULTS Maternal smoking has significant effects on upper and lower lip contours, Cupid's bow, lower lip-chin shape and lower lip tone (all P < 0.05). There was also an indication of a potential epigenetic effect of smoking pre-pregnancy on upper lip contour (P = 0.0573). Alcohol consumption is significantly associated with philtrum shape, particularly when >6 units of alcohol are consumed per week (P = 0.0149, 32 weeks). Overall results suggest a deeply grooved philtrum is more likely if alcohol is consumed. Investigating the combined effect of smoking and alcohol consumption, lower lip contour (P = 0.00923) and lower lip-chin shape (P = 0.0171) are statistically significant, with lower lip contour more likely to be narrow in the midline, and lower lip-chin shape more likely to be an angular concavity. CONCLUSION Maternal smoking influences a number of lip traits, including a possible epigenetic effect on upper lip contour. Maternal alcohol consumption, particularly at a high level, influences philtrum shape. Maternal smoking and alcohol consumption have a combined effect on lower lip contour and lower lip-chin shape.
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Affiliation(s)
| | - Stephen Richmond
- Department of Orthodontics, School of Dentistry, Cardiff University, Cardiff, UK
| | | | - Hawraa Hassan Abbas
- Department of Orthodontics, School of Dentistry, Cardiff University, Cardiff, UK
| | | | - Megan Gael Davis
- Department of Orthodontics, School of Dentistry, Cardiff University, Cardiff, UK
| | - Alexei Zhurov
- Department of Orthodontics, School of Dentistry, Cardiff University, Cardiff, UK
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17
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Lancaster EE, Vladimirov VI, Riley BP, Landry JW, Roberson-Nay R, York TP. LARGE-SCALE INTEGRATION OF DNA METHYLATION AND GENE EXPRESSION ARRAY PLATFORMS IDENTIFIES BOTH cis AND trans RELATIONSHIPS. Epigenetics 2022; 17:1753-1773. [PMID: 35608069 PMCID: PMC9621057 DOI: 10.1080/15592294.2022.2079293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although epigenome-wide association studies (EWAS) have been successful in identifying DNA methylation (DNAm) patterns associated with disease states, any further characterization of etiologic mechanisms underlying disease remains elusive. This knowledge gap does not originate from a lack of DNAm–trait associations, but rather stems from study design issues that affect the interpretability of EWAS results. Despite known limitations in predicting the function of a particular CpG site, most EWAS maintain the broad assumption that altered DNAm results in a concomitant change of transcription at the most proximal gene. This study integrated DNAm and gene expression (GE) measurements in two cohorts, the Adolescent and Young Adult Twin Study (AYATS) and the Pregnancy, Race, Environment, Genes (PREG) study, to improve the understanding of epigenomic regulatory mechanisms. CpG sites associated with GE in cis were enriched in areas of transcription factor binding and areas of intermediate-to-low CpG density. CpG sites associated with trans GE were also enriched in areas of known regulatory significance, including enhancer regions. These results highlight issues with restricting DNAm-transcript annotations to small genomic intervals and question the validity of assuming a cis DNAm–GE pathway. Based on these findings, the interpretation of EWAS results is limited in studies without multi-omic support and further research should identify genomic regions in which GE-associated DNAm is overrepresented. An in-depth characterization of GE-associated CpG sites could improve predictions of the downstream functional impact of altered DNAm and inform best practices for interpreting DNAm–trait associations generated by EWAS.
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Affiliation(s)
- Eva E Lancaster
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23220
| | | | - Brien P Riley
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23220.,Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23220
| | - Joseph W Landry
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23220
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23220.,Department of Psychology, Virginia Commonwealth University, Richmond, VA 23220
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23220.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA 23220
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18
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Chen L, Peng K, Han Z, Yu S, Huang Z, Xu H, Kang M. Development and validation of a nomogram for preoperative prediction of lymph node metastasis in pathological T1 esophageal squamous cell carcinoma. Medicine (Baltimore) 2022; 101:e29299. [PMID: 35608431 PMCID: PMC9276106 DOI: 10.1097/md.0000000000029299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 03/28/2022] [Indexed: 01/04/2023] Open
Abstract
Endoscopic resection is increasingly used to treat patients with pathological T1 (pT1) esophageal squamous cell carcinoma (ESCC) because of its small surgical trauma. However, reports of the risk factors for lymph node metastasis (LNM) have been controversial. Therefore, we aim to build a nomogram to individually predict the risk of LNM in pT1 ESCC patients, to make an optimal balance between surgical trauma and surgical income.One hundred seventy patients with pT1 esophageal cancer in our hospital were analyzed retrospectively. Logistic proportional hazards models were conducted to find out the risk factor associated with LNM independently, and those were imported into R library "RMS" for analysis. A nomogram is generated based on the contribution weights of variables. Finally, decision analysis and clinical impact curve were used to determine the optimal decision point.Twenty-five (14.7%) of the 170 patients with pT1 ESCC exhibited LNM. Multivariable logistic regression analysis showed that smoking, carcinoembryonic antigen, vascular tumor thromboembolus, and tumor differentiation degree were independent risk factors for LNM. The nomogram had relatively high accuracy (C index of 0.869, 95% confidence interval: 0.794-0.914, P < .0001). The decision curve analysis provided the most significant clinical benefit for the entire included population, with scores falling just above the total score of 85 in the nomogram.Smoking, carcinoembryonic antigen, vascular tumor thromboembolus, and tumor differentiation degree may predict the risk of LNM in tumor 1 ESCC. The risk of LNM can be predicted by the nomogram.
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Affiliation(s)
- Ling Chen
- Department of Cardiac Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Kaiming Peng
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Ziyan Han
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Shaobin Yu
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Zhixin Huang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Hui Xu
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
| | - Mingqiang Kang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, China
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Olmedo-Suárez MÁ, Ramírez-Díaz I, Pérez-González A, Molina-Herrera A, Coral-García MÁ, Lobato S, Sarvari P, Barreto G, Rubio K. Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs. Biomolecules 2022; 12:513. [PMID: 35454102 PMCID: PMC9032613 DOI: 10.3390/biom12040513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Environmental factors, including pollutants and lifestyle, constitute a significant role in severe, chronic pathologies with an essential societal, economic burden. The measurement of all environmental exposures and assessing their correlation with effects on individual health is defined as the exposome, which interacts with our unique characteristics such as genetics, physiology, and epigenetics. Epigenetics investigates modifications in the expression of genes that do not depend on the underlying DNA sequence. Some studies have confirmed that environmental factors may promote disease in individuals or subsequent progeny through epigenetic alterations. Variations in the epigenetic machinery cause a spectrum of different disorders since these mechanisms are more sensitive to the environment than the genome, due to the inherent reversible nature of the epigenetic landscape. Several epigenetic mechanisms, including modifications in DNA (e.g., methylation), histones, and noncoding RNAs can change genome expression under the exogenous influence. Notably, the role of long noncoding RNAs in epigenetic processes has not been well explored in the context of exposome-induced tumorigenesis. In the present review, our scope is to provide relevant evidence indicating that epigenetic alterations mediate those detrimental effects caused by exposure to environmental toxicants, focusing mainly on a multi-step regulation by diverse noncoding RNAs subtypes.
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Affiliation(s)
- Miguel Ángel Olmedo-Suárez
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Andrea Pérez-González
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Alejandro Molina-Herrera
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Miguel Ángel Coral-García
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Decanato de Ciencias de la Salud, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Sagrario Lobato
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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Eriksson Ström J, Kebede Merid S, Pourazar J, Blomberg A, Lindberg A, Ringh MV, Hagemann-Jensen M, Ekström TJ, Behndig AF, Melén E. COPD is Associated with Epigenome-wide Differential Methylation in BAL Lung Cells. Am J Respir Cell Mol Biol 2022; 66:638-647. [PMID: 35286818 PMCID: PMC9163645 DOI: 10.1165/rcmb.2021-0403oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
DNA methylation patterns in chronic pulmonary obstructive disease (COPD) might offer new insights into disease pathogenesis. To assess methylation profiles in the main COPD target organ, we performed an epigenome-wide association study on bronchoalveolar lavage (BAL) cells. Bronchoscopies were performed in 18 COPD subjects and 15 controls (ex- and current smokers). DNA methylation was measured with Illumina MethylationEPIC BeadChip covering >850,000 CpGs. Differentially methylated positions (DMPs) were examined for 1) enrichment in pathways and functional gene relationships using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology; 2) accelerated aging using Horvath's epigenetic clock; 3) correlation with gene expression; and 4) co-localization with genetic variation. We found 1,155 Bonferroni significant (P < 6.74 × 10-8) DMPs associated with COPD, many with large effect sizes. Functional analysis identified biologically plausible pathways and gene relationships, including enrichment for transcription factor activity. Strong correlation was found between COPD and chronological age, but not with accelerated epigenetic aging. For 79 unique DMPs, DNA methylation correlated significantly with gene expression in BAL cells. Thirty-nine percent of DMPs were co-localized with COPD-associated SNPs. To the best of our knowledge, this is the first EWAS of COPD on BAL cells, and our analyses revealed many differential methylation sites. Integration with mRNA data showed a strong functional readout for relevant genes, identifying sites where DNA methylation might directly impact expression. Almost half of DMPs were co-located with SNPs identified in previous GWAS of COPD, suggesting joint genetic and epigenetic pathways related to disease.
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Affiliation(s)
- Jonas Eriksson Ström
- Department of Public Health and Clinical Medicine, Division of Medicine/Respiratory Medicine, Umeå University, Umeå, Sweden;
| | - Simon Kebede Merid
- Karolinska Institutet, 27106, Institute of Environmental Medicine, Stockholm, Sweden
| | - Jamshid Pourazar
- Umeå Universitet Medicinska fakulteten, 59588, Dept. of Public Health and Clinical Medicine, Umeå, Sweden
| | - Anders Blomberg
- Umea University, 8075, Dept. of Public Health and Clinical Medicine, Umea, Sweden
| | - Anne Lindberg
- Umeå Universitet, 8075, Department of Public Health and Clinical Medicine, Section of Medicine, Umea, Sweden
| | - Mikael V Ringh
- Karolinska Institutet, 27106, Department of Clinical Neuroscience and Center for Molecular Medicine, Stockholm, Sweden
| | | | - Tomas J Ekström
- Karolinska Institutet, 27106, Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Stockholm, Sweden
| | - Annelie F Behndig
- Department of Public Health and Clinical Medicine, Division of Medicine/Respiratory Medicine, Umeå University, Umeå, Sweden
| | - Erik Melén
- Karolinska Institutet Department of Clinical Science and Education Sodersjukhuset, 411435, Karolinska Institutet, Stockholm, Sweden
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21
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Aguilera J, Han X, Cao S, Balmes J, Lurmann F, Tyner T, Lutzker L, Noth E, Hammond SK, Sampath V, Burt T, Utz PJ, Khatri P, Aghaeepour N, Maecker H, Prunicki M, Nadeau K. Increases in ambient air pollutants during pregnancy are linked to increases in methylation of IL4, IL10, and IFNγ. Clin Epigenetics 2022; 14:40. [PMID: 35287715 PMCID: PMC8919561 DOI: 10.1186/s13148-022-01254-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ambient air pollutant (AAP) exposure is associated with adverse pregnancy outcomes, such as preeclampsia, preterm labor, and low birth weight. Previous studies have shown methylation of immune genes associate with exposure to air pollutants in pregnant women, but the cell-mediated response in the context of typical pregnancy cell alterations has not been investigated. Pregnancy causes attenuation in cell-mediated immunity with alterations in the Th1/Th2/Th17/Treg environment, contributing to maternal susceptibility. We recruited women (n = 186) who were 20 weeks pregnant from Fresno, CA, an area with chronically elevated AAP levels. Associations of average pollution concentration estimates for 1 week, 1 month, 3 months, and 6 months prior to blood draw were associated with Th cell subset (Th1, Th2, Th17, and Treg) percentages and methylation of CpG sites (IL4, IL10, IFNγ, and FoxP3). Linear regression models were adjusted for weight, age, season, race, and asthma, using a Q value as the false-discovery-rate-adjusted p-value across all genes. RESULTS Short-term and mid-term AAP exposures to fine particulate matter (PM2.5), nitrogen dioxide (NO2) carbon monoxide (CO), and polycyclic aromatic hydrocarbons (PAH456) were associated with percentages of immune cells. A decrease in Th1 cell percentage was negatively associated with PM2.5 (1 mo/3 mo: Q < 0.05), NO2 (1 mo/3 mo/6 mo: Q < 0.05), and PAH456 (1 week/1 mo/3 mo: Q < 0.05). Th2 cell percentages were negatively associated with PM2.5 (1 week/1 mo/3 mo/6 mo: Q < 0.06), and NO2 (1 week/1 mo/3 mo/6 mo: Q < 0.06). Th17 cell percentage was negatively associated with NO2 (3 mo/6 mo: Q < 0.01), CO (1 week/1 mo: Q < 0.1), PM2.5 (3 mo/6 mo: Q < 0.05), and PAH456 (1 mo/3 mo/6 mo: Q < 0.08). Methylation of the IL10 gene was positively associated with CO (1 week/1 mo/3 mo: Q < 0.01), NO2 (1 mo/3 mo/6 mo: Q < 0.08), PAH456 (1 week/1 mo/3 mo: Q < 0.01), and PM2.5 (3 mo: Q = 0.06) while IL4 gene methylation was positively associated with concentrations of CO (1 week/1 mo/3 mo/6 mo: Q < 0.09). Also, IFNγ gene methylation was positively associated with CO (1 week/1 mo/3 mo: Q < 0.05) and PAH456 (1 week/1 mo/3 mo: Q < 0.06). CONCLUSION Exposure to several AAPs was negatively associated with T-helper subsets involved in pro-inflammatory and anti-inflammatory responses during pregnancy. Methylation of IL4, IL10, and IFNγ genes with pollution exposure confirms previous research. These results offer insights into the detrimental effects of air pollution during pregnancy, the demand for more epigenetic studies, and mitigation strategies to decrease pollution exposure during pregnancy.
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Affiliation(s)
- Juan Aguilera
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, 240 Pasteur, Stanford, CA, 94305, USA
| | - Xiaorui Han
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, 240 Pasteur, Stanford, CA, 94305, USA
| | - Shu Cao
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, 240 Pasteur, Stanford, CA, 94305, USA
| | - John Balmes
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Tim Tyner
- University of California, San Francisco-Fresno, Fresno, CA, USA
- Central California Asthma Collaborative, Fresno, USA
| | - Liza Lutzker
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Elizabeth Noth
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - S Katharine Hammond
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, 240 Pasteur, Stanford, CA, 94305, USA
| | - Trevor Burt
- Department of Pediatrics, Division of Neonatology and the Translating Duke Health Children's Health and Discovery Initiative, Duke University School of Medicine, 701 W Main St., Chesterfield Building, Suite 510, Durham, NC, 27701, USA
| | - P J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford University, 291 Campus Drive, Stanford, CA, 94305, USA
| | - Purvesh Khatri
- Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford University, 291 Campus Drive, Stanford, CA, 94305, USA
| | - Nima Aghaeepour
- Departments of Biomedical Data Sciences, Stanford University, 291 Campus Drive, Stanford, CA, 94305, USA
| | - Holden Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, 291 Campus Drive, Stanford, CA, 94305, USA
| | - Mary Prunicki
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, 240 Pasteur, Stanford, CA, 94305, USA
| | - Kari Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, 240 Pasteur, Stanford, CA, 94305, USA.
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22
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Mesnage R, Ibragim M, Mandrioli D, Falcioni L, Tibaldi E, Belpoggi F, Brandsma I, Bourne E, Savage E, Mein CA, Antoniou MN. Comparative Toxicogenomics of Glyphosate and Roundup Herbicides by Mammalian Stem Cell-Based Genotoxicity Assays and Molecular Profiling in Sprague-Dawley Rats. Toxicol Sci 2022; 186:83-101. [PMID: 34850229 PMCID: PMC8883356 DOI: 10.1093/toxsci/kfab143] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Whether glyphosate-based herbicides (GBHs) are more potent than glyphosate alone at activating cellular mechanisms, which drive carcinogenesis remain controversial. As GBHs are more cytotoxic than glyphosate, we reasoned they may also be more capable of activating carcinogenic pathways. We tested this hypothesis by comparing the effects of glyphosate with Roundup GBHs both in vitro and in vivo. First, glyphosate was compared with representative GBHs, namely MON 52276 (European Union), MON 76473 (United Kingdom), and MON 76207 (United States) using the mammalian stem cell-based ToxTracker system. Here, MON 52276 and MON 76473, but not glyphosate and MON 76207, activated oxidative stress and unfolded protein responses. Second, molecular profiling of liver was performed in female Sprague-Dawley rats exposed to glyphosate or MON 52276 (at 0.5, 50, and 175 mg/kg bw/day glyphosate) for 90 days. MON 52276 but not glyphosate increased hepatic steatosis and necrosis. MON 52276 and glyphosate altered the expression of genes in liver reflecting TP53 activation by DNA damage and circadian rhythm regulation. Genes most affected in liver were similarly altered in kidneys. Small RNA profiling in liver showed decreased amounts of miR-22 and miR-17 from MON 52276 ingestion. Glyphosate decreased miR-30, whereas miR-10 levels were increased. DNA methylation profiling of liver revealed 5727 and 4496 differentially methylated CpG sites between the control and glyphosate and MON 52276 exposed animals, respectively. Apurinic/apyrimidinic DNA damage formation in liver was increased with glyphosate exposure. Altogether, our results show that Roundup formulations cause more biological changes linked with carcinogenesis than glyphosate.
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Affiliation(s)
- Robin Mesnage
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, Faculty of Life Sciences & Medicine, Guy’s Hospital, King’s College London, London SE1 9RT, UK
| | - Mariam Ibragim
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, Faculty of Life Sciences & Medicine, Guy’s Hospital, King’s College London, London SE1 9RT, UK
| | - Daniele Mandrioli
- Cesare Maltoni Cancer Research Center, Ramazzini Institute (RI), Bentivoglio, Bologna 40010, Italy
| | - Laura Falcioni
- Cesare Maltoni Cancer Research Center, Ramazzini Institute (RI), Bentivoglio, Bologna 40010, Italy
| | - Eva Tibaldi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute (RI), Bentivoglio, Bologna 40010, Italy
| | - Fiorella Belpoggi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute (RI), Bentivoglio, Bologna 40010, Italy
| | | | - Emma Bourne
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London E1 2AT, UK
| | - Emanuel Savage
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London E1 2AT, UK
| | - Charles A Mein
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London E1 2AT, UK
| | - Michael N Antoniou
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, Faculty of Life Sciences & Medicine, Guy’s Hospital, King’s College London, London SE1 9RT, UK
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Chakravarti R, Lenka SK, Gautam A, Singh R, Ravichandiran V, Roy S, Ghosh D. A Review on CRISPR-Mediated Epigenome Editing: A Future Directive for Therapeutic Management of Cancer. Curr Drug Targets 2022; 23:836-853. [DOI: 10.2174/1389450123666220117105531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/15/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Recent studies have shed light on the role of epigenetic marks in certain diseases like cancer, type II diabetes mellitus (T2DM), obesity, and cardiovascular dysfunction, to name a few. Epigenetic marks like DNA methylation and histone acetylation are randomly altered in the disease state. It has been seen that methylation of DNA and histones can result in down-regulation of gene expression, whereas histone acetylation, ubiquitination, and phosphorylation are linked to enhanced expression of genes. How can we precisely target such epigenetic aberrations to prevent the advent of diseases? The answer lies in the amalgamation of the efficient genome editing technique, CRISPR, with certain effector molecules that can alter the status of epigenetic marks as well as employ certain transcriptional activators or repressors. In this review, we have discussed the rationale of epigenetic editing as a therapeutic strategy and how CRISPR-Cas9 technology coupled with epigenetic effector tags can efficiently edit epigenetic targets. In the later part, we have discussed how certain epigenetic effectors are tagged with dCas9 to elicit epigenetic changes in cancer. Increased interest in exploring the epigenetic background of cancer and non-communicable diseases like type II diabetes mellitus and obesity accompanied with technological breakthroughs has made it possible to perform large-scale epigenome studies.
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Affiliation(s)
- Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Swadhin Kumar Lenka
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Syamal Roy
- CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
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C L, H Z, P K, K M. Recurrence index predicts prognosis of patients with pathological T1 esophageal squamous cell carcinoma. Asian J Surg 2022; 45:928-929. [PMID: 35000851 DOI: 10.1016/j.asjsur.2021.12.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/03/2021] [Indexed: 11/02/2022] Open
Affiliation(s)
- Ling C
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350122, China
| | - Zhixin H
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou 350001, China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350122, China
| | - Kaiming P
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350122, China
| | - Mingqiang K
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China; Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350122, China.
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Panariello F, Fanelli G, Fabbri C, Atti AR, De Ronchi D, Serretti A. Epigenetic Basis of Psychiatric Disorders: A Narrative Review. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2022; 21:302-315. [PMID: 34433406 DOI: 10.2174/1871527320666210825101915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/02/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Psychiatric disorders are complex, multifactorial illnesses with a demonstrated biological component in their etiopathogenesis. Epigenetic modifications, through the modulation of DNA methylation, histone modifications and RNA interference, tune tissue-specific gene expression patterns and play a relevant role in the etiology of psychiatric illnesses. OBJECTIVE This review aims to discuss the epigenetic mechanisms involved in psychiatric disorders, their modulation by environmental factors and their interactions with genetic variants, in order to provide a comprehensive picture of their mutual crosstalk. METHODS In accordance with the PRISMA guidelines, systematic searches of Medline, EMBASE, PsycINFO, Web of Science, Scopus, and the Cochrane Library were conducted. RESULTS Exposure to environmental factors, such as poor socio-economic status, obstetric complications, migration, and early life stressors, may lead to stable changes in gene expression and neural circuit function, playing a role in the risk of psychiatric diseases. The most replicated genes involved by studies using different techniques are discussed. Increasing evidence indicates that these sustained abnormalities are maintained by epigenetic modifications in specific brain regions and they interact with genetic variants in determining the risk of psychiatric disorders. CONCLUSION An increasing amount of evidence suggests that epigenetics plays a pivotal role in the etiopathogenesis of psychiatric disorders. New therapeutic approaches may work by reversing detrimental epigenetic changes that occurred during the lifespan.
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Affiliation(s)
- Fabio Panariello
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Giuseppe Fanelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Chiara Fabbri
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Anna Rita Atti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Diana De Ronchi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
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Aryl Hydrocarbon Receptor Repressor Is Hypomethylated in Psoriasis and Promotes Psoriasis-like Inflammation in HaCaT Cells. Int J Mol Sci 2021; 22:ijms222312715. [PMID: 34884515 PMCID: PMC8657998 DOI: 10.3390/ijms222312715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
It is known that DNA hypomethylation of aryl hydrocarbon receptor repressor (AhRR), one of the epigenetic markers of environmental pollutants, causes skin diseases. However, the function and mechanisms are still unknown. We aimed to determine whether AhRR is hypomethylated in PBMC of psoriasis patients, as well as to examine the expression of psoriasis-related inflammatory cytokines and antimicrobial peptides after 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) treatment in HaCaT cells overexpressing or silencing AhRR. AhRR was determined by qPCR, Western blot, immunohistochemistry, and immunocytochemistry in skin tissue and HaCaT cells. DNA methylation of AhRR was performed by Infinium Human Methylation450 BeadChip in PBMC of psoriasis patients and methylation-specific PCR (MSP) in HaCaT cells. NF-κB pp50 translocation and activity were performed by immunocytochemistry and luciferase reporter assay, respectively. We verified AhRR gene expression in the epidermis from psoriasis patients and healthy controls. AhRR hypomethylation in PBMC of psoriasis patients and pAhRR-HaCaT cells was confirmed. The expression level of AhRR was increased in both TCDD-treated HaCaT cells and pAhRR-HaCaT cells. NF-κB pp50 translocation and activity increased with TCDD. Our results showed that AhRR was hypomethylated and overexpressed in the lesional skin of patients with psoriasis, thereby increasing AhRR gene expression and regulating pro-inflammatory cytokines through the NF-κB signaling pathway in TCDD-treated HaCaT cells.
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Smoking-associated upregulation of CBX3 suppresses ARHGAP24 expression to activate Rac1 signaling and promote tumor progression in lung adenocarcinoma. Oncogene 2021; 41:538-549. [PMID: 34785774 PMCID: PMC8782721 DOI: 10.1038/s41388-021-02114-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 01/10/2023]
Abstract
Although tobacco smoking is a risk factor for lung adenocarcinoma (LUAD), the mechanisms by which tobacco smoking induces LUAD development remain elusive. Histone methylation levels in human bronchial epithelial cells have been reported to increase after exposure to cigarettes. In this study, we explored the mechanisms regulating histone methylation in LUAD in response to smoking. We found that the histone H3K9 methylation reader CBX3 was upregulated in current smokers with LUAD, and that CBX3 overexpression promoted LUAD progression. Functional enrichment analyses revealed that CBX3 regulated the activation of Rho GTPases in LUAD. We also found that by forming a complex with TRIM28, TRIM24, and RBBP4, CBX3 repressed the expression of ARHGAP24 and increased the amount of active Rac1 in LUAD cells. Collectively, these results suggest that smoking associated upregulation of CBX3 promotes LUAD progression by activating the ARHGAP24/Rac1 pathway. Hence, the CBX3/ARHGAP24/Rac1 axis may represent a promising therapeutic target in smoking-induced LUAD.
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Dawes K, Andersen A, Reimer R, Mills JA, Hoffman E, Long JD, Miller S, Philibert R. The relationship of smoking to cg05575921 methylation in blood and saliva DNA samples from several studies. Sci Rep 2021; 11:21627. [PMID: 34732805 PMCID: PMC8566492 DOI: 10.1038/s41598-021-01088-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
Numerous studies have shown that cg05575921 methylation decreases in response to smoking. However, secondary to methodological issues, the magnitude and dose dependency of that response is as of yet unclear. This lack of certainty is a barrier to the use of DNA methylation clinically to assess and monitor smoking status. To better define this relationship, we conducted a joint analysis of methylation sensitive PCR digital (MSdPCR) assessments of cg05575921 methylation in whole blood and/or saliva DNA to smoking using samples from 421 smokers and 423 biochemically confirmed non-smokers from 4 previously published studies. We found that cg05575921 methylation manifested a curvilinear dose dependent decrease in response to increasing cigarette consumption. In whole blood DNA, the Receiver Operating Characteristic (ROC) Area Under the Curve (AUC) of cg05575921 methylation for predicting daily smoking status was 0.98. In saliva DNA, the gross AUC was 0.91 with correction for cellular heterogeneity improving the AUC to 0.94. Methylation status was significantly associated with the Fagerstrom Test for Nicotine Dependence score, but with significant sampling heterogeneity. We conclude that MSdPCR assessments of cg05575921 methylation are a potentially powerful, clinically implementable tool for the assessment and management of smoking.
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Affiliation(s)
- Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
- Molecular Medicine Program, University of Iowa, Iowa City, IA, 52242, USA
| | - Allan Andersen
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
| | - Rachel Reimer
- Department of Public Health, Des Moines University, Des Moines, IA, 50312, USA
| | - James A Mills
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
| | - Eric Hoffman
- Department of Radiology, University of Iowa, Iowa City, IA, 52242, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - Jeffrey D Long
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
- Department of Biostatistics, University of Iowa, Iowa City, IA, 52242, USA
| | - Shelly Miller
- Behavioral Diagnostics LLC, Coralville, IA, 52241, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA.
- Behavioral Diagnostics LLC, Coralville, IA, 52241, USA.
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Abstract
Substance use disorders (SUDs) are conditions in which the use of legal or illegal substances, such as nicotine, alcohol or opioids, results in clinical and functional impairment. SUDs and, more generally, substance use are genetically complex traits that are enormously costly on an individual and societal basis. The past few years have seen remarkable progress in our understanding of the genetics, and therefore the biology, of substance use and abuse. Various studies - including of well-defined phenotypes in deeply phenotyped samples, as well as broadly defined phenotypes in meta-analysis and biobank samples - have revealed multiple risk loci for these common traits. A key emerging insight from this work establishes a biological and genetic distinction between quantity and/or frequency measures of substance use (which may involve low levels of use without dependence), versus symptoms related to physical dependence.
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Associations between Second-Hand Tobacco Smoke Exposure and Cardiorespiratory Fitness, Physical Activity, and Respiratory Health in Children. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111445. [PMID: 34769962 PMCID: PMC8582797 DOI: 10.3390/ijerph182111445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cardiorespiratory fitness (CRF) and physical activity (PA) are associated with a plethora of positive health effects. Many UK children fail to meet the recommended level of PA, with an observed decline in CRF levels over recent decades. Second-hand tobacco smoke (SHS) is responsible for a significant proportion of the worldwide burden of disease, but little is understood regarding the impact of SHS exposure on CRF and PA in children. The aim of this study was to test the associations between SHS exposure and CRF, PA, and respiratory health in children. METHOD Children (9-11 years) from UK primary schools in deprived areas participated (n = 104, 38 smoking households). Surveys determined household smoking, and exhaled carbon monoxide was used to indicate children's recent SHS exposure. CRF (VO2peak) was assessed via maximal treadmill protocol using breath-by-breath analysis. Fractional exhaled nitric oxide and spirometry were utilised as indicators of respiratory health. RESULTS Linear regression models demonstrated that SHS exposure was negatively associated with allometrically scaled VO2peak (B = -3.8, p = 0.030) but not PA or respiratory health. CONCLUSION The results indicate that SHS is detrimental to children's CRF; given that approximately one-third of children are regularly exposed to SHS, this important finding has implications for both public health and the sport and exercise sciences.
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Nicotine Exacerbates TAAD Formation Induced by Smooth Muscle-Specific Deletion of the TGF- β Receptor 2. J Immunol Res 2021; 2021:6880036. [PMID: 34646889 PMCID: PMC8505064 DOI: 10.1155/2021/6880036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/04/2021] [Indexed: 01/22/2023] Open
Abstract
Tobacco smoke is an established risk factor for thoracic aortic aneurysms and dissections (TAAD). However, little is known about its underlying mechanisms due to the lack of validated animal models. The present study developed a mouse model that may be utilized to investigate exacerbation of TAAD formation by mimetics of tobacco smoke. TAADs were created via inducible deletion of smooth muscle cell-specific Tgfbr2 receptors. Using this model, the first set of experiments evaluated the efficacy of nicotine salt (34.0 mg/kg/day), nicotine free base (NFB, 5.0 mg 90-day pellets), and cigarette smoke extract (0.1 ml/mouse/day). Compared with their respective control groups, only NFB pellets promoted TAAD dilation (23 ± 3% vs. 12 ± 2%, P = 0.014), and this efficacy was achieved at a cost of >50% acute mortality. Infusion of NFB with osmotic minipumps at extremely high, but nonlethal, doses (15.0 or 45.0 mg/kg/day) failed to accelerate TAAD dilation. Interestingly, costimulation with β-aminopropionitrile (BAPN) promoted TAAD dilation and aortic rupture at dosages of 3.0 and 45.0 mg/kg/day, respectively, indicating that BAPN sensitizes the response of TAADs to NFB. In subsequent analyses, the detrimental effects of NFB were associated with clustering of macrophages, neutrophils, and T-cells in areas with structural destruction, enhanced matrix metalloproteinase- (MMP-) 2 production, and pathological angiogenesis with attenuated fibrosis in the adventitia. In conclusion, modeling nicotine exacerbation of TAAD formation requires optimization of chemical form, route of delivery, and dosage of the drug as well as the pathologic complexity of TAADs. Under the optimized conditions of the present study, chronic inflammation and adventitial mal-remodeling serve as critical pathways through which NFB exacerbates TAAD formation.
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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Merrill SM, Moore SR, Gladish N, Giesbrecht GF, Dewey D, Konwar C, MacIssac JL, Kobor MS, Letourneau NL. Paternal adverse childhood experiences: Associations with infant DNA methylation. Dev Psychobiol 2021; 63:e22174. [PMID: 34333774 DOI: 10.1002/dev.22174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022]
Abstract
Adverse childhood experiences (ACEs), or cumulative childhood stress exposures, such as abuse, neglect, and household dysfunction, predict later health problems in both the exposed individuals and their offspring. One potential explanation suggests exposure to early adversity predicts epigenetic modification, especially DNA methylation (DNAm), linked to later health. Stress experienced preconception by mothers may associate with DNAm in the next generation. We hypothesized that fathers' exposure to ACEs also associates with their offspring DNAm, which, to our knowledge, has not been previously explored. An epigenome-wide association study (EWAS) of blood DNAm (n = 45) from 3-month-old infants was regressed onto fathers' retrospective ACEs at multiple Cytosine-phosphate-Guanosine (CpG) sites to discover associations. This accounted for infants' sex, age, ethnicity, cell type proportion, and genetic variability. Higher ACE scores associated with methylation values at eight CpGs. Post-hoc analysis found no contribution of paternal education, income, marital status, and parental postpartum depression, but did with paternal smoking and BMI along with infant sleep latency. These same CpGs also contributed to the association between paternal ACEs and offspring attention problems at 3 years. Collectively, these findings suggested there were biological associations with paternal early life adversity and offspring DNAm in infancy, potentially affecting offspring later childhood outcomes.
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Affiliation(s)
- Sarah M Merrill
- BC Children's Hospital Research Institute Vancouver, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Sarah R Moore
- BC Children's Hospital Research Institute Vancouver, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Nicole Gladish
- BC Children's Hospital Research Institute Vancouver, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Gerald F Giesbrecht
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada.,Owerko Centre at the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Deborah Dewey
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada.,Owerko Centre at the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada.,Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Chaini Konwar
- BC Children's Hospital Research Institute Vancouver, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Julia L MacIssac
- BC Children's Hospital Research Institute Vancouver, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Michael S Kobor
- BC Children's Hospital Research Institute Vancouver, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada.,Program in Child and Brain Development, CIFAR, Toronto, Ontario, Canada
| | - Nicole L Letourneau
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada.,Owerko Centre at the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada.,Department of Psychiatry, University of Calgary, Calgary, Alberta, Canada.,Faculty of Nursing, University of Calgary, Calgary, Alberta, Canada
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Jadhav KB, Shah V, Chauhan N, Shah N, Parmar G. Expression of microRNA-21 in saliva and tumor tissue of patients with oral squamous cell carcinoma: a predictor of cervical lymph node metastasis. Oral Surg Oral Med Oral Pathol Oral Radiol 2021; 133:60-69. [PMID: 34518132 DOI: 10.1016/j.oooo.2021.07.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Evaluation of diagnostic accuracy of microRNA-21 (miR-21) in saliva and tumor tissue for presurgical assessment of lymph node metastasis in patients with oral squamous cell carcinoma (OSCC). STUDY DESIGN Unstimulated whole saliva and tumor tissue was obtained from clinically suspected patients with OSCC. A total of 130 patients diagnosed with OSCC were included as study participants. The assessment of cervical lymph node metastasis was done before surgery using imaging scans and post surgically confirmed by histopathologic examination of excised lymph nodes. miR-21 expression was evaluated using real-time polymerase chain reaction. The data was statistically analyzed for correlation analysis, cutoff values, sensitivity, and specificity. The κ statistic was applied to assess the degree of agreement between the lymph node metastasis and miR-21 expression. RESULTS miR-21 expression showed a statistically significant correlation with cervical lymph node metastasis with a diagnostic accuracy of 65% to 71.54% in saliva and 69% to 81.54% in tumor tissue. Very good agreement was observed between tumor tissue miR-21-3p and cervical lymph node metastasis with a specificity of 80.60% and a sensitivity of 82.40%. CONCLUSIONS miR-21 expression in saliva and tumor tissue of patients with OSCC showed high diagnostic accuracy for assessment of cervical lymph node metastasis. It can be used as an alternative for assessment of cervical lymph node metastasis before surgery.
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Affiliation(s)
- Kiran B Jadhav
- PhD Scholar, Department of Oral Pathology and Microbiology, K M Shah Dental College and Hospital, Sumandeep Vidyapeeth, Piparia, Vadodara, Gujarat, India; Professor, Department of Oral Pathology and Microbiology, Vasant Dada Patil Dental College and Hospital, Maharashtra University of Health Sciences, Sangli, India.
| | - Vandana Shah
- Professor and Head, Department of Oral Pathology and Microbiology, K M Shah Dental College and Hospital, Sumandeep Vidyapeeth, Piparia, Vadodara, Gujarat, India
| | - Nirali Chauhan
- Professor, Department of ENT, Smt. B K Shah Medical College and Research Centre, Sumandeep Vidyapeeth, Piparia, Vadodara, Gujarat, India
| | - Naveen Shah
- Professor and Head, Department of Oral and Maxillofacial Surgery, K M Shah Dental College and Hospital, Sumandeep Vidyapeeth, Piparia, Vadodara. Gujarat, India
| | - Ghanshyam Parmar
- Associate Professor, Department of Pharmacy, Sumandeep Vidyapeeth, Piparia, Vadodara, Gujarat, India
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Huo X, Jin S, Wang Y, Ma L. DNA methylation in chronic obstructive pulmonary disease. Epigenomics 2021; 13:1145-1155. [PMID: 34142873 DOI: 10.2217/epi-2021-0111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), a complex disease with polygenetic tendency, is one of the most important health problems in the world. Recently, in the study of the pathogenesis of the COPD, epigenetic changes caused by environmental factors, such as DNA methylation, started to attract more attention than genetic factors. In this review, we discuss the main features of DNA methylation, such as DNA methyltransferases and the methylation sites that modulate the DNA methylation level, and their roles in COPD progression. Finally, to promote new ideas for the prevention and treatment of COPD, we focus on the potential of DNA methylation as a COPD therapeutic target.
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Affiliation(s)
- XinXin Huo
- School of Public Health, Lanzhou University, Lanzhou, China
| | - SiHui Jin
- School of Public Health, Lanzhou University, Lanzhou, China
| | - YiGe Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Li Ma
- School of Public Health, Lanzhou University, Lanzhou, China
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36
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Peng XX, Yu R, Wu X, Wu SY, Pi C, Chen ZH, Zhang XC, Gao CY, Shao YW, Liu L, Wu YL, Zhou Q. Correlation of plasma exosomal microRNAs with the efficacy of immunotherapy in EGFR / ALK wild-type advanced non-small cell lung cancer. J Immunother Cancer 2021; 8:jitc-2019-000376. [PMID: 31959728 PMCID: PMC7057418 DOI: 10.1136/jitc-2019-000376] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2019] [Indexed: 12/13/2022] Open
Abstract
Background Immunotherapy has become an important treatment option for patients with advanced non-small cell lung cancer (NSCLC). At present, none of these existing biomarkers can effectively stratify true responders and there is an urgent need for identifying novel biomarkers. Exosomes derived from the serum of patients with cancer have been proven to be reliable markers for cancer diagnosis. Here, we explored the possibility of using plasma-derived exosomal microRNAs as potential biomarkers for optimal selection of patients with advanced EGFR/ALK negative NSCLC to immunotherapy. Methods From June 2017 to February 2019, 30 patients with advanced EGFR/ALK wild-type (WT) NSCLC who received PD-1/PD-L1 inhibitors were enrolled. The efficacy evaluation was conducted after every three cycles of treatment according to RECIST 1.1. Plasma samples of these patients were collected before the administration of PD-1/PD-L1 inhibitors as baseline, and after every three cycles if the patients achieved partial response (PR) or complete response. Plasma from seven healthy individuals was also collected as normal control. Exosomes were prepared by ultracentrifugation followed by total RNA extraction, and exosome-derived miRNAs were profiled using small RNA next-generation sequencing followed by differential expression analysis. Results In order to identify biomarker for better response, all five patients who achieved PR and four patients with progressive disease (PD) at efficacy evaluation were included for differential expression analysis. Based on unsupervised hierarchical clustering, exosomal miRNA expression profile was significantly altered in patients with NSCLC compared with normal controls with a total of 155 differentially expressed exosomal miRNAs. Interestingly, hsa-miR-320d, hsa-miR-320c, and hsa-miR-320b were identified significantly upregulated in the PD groups compared with the PR group at baseline before the treatment. In addition, we identified that hsa-miR-125b-5p, a T-cell suppressor, showed a trend of increased expression in the PD group at baseline and was significantly downregulated in the post-treatment plasma exosomes compared with pre-treatment samples of the PR patients. Conclusion Patients with NSCLC represent unique plasma exosomal miRNA profiles. Hsa-miR-320d, hsa-miR-320c, and hsa-miR-320b were identified as potential biomarkers for predicting the efficacy of immunotherapy in advanced NSCLCs. When T-cell suppressor hsa-miR-125b-5p was downregulated during the treatment, the patients may obtain increased T-cell function and respond well to immunotherapy.
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Affiliation(s)
- Xiao-Xiao Peng
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ruoying Yu
- Translational Medicine Research Institute, Geneseeq Technology Inc, Toronto, Ontario, Canada
| | - Xue Wu
- Translational Medicine Research Institute, Geneseeq Technology Inc, Toronto, Ontario, Canada
| | - Shu-Yu Wu
- Department of Research and Development, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Can Pi
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhi-Hong Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cun-Yi Gao
- Department of Research and Development, Nanjing Geneseeq Technology Inc, Nanjing, China
| | - Yang W Shao
- Department of Research and Development, Nanjing Geneseeq Technology Inc, Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
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37
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Epigenetic Alterations of Maternal Tobacco Smoking during Pregnancy: A Narrative Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18105083. [PMID: 34064931 PMCID: PMC8151244 DOI: 10.3390/ijerph18105083] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022]
Abstract
In utero exposure to maternal tobacco smoking is the leading cause of birth complications in addition to being associated with later impairment in child’s development. Epigenetic alterations, such as DNA methylation (DNAm), miRNAs expression, and histone modifications, belong to possible underlying mechanisms linking maternal tobacco smoking during pregnancy and adverse birth outcomes and later child’s development. The aims of this review were to provide an update on (1) the main results of epidemiological studies on the impact of in utero exposure to maternal tobacco smoking on epigenetic mechanisms, and (2) the technical issues and methods used in such studies. In contrast with miRNA and histone modifications, DNAm has been the most extensively studied epigenetic mechanism with regard to in utero exposure to maternal tobacco smoking. Most studies relied on cord blood and children’s blood, but placenta is increasingly recognized as a powerful tool, especially for markers of pregnancy exposures. Some recent studies suggest reversibility in DNAm in certain genomic regions as well as memory of smoking exposure in DNAm in other regions, upon smoking cessation before or during pregnancy. Furthermore, reversibility could be more pronounced in miRNA expression compared to DNAm. Increasing evidence based on longitudinal data shows that maternal smoking-associated DNAm changes persist during childhood. In this review, we also discuss some issues related to cell heterogeneity as well as downstream statistical analyses used to relate maternal tobacco smoking during pregnancy and epigenetics. The epigenetic effects of maternal smoking during pregnancy have been among the most widely investigated in the epigenetic epidemiology field. However, there are still huge gaps to fill in, including on the impact on miRNA expression and histone modifications to get a better view of the whole epigenetic machinery. The consistency of maternal tobacco smoking effects across epigenetic marks and across tissues will also provide crucial information for future studies. Advancement in bioinformatic and biostatistics approaches is key to develop a comprehensive analysis of these biological systems.
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Devóz PP, Reis MBD, Gomes WR, Maraslis FT, Ribeiro DL, Antunes LMG, Batista BL, Grotto D, Reis RM, Barbosa F, Barcelos GRM. Adaptive epigenetic response of glutathione (GSH)-related genes against lead (Pb)-induced toxicity, in individuals chronically exposed to the metal. CHEMOSPHERE 2021; 269:128758. [PMID: 33143897 DOI: 10.1016/j.chemosphere.2020.128758] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/15/2020] [Accepted: 10/25/2020] [Indexed: 06/11/2023]
Abstract
It is well known that one of the most outstanding adverse effects related to lead (Pb) exposure is oxidative stress; moreover, recent findings suggest that disturbances of the redox status of cells are associated with epigenetic responses, and metabolism of glutathione (GSH) plays an important role in this process. This study aimed to assess Pb exposure on % methylation of GSH-related genes' promoter regions (%CH3-CpG) and their influence on biomarkers of oxidative stress, in workers exposed to the metal. One hundred nine male workers participated in the study; ICP-MS determined blood lead levels (BLL); biochemical parameters related to redox status, named GSH, glutathione peroxidase (GPX) and glutathione-S-transferase (GST) were quantified by UV/Vis spectrophotometry. Determination of %CH3-CpG of genes GCLC, GPX1, GSR, and GSTP1 were done by pyrosequencing. Inverse associations were seen between BLL and %CH3-CpG-GCLC, and %CH3-CpG-GSTP1. Moreover, metal exposure did not impact GSH, GPX, and GST; however, negative associations were observed between %CH3-CpG-GPX1 and %CH3-CpG-GSTP1, and the activities of GPX and GST, respectively. Taken together, our results give further evidence about adaptive epigenetic response to avoid oxidative damage induced by Pb exposure, allowing a better understanding of the molecular mechanisms related to the metal toxicity.
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Affiliation(s)
- Paula Pícoli Devóz
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/n, CEP 14040-903, Ribeirão Preto, SP, Brazil
| | - Mariana Bisarro Dos Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela 1331, CEP 14784-400, Barretos, SP, Brazil
| | - Willian Robert Gomes
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/n, CEP 14040-903, Ribeirão Preto, SP, Brazil
| | - Flora Troina Maraslis
- Department of Biosciences, Institute of Health and Society, Federal University of São Paulo, Avenida Ana Costa 95, CEP 11060-001, Santos, SP, Brazil
| | - Diego Luis Ribeiro
- Departament of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida dos Bandeirantes 3900, CEP 14040-901, Ribeirão Preto, SP, Brazil
| | - Lusânia Maria Greggi Antunes
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/n, CEP 14040-903, Ribeirão Preto, SP, Brazil
| | - Bruno Lemos Batista
- Center of Natural and Human Sciences, Federal University of ABC, Avenida Dos Estados 5001, CEP 09210-580, Santo André, SP, Brazil
| | - Denise Grotto
- University of Sorocaba, Rodovia Raposo Tavares km 92.5, CEP 18023-000, Sorocaba, SP, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela 1331, CEP 14784-400, Barretos, SP, Brazil; Life and Health Sciences Research Institute, School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Gualtar Campus, 4710-057, Braga, Portugal
| | - Fernando Barbosa
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida Do Café S/n, CEP 14040-903, Ribeirão Preto, SP, Brazil
| | - Gustavo Rafael Mazzaron Barcelos
- Department of Biosciences, Institute of Health and Society, Federal University of São Paulo, Avenida Ana Costa 95, CEP 11060-001, Santos, SP, Brazil.
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Clausing ES, Binder AM, Non AL. Epigenetic age associates with psychosocial stress and resilience in children of Latinx immigrants. Epigenomics 2021; 13:1677-1699. [PMID: 33749330 DOI: 10.2217/epi-2019-0343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Aim: To investigate associations of psychosocial stressors and resilience factors with DNA methylation age in saliva of Latinx children of immigrants before and after the 2016 presidential election (2015-2018). Materials & methods: We compared psychosocial exposures with four distinct measures of epigenetic age assessed in saliva of children (6-13 years, n = 71 pre-election; n = 35 post-election). Exploratory genome-wide analyses were also conducted. Results: We found distinct associations across epigenetic clocks and time points: for example, greater maternal social status pre-election and fear of parent deportation post-election both associated with decreased Hannum Age (p ≤ 0.01). Conclusion: Though limited in size, our unique study design provides novel hypotheses regarding how the social environment may influence epigenetic aging and genome-wide methylation, potentially contributing to racial/ethnic health inequalities.
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Affiliation(s)
- Elizabeth S Clausing
- Department of Anthropology at The University of California, San Diego, 92093 CA, USA
| | - Alexandra M Binder
- Department of Epidemiology at The University of California, Los Angeles, 90095 CA, USA
| | - Amy L Non
- Department of Anthropology at The University of California, San Diego, 92093 CA, USA
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Salavrakos M, Leclercq S, De Timary P, Dom G. Microbiome and substances of abuse. Prog Neuropsychopharmacol Biol Psychiatry 2021; 105:110113. [PMID: 32971216 DOI: 10.1016/j.pnpbp.2020.110113] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022]
Abstract
There is a growing amount of evidence showing a reciprocal relation between the gut microbiota and the brain. Substance use disorders (SUD), which are a major cause of preventable morbidity and mortality worldwide, have an influence on the gut microbiota and on the gut-brain axis. The communication between the microbiota and the brain exists through different pathways: (1) the immune response elicited by bacterial products, coupled with alterations of the intestinal barrier allowing these products to enter the bloodstream, (2) the direct and indirect effects of bacterial metabolites such as short chain fatty acids (SCFAs) or tryptophan on the brain, (3) and the hypothalamic-pituitary-adrenal (HPA) axis, whose peripheral afferents can be influenced by the microbiota, and can in turn activate microglia. Among substances of abuse, alcohol has been the subject of the greatest number of studies in this field. In some but not all patients suffering from alcohol-use-disorder (AUD), alcohol alters the composition of the gut microbiota and the permeability of the intestinal barrier, directly and through dysbiosis. It has also been well demonstrated that alcohol induces a peripheral inflammation; it is still unclear whether it induces a central inflammation, as there are contradictory results in human studies. In animal studies, it has been shown that neuroinflammation increases during alcohol withdrawal. Literature on opioids and stimulants is less numerous. Chronic morphine intake induces dysbiosis, increased intestinal permeability and a probable neuroinflammation, which could explain symptoms such as tolerance, hyperalgesia and deficit in reward behavior. Cocaine induces a dysbiosis and conversely the microbiome can modulate the behavioral response to stimulant drugs. Tobacco cessation is associated with an increase in microbiota diversity. Taken together, the findings of our narrative literature review suggest a bidirectional influence in the pathogenesis of substance use disorders.
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Affiliation(s)
- M Salavrakos
- Target Journal Progress in Neuropsychopharmacology and Biological Psychiatry, Belgium
| | - S Leclercq
- Target Journal Progress in Neuropsychopharmacology and Biological Psychiatry, Belgium
| | - P De Timary
- Target Journal Progress in Neuropsychopharmacology and Biological Psychiatry, Belgium
| | - G Dom
- Target Journal Progress in Neuropsychopharmacology and Biological Psychiatry, Belgium.
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Pereira-da-Silva T, Napoleão P, Costa MC, Gabriel AF, Selas M, Silva F, Enguita FJ, Ferreira RC, Carmo MM. Cigarette Smoking, miR-27b Downregulation, and Peripheral Artery Disease: Insights into the Mechanisms of Smoking Toxicity. J Clin Med 2021; 10:jcm10040890. [PMID: 33671744 PMCID: PMC7926909 DOI: 10.3390/jcm10040890] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/14/2021] [Accepted: 02/17/2021] [Indexed: 12/26/2022] Open
Abstract
Cigarette smoking is a risk factor for the development of peripheral artery disease (PAD), although the proatherosclerotic mediators of cigarette smoking are not entirely known. We explored whether circulating microRNAs (miRNAs) are dysregulated in cigarette smokers and associated with the presence of PAD. Ninety-four participants were recruited, including 58 individuals without and 36 with PAD, 51 never smokers, 28 prior smokers, and 15 active smokers. The relative expression of six circulating miRNAs with distinct biological roles (miR-21, miR-27b, miR-29a, miR-126, miR-146, and miR-218) was assessed. Cigarette smoking was associated with the presence of PAD in multivariate analysis. Active smokers, but not prior smokers, presented miR-27b downregulation and higher leukocyte, neutrophil, and lymphocyte counts; miR-27b expression levels were independently associated with active smoking. Considering the metabolic and/or inflammatory abnormalities induced by cigarette smoking, miR-27b was independently associated with the presence of PAD and downregulated in patients with more extensive PAD. In conclusion, the atheroprotective miR-27b was downregulated in active smokers, but not in prior smokers, and miR-27b expression was independently associated with the presence of PAD. These unreported data suggest that the proatherogenic properties of cigarette smoking are mediated by a downregulation of miR-27b, which may be attenuated by smoking cessation.
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Affiliation(s)
- Tiago Pereira-da-Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
- NOVA Doctoral School, NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Correspondence: ; Tel.: +351-919908505
| | - Patrícia Napoleão
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
| | - Marina C. Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - André F. Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Mafalda Selas
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Filipa Silva
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (P.N.); (M.C.C.); (A.F.G.); (F.J.E.)
- Cardiomics Unit, Centro Cardiovascular da Universidade de Lisboa, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Rui Cruz Ferreira
- Department of Cardiology, Hospital de Santa Marta, Centro Hospitalar Universitário de Lisboa Central, 1169-024 Lisbon, Portugal; (M.S.); (F.S.); (R.C.F.)
| | - Miguel Mota Carmo
- Chronic Diseases Research Center (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal;
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Richetto J, Meyer U. Epigenetic Modifications in Schizophrenia and Related Disorders: Molecular Scars of Environmental Exposures and Source of Phenotypic Variability. Biol Psychiatry 2021; 89:215-226. [PMID: 32381277 DOI: 10.1016/j.biopsych.2020.03.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/19/2020] [Accepted: 03/16/2020] [Indexed: 12/18/2022]
Abstract
Epigenetic modifications are increasingly recognized to play a role in the etiology and pathophysiology of schizophrenia and other psychiatric disorders with developmental origins. Here, we summarize clinical and preclinical findings of epigenetic alterations in schizophrenia and relevant disease models and discuss their putative origin. Recent findings suggest that certain schizophrenia risk loci can influence stochastic variation in gene expression through epigenetic processes, highlighting the intricate interaction between genetic and epigenetic control of neurodevelopmental trajectories. In addition, a substantial portion of epigenetic alterations in schizophrenia and related disorders may be acquired through environmental factors and may be manifested as molecular "scars." Some of these scars can influence brain functions throughout the entire lifespan and may even be transmitted across generations via epigenetic germline inheritance. Epigenetic modifications, whether caused by genetic or environmental factors, are plausible molecular sources of phenotypic heterogeneity and offer a target for therapeutic interventions. The further elucidation of epigenetic modifications thus may increase our knowledge regarding schizophrenia's heterogeneous etiology and pathophysiology and, in the long term, may advance personalized treatments through the use of biomarker-guided epigenetic interventions.
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Affiliation(s)
- Juliet Richetto
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, and Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.
| | - Urs Meyer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, and Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
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Clausing ES, Non AL. Epigenetics as a Mechanism of Developmental Embodiment of Stress, Resilience, and Cardiometabolic Risk Across Generations of Latinx Immigrant Families. Front Psychiatry 2021; 12:696827. [PMID: 34354616 PMCID: PMC8329078 DOI: 10.3389/fpsyt.2021.696827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022] Open
Abstract
Psychosocial stressors can become embodied to alter biology throughout the life course in ways that may have lasting health consequences. Immigrants are particularly vulnerable to high burdens of stress, which have heightened in the current sociopolitical climate. This study is an investigation of how immigration-related stress (IRS) may impact the cardiometabolic risk and epigenetic markers of Latinx immigrant mothers and children in Nashville, TN. We compared stress and resilience factors reported by Latina immigrant mothers and their children (aged 5-13) from two time points spanning the 2016 U.S. presidential election (June 2015-June 2016 baseline, n = 81; March-September 2018 follow-up, n = 39) with cardiometabolic risk markers (BMI, waist circumference, and blood pressure). We also analyzed these factors in relation to DNA methylation in saliva of stress-related candidate genes (SLC6A4 and FKBP5), generated via bisulfite pyrosequencing (complete case n's range from 67-72 baseline and 29-31 follow-up) (n's range from 80 baseline to 36 follow-up). We found various associations with cardiometabolic risk, such as higher social support and greater acculturation were associated with lower BMI in mothers; discrimination and school stress associated with greater waist circumferences in children. Very few exposures associated with FKBP5, but various stressors associated with methylation at many sites in SLC6A4, including immigrant-related stress in both mothers and children, and fear of parent deportation in children. Additionally, in the mothers, total maternal stress, health stress, and subjective social status associated with methylation at multiple sites of SLC6A4. Acculturation associated with methylation in mothers in both genes, though directions of effect varied over time. We also find DNA methylation at SLC6A4 associates with measures of adiposity and blood pressure, suggesting that methylation may be on the pathway linking stress with cardiometabolic risk. More research is needed to determine the role of these epigenetic differences in contributing to embodiment of stress across generations.
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Affiliation(s)
- Elizabeth S Clausing
- Department of Anthropology, University of California San Diego (UCSD), La Jolla, CA, United States
| | - Amy L Non
- Department of Anthropology, University of California San Diego (UCSD), La Jolla, CA, United States
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Zhan S, Huang J. Effects of Cigarette Smoking on Preimplantation Embryo Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1300:137-150. [PMID: 33523432 DOI: 10.1007/978-981-33-4187-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
In this chapter, we first gave a brief introduction to the detriments of cigarette smoking, with an emphasis on its adverse effects on female reproductive health. Then, we outlined recent advances about the impacts of cigarette smoke on preimplantation embryo development. Additionally, toxicities of cadmium and benzo(a)pyrene (BaP) at this specific developmental window were also discussed, to illustrate the potential mechanisms involved in cigarette smoke-associated embryotoxicity. Finally, we provide an overview of the issues to be solved in the future research. Further studies about the molecular mechanism of cigarette smoking-associated female infertility may provide vital insights into developing new interventions for the women smokers and thus improving their reproductive outcomes.
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Affiliation(s)
- Shaoquan Zhan
- Center for Reproductive Medicine, the Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junjiu Huang
- Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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Stephenson M, Bollepalli S, Cazaly E, Salvatore JE, Barr P, Rose RJ, Dick D, Kaprio J, Ollikainen M. Associations of Alcohol Consumption With Epigenome-Wide DNA Methylation and Epigenetic Age Acceleration: Individual-Level and Co-twin Comparison Analyses. Alcohol Clin Exp Res 2020; 45:318-328. [PMID: 33277923 DOI: 10.1111/acer.14528] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND DNA methylation may play a role in the progression from normative to problematic drinking and underlie adverse health outcomes associated with alcohol misuse. We examined the association between alcohol consumption and DNA methylation patterns using 3 approaches: a conventional epigenome-wide association study (EWAS); a co-twin comparison design, which controls for genetic and environmental influences that twins share; and a regression of age acceleration, defined as a discrepancy between chronological age and DNA methylation age, on alcohol consumption. METHODS Participants came from the Finnish Twin Cohorts (FinnTwin12/FinnTwin16; N = 1,004; 55% female; average age = 23 years). Individuals reported the number of alcoholic beverages consumed in the past week, and epigenome-wide DNA methylation was assessed in whole blood using the Infinium HumanMethylation450 BeadChip. RESULTS In the EWAS, alcohol consumption was significantly related to methylation at 24 CpG sites. When evaluating whether differences between twin siblings (185 monozygotic pairs) in alcohol consumption predicted differences in DNA methylation, co-twin comparisons replicated 4 CpG sites from the EWAS and identified 23 additional sites. However, when we examined qualitative differences in drinking patterns between twins (heavy drinker vs. light drinker/abstainer or moderate drinker vs. abstainer; 44 pairs), methylation patterns did not significantly differ within twin pairs. Finally, individuals who reported higher alcohol consumption also exhibited greater age acceleration, though results were no longer significant after controlling for genetic and environmental influences shared by co-twins. CONCLUSIONS Our analyses offer insight into the associations between epigenetic variation and levels of alcohol consumption in young adulthood.
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Affiliation(s)
- Mallory Stephenson
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland
| | - Emma Cazaly
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland
| | - Jessica E Salvatore
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia.,Virginia Institute for Psychiatric and Behavioral Genetics, (JES), Virginia Commonwealth University, Richmond, Virginia
| | - Peter Barr
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia
| | - Richard J Rose
- Department of Psychological and Brain Sciences, (RJR), Indiana University, Bloomington, Indiana
| | - Danielle Dick
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia.,Department of Human and Molecular Genetics, (DD), Virginia Commonwealth University, Richmond, Virginia
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland.,Department of Public Health, (JK, MO), University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland.,Department of Public Health, (JK, MO), University of Helsinki, Helsinki, Finland
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Smoking-related changes in DNA methylation and gene expression are associated with cardio-metabolic traits. Clin Epigenetics 2020; 12:157. [PMID: 33092652 PMCID: PMC7579899 DOI: 10.1186/s13148-020-00951-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Tobacco smoking is a well-known modifiable risk factor for many chronic diseases, including cardiovascular disease (CVD). One of the proposed underlying mechanism linking smoking to disease is via epigenetic modifications, which could affect the expression of disease-associated genes. Here, we conducted a three-way association study to identify the relationship between smoking-related changes in DNA methylation and gene expression and their associations with cardio-metabolic traits. RESULTS We selected 2549 CpG sites and 443 gene expression probes associated with current versus never smokers, from the largest epigenome-wide association study and transcriptome-wide association study to date. We examined three-way associations, including CpG versus gene expression, cardio-metabolic trait versus CpG, and cardio-metabolic trait versus gene expression, in the Rotterdam study. Subsequently, we replicated our findings in The Cooperative Health Research in the Region of Augsburg (KORA) study. After correction for multiple testing, we identified both cis- and trans-expression quantitative trait methylation (eQTM) associations in blood. Specifically, we found 1224 smoking-related CpGs associated with at least one of the 443 gene expression probes, and 200 smoking-related gene expression probes to be associated with at least one of the 2549 CpGs. Out of these, 109 CpGs and 27 genes were associated with at least one cardio-metabolic trait in the Rotterdam Study. We were able to replicate the associations with cardio-metabolic traits of 26 CpGs and 19 genes in the KORA study. Furthermore, we identified a three-way association of triglycerides with two CpGs and two genes (GZMA; CLDND1), and BMI with six CpGs and two genes (PID1; LRRN3). Finally, our results revealed the mediation effect of cg03636183 (F2RL3), cg06096336 (PSMD1), cg13708645 (KDM2B), and cg17287155 (AHRR) within the association between smoking and LRRN3 expression. CONCLUSIONS Our study indicates that smoking-related changes in DNA methylation and gene expression are associated with cardio-metabolic risk factors. These findings may provide additional insights into the molecular mechanisms linking smoking to the development of CVD.
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Mishra P, Hänninen I, Raitoharju E, Marttila S, Mishra B, Mononen N, Kähönen M, Hurme M, Raitakari O, Törönen P, Holm L, Lehtimäki T. Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study. Biosci Rep 2020; 40:BSR20200596. [PMID: 32583859 PMCID: PMC7340865 DOI: 10.1042/bsr20200596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022] Open
Abstract
Smoking as a major risk factor for morbidity affects numerous regulatory systems of the human body including DNA methylation. Most of the previous studies with genome-wide methylation data are based on conventional association analysis and earliest threshold-based gene set analysis that lacks sensitivity to be able to reveal all the relevant effects of smoking. The aim of the present study was to investigate the impact of active smoking on DNA methylation at three biological levels: 5'-C-phosphate-G-3' (CpG) sites, genes and functionally related genes (gene sets). Gene set analysis was done with mGSZ, a modern threshold-free method previously developed by us that utilizes all the genes in the experiment and their differential methylation scores. Application of such method in DNA methylation study is novel. Epigenome-wide methylation levels were profiled from Young Finns Study (YFS) participants' whole blood from 2011 follow-up using Illumina Infinium HumanMethylation450 BeadChips. We identified three novel smoking related CpG sites and replicated 57 of the previously identified ones. We found that smoking is associated with hypomethylation in shore (genomic regions 0-2 kilobases from CpG island). We identified smoking related methylation changes in 13 gene sets with false discovery rate (FDR) ≤ 0.05, among which is olfactory receptor activity, the flagship novel finding of the present study. Overall, we extended the current knowledge by identifying: (i) three novel smoking related CpG sites, (ii) similar effects as aging on average methylation in shore, and (iii) a novel finding that olfactory receptor activity pathway responds to tobacco smoke and toxin exposure through epigenetic mechanisms.
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Affiliation(s)
- Pashupati P. Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Ismo Hänninen
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Saara Marttila
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Gerontology Research Center (GEREC), Tampere University, Tampere, Finland
| | - Binisha H. Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Mikko Hurme
- Gerontology Research Center (GEREC), Tampere University, Tampere, Finland
- Department of Microbiology and Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Petri Törönen
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland
| | - Liisa Holm
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
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Zalewski DP, Ruszel KP, Stępniewski A, Gałkowski D, Bogucki J, Komsta Ł, Kołodziej P, Chmiel P, Zubilewicz T, Feldo M, Kocki J, Bogucka-Kocka A. Dysregulation of microRNA Modulatory Network in Abdominal Aortic Aneurysm. J Clin Med 2020; 9:jcm9061974. [PMID: 32599769 PMCID: PMC7355415 DOI: 10.3390/jcm9061974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/13/2020] [Accepted: 06/22/2020] [Indexed: 12/16/2022] Open
Abstract
Abdominal artery aneurysm (AAA) refers to abdominal aortic dilatation of 3 cm or greater. AAA is frequently underdiagnosed due to often asymptomatic character of the disease, leading to elevated mortality due to aneurysm rupture. MiRNA constitute a pool of small RNAs controlling gene expression and is involved in many pathologic conditions in human. Targeted panel detecting altered expression of miRNA and genes involved in AAA would improve early diagnosis of this disease. In the presented study, we selected and analyzed miRNA and gene expression signatures in AAA patients. Next, generation sequencing was applied to obtain miRNA and gene-wide expression profiles from peripheral blood mononuclear cells in individuals with AAA and healthy controls. Differential expression analysis was performed using DESeq2 and uninformative variable elimination by partial least squares (UVE-PLS) methods. A total of 31 miRNAs and 51 genes were selected as the most promising biomarkers of AAA. Receiver operating characteristics (ROC) analysis showed good diagnostic ability of proposed biomarkers. Genes regulated by selected miRNAs were determined in silico and associated with functional terms closely related to cardiovascular and neurological diseases. Proposed biomarkers may be used for new diagnostic and therapeutic approaches in management of AAA. The findings will also contribute to the pool of knowledge about miRNA-dependent regulatory mechanisms involved in pathology of that disease.
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Affiliation(s)
- Daniel P. Zalewski
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland; (D.P.Z.); (P.C.)
| | - Karol P. Ruszel
- Chair of Medical Genetics, Department of Clinical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland; (K.P.R.); (J.B.); (J.K.)
| | - Andrzej Stępniewski
- Ecotech Complex Analytical and Programme Centre for Advanced Environmentally Friendly Technologies, University of Marie Curie-Skłodowska, 39 Głęboka St., 20-612 Lublin, Poland;
| | - Dariusz Gałkowski
- Department of Pathology and Laboratory Medicine, Rutgers - Robert Wood Johnson Medical School, One Robert Wood Johnson Place, New Brunswick, NJ 08903-0019, USA;
| | - Jacek Bogucki
- Chair of Medical Genetics, Department of Clinical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland; (K.P.R.); (J.B.); (J.K.)
| | - Łukasz Komsta
- Chair and Department of Medicinal Chemistry, Medical University of Lublin, 4 Jaczewskiego St., 20-090 Lublin, Poland;
| | - Przemysław Kołodziej
- Laboratory of Diagnostic Parasitology, Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland;
| | - Paulina Chmiel
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland; (D.P.Z.); (P.C.)
| | - Tomasz Zubilewicz
- Chair and Department of Vascular Surgery and Angiology, Medical University of Lublin, 11 Staszica St., 20-081 Lublin, Poland; (T.Z.); (M.F.)
| | - Marcin Feldo
- Chair and Department of Vascular Surgery and Angiology, Medical University of Lublin, 11 Staszica St., 20-081 Lublin, Poland; (T.Z.); (M.F.)
| | - Janusz Kocki
- Chair of Medical Genetics, Department of Clinical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland; (K.P.R.); (J.B.); (J.K.)
| | - Anna Bogucka-Kocka
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland; (D.P.Z.); (P.C.)
- Correspondence: ; Tel.: +48-81-448-7232
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Papoutsopoulou S, Satsangi J, Campbell BJ, Probert CS. Review article: impact of cigarette smoking on intestinal inflammation-direct and indirect mechanisms. Aliment Pharmacol Ther 2020; 51:1268-1285. [PMID: 32372449 DOI: 10.1111/apt.15774] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/13/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND The inflammatory bowel diseases, Crohn's disease and ulcerative colitis are related multifactorial diseases. Their pathogenesis is influenced by each individual's immune system, the environmental factors within exposome and genetic predisposition. Smoking habit is the single best-established environmental factor that influences disease phenotype, behaviour and response to therapy. AIM To assess current epidemiological, experimental and clinical evidence that may explain how smoking impacts on the pathogenesis of inflammatory bowel disease. METHODS A Medline search for 'cigarette smoking', in combination with terms including 'passive', 'second-hand', 'intestinal inflammation', 'Crohn's disease', 'ulcerative colitis', 'colitis'; 'intestinal epithelium', 'immune system', 'intestinal microbiota', 'tight junctions', 'mucus', 'goblet cells', 'Paneth cells', 'autophagy'; 'epigenetics', 'genes', 'DNA methylation', 'histones', 'short noncoding/long noncoding RNAs'; 'carbon monoxide/CO' and 'nitric oxide/NO' was performed. RESULTS Studies found evidence of direct and indirect effects of smoking on various parameters, including oxidative damage, impairment of intestinal barrier and immune cell function, epigenetic and microbiota composition changes, that contribute to the pathogenesis of inflammatory bowel disease. CONCLUSIONS Cigarette smoking promotes intestinal inflammation by affecting the function and interactions among intestinal epithelium, immune system and microbiota/microbiome.
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Affiliation(s)
- Stamatia Papoutsopoulou
- Gastroenterology Research Unit, Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Jack Satsangi
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Barry J Campbell
- Gastroenterology Research Unit, Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Chris S Probert
- Gastroenterology Research Unit, Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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Kaur G, Batra S. Regulation of DNA methylation signatures on NF-κB and STAT3 pathway genes and TET activity in cigarette smoke extract-challenged cells/COPD exacerbation model in vitro. Cell Biol Toxicol 2020; 36:459-480. [PMID: 32342329 DOI: 10.1007/s10565-020-09522-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/19/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a global health problem. Currently, there is a lack of knowledge about the pathobiology of this disease and available therapies are ineffective. Cigarette smoking is the leading cause of COPD; however, not all smokers develop COPD. Exacerbations of COPD caused by microbes are common and detrimental. Approximately 20-50% of patient exacerbations are caused by bacterial colonization in the lower airways. It is generally accepted that epigenetic mechanisms, especially DNA methylation, play an important role during progression of COPD. Thus, we hypothesized that DNA methylation patterns vary significantly following smoke exposure and during exacerbations caused by bacterial infections. To test our hypothesis, we used an in vitro study model that mimics COPD exacerbations and performed extensive studies to understand the role of CpG promoter methylation of NF-κB and STAT3-mediated pathway genes. Both NF-κB and STAT3 transcription factors play critical roles in orchestrating inflammatory responses during cigarette smoke exposure. In brief, human lung adenocarcinoma cells with type II alveolar epithelium characteristics (A549) were challenged with cigarette smoke extract (CSE) or DMSO (control) followed by a 3-h challenge with bacterial lipopolysaccharide (LPS; from Pseudomonas aeruginosa) prior to the termination of CSE exposure (COPD exacerbation group). The production of cytokines/chemokines, regulation of transcription factors, and DNA methylation of specific genes were then assessed. We also studied changes in the expression and activity of ten-eleven translocases (TETs), the enzymes responsible for DNA demethylation, and assessed their role in regulating DNA methylation in the CSE-challenged group. RESULTS There was a significant increase in the release of cytokines/chemokines (IL-8, MCP-1, IL-6 and CCL5) in the COPD exacerbation group as compared to the control group. Hypomethylation of NF-κB-mediated pathway genes correlated with their induction in our COPD exacerbation study model. Further, we observed an important role of TET1/2 in regulating the DNA methylation of NF-κB, STAT3, IKK, and NIK genes and cytokine/chemokine production by A549 cells during CSE challenge. CONCLUSIONS Studies to further define the role of TETs in CSE-mediated epigenetic regulation may lead to the development of better and more effective therapeutic intervention strategies for COPD.
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Affiliation(s)
- Gagandeep Kaur
- Laboratory of Pulmonary Immunotoxicology, Department of Environmental Toxicology, Southern University and A&M College, Baton Rouge, LA, 70813, USA
| | - Sanjay Batra
- Laboratory of Pulmonary Immunotoxicology, Department of Environmental Toxicology, Southern University and A&M College, Baton Rouge, LA, 70813, USA.
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