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Mohsin R, Fujimoto VY, Galusha AL, Parsons PJ, Krall JR, Butts-Jackson CD, Mok-Lin E, Bloom MS. Associations between follicular fluid trace elements and ovarian response during in vitro fertilization. ENVIRONMENTAL RESEARCH 2024; 252:118801. [PMID: 38555083 PMCID: PMC11156565 DOI: 10.1016/j.envres.2024.118801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/04/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
INTRODUCTION Exposure to trace elements has been associated with ovarian response in experimental studies. We conducted a hypothesis-generating study of associations between ovarian follicular fluid (FF) trace elements and measures of ovarian response among women using in vitro fertilization (IVF). METHODS We collected ovarian FF specimens from 56 women. We determined concentrations (μg/L) of 11 trace elements using inductively coupled plasma-tandem mass spectrometry. We estimated associations between women's FF trace elements per interquartile range difference, and measures of ovarian response using linear (peak estradiol (E2), baseline anti-mullerian hormone (AMH), and follicle stimulating hormone (FSH)) and negative binomial (baseline antral follicle count (AFC) and oocyte count) regression, adjusting for confounding factors. We used principal component analysis (PCA) to estimate the associations of the FF trace elements mixture. We also explored FF oxidative stress enzymes as causal mediators of the associations. RESULTS Higher FF cobalt was associated with greater peak E2 (mean difference = 351.48 pg/mL; 95%CI: 21.76, 724.71) and AFC (rate ratio = 1.14; 95%CI: 1.01, 1.28), and higher FF copper was associated with greater peak E2 (mean difference = 335.66 pg/mL; 95%CI: 81.77, 753.08) and oocyte count (rate ratio = 1.19; 95%CI: 1.02, 1.43). Higher FF mercury was also associated with greater peak E2 (mean difference = 410.70 pg/mL; 95%CI: 61.90, 883.39). Higher FF lead was associated with lesser AFC (rate ratio = 0.85; 95%CI: 0.73, 0.98). Using PCA, the mixture of Sr, Hg, and As was associated with higher peak estradiol, AFC, and oocyte count. FF glutathione peroxidase, paraoxonase, and arylesterase activities were inconsistent mediators of the associations, but the effect estimates were imprecise. CONCLUSION Our results suggest that essential and non-essential trace elements in FF were associated with ovarian response during IVF.
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Affiliation(s)
- Rooshna Mohsin
- Department of Global and Community Health, George Mason University, Fairfax, VA, 22030, United States
| | - Victor Y Fujimoto
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California at San Francisco, San Francisco, CA, 94158, United States
| | - Aubrey L Galusha
- Laboratory of Inorganic & Nuclear Chemistry, Wadsworth Center, New York State Department of Health, Albany, NY, 12237, United States; Department of Environmental Health Sciences, University at Albany, State University of New York, Rensselaer, NY, 12144, United States
| | - Patrick J Parsons
- Laboratory of Inorganic & Nuclear Chemistry, Wadsworth Center, New York State Department of Health, Albany, NY, 12237, United States; Department of Environmental Health Sciences, University at Albany, State University of New York, Rensselaer, NY, 12144, United States
| | - Jenna R Krall
- Department of Global and Community Health, George Mason University, Fairfax, VA, 22030, United States
| | - Celeste D Butts-Jackson
- Department of Health Services Management, North Carolina Agricultural and Technical State University, Greensboro, NC, 27411, United States; Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27599, United States
| | - Evelyn Mok-Lin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California at San Francisco, San Francisco, CA, 94158, United States
| | - Michael S Bloom
- Department of Global and Community Health, George Mason University, Fairfax, VA, 22030, United States.
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Zhao R, Lin S, Han M, Lin Z, Yu M, Zhang B, Ma L, Li D, Peng L. Association between machine learning-assisted heavy metal exposures and diabetic kidney disease: a cross-sectional survey and Mendelian randomization analysis. Front Public Health 2024; 12:1367061. [PMID: 38947355 PMCID: PMC11212833 DOI: 10.3389/fpubh.2024.1367061] [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: 04/14/2024] [Accepted: 05/30/2024] [Indexed: 07/02/2024] Open
Abstract
Background and objective Heavy metals, ubiquitous in the environment, pose a global public health concern. The correlation between these and diabetic kidney disease (DKD) remains unclear. Our objective was to explore the correlation between heavy metal exposures and the incidence of DKD. Methods We analyzed data from the NHANES (2005-2020), using machine learning, and cross-sectional survey. Our study also involved a bidirectional two-sample Mendelian randomization (MR) analysis. Results Machine learning reveals correlation coefficients of -0.5059 and - 0.6510 for urinary Ba and urinary Tl with DKD, respectively. Multifactorial logistic regression implicates urinary Ba, urinary Pb, blood Cd, and blood Pb as potential associates of DKD. When adjusted for all covariates, the odds ratios and 95% confidence intervals are 0.87 (0.78, 0.98) (p = 0.023), 0.70 (0.53, 0.92) (p = 0.012), 0.53 (0.34, 0.82) (p = 0.005), and 0.76 (0.64, 0.90) (p = 0.002) in order. Furthermore, multiplicative interactions between urinary Ba and urinary Sb, urinary Cd and urinary Co, urinary Cd and urinary Pb, and blood Cd and blood Hg might be present. Among the diabetic population, the OR of urinary Tl with DKD is a mere 0.10, with a 95%CI of (0.01, 0.74), urinary Co 0.73 (0.54, 0.98) in Model 3, and urinary Pb 0.72 (0.55, 0.95) in Model 2. Restricted Cubic Splines (RCS) indicate a linear linkage between blood Cd in the general population and urinary Co, urinary Pb, and urinary Tl with DKD among diabetics. An observable trend effect is present between urinary Pb and urinary Tl with DKD. MR analysis reveals odds ratios and 95% confidence intervals of 1.16 (1.03, 1.32) (p = 0.018) and 1.17 (1.00, 1.36) (p = 0.044) for blood Cd and blood Mn, respectively. Conclusion In the general population, urinary Ba demonstrates a nonlinear inverse association with DKD, whereas in the diabetic population, urinary Tl displays a linear inverse relationship with DKD.
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Affiliation(s)
- Ruiqi Zhao
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Sen Lin
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Mengyao Han
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhimei Lin
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Mengjiao Yu
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Bei Zhang
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Lanyue Ma
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Danfei Li
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Lisheng Peng
- Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong, China
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Pepke ML, Hansen SB, Limborg MT. Unraveling host regulation of gut microbiota through the epigenome-microbiome axis. Trends Microbiol 2024:S0966-842X(24)00137-9. [PMID: 38839511 DOI: 10.1016/j.tim.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
Recent studies of dynamic interactions between epigenetic modifications of a host organism and the composition or activity of its associated gut microbiota suggest an opportunity for the host to shape its microbiome through epigenetic alterations that lead to changes in gene expression and noncoding RNA activity. We use insights from microbiota-induced epigenetic changes to review the potential of the host to epigenetically regulate its gut microbiome, from which a bidirectional 'epigenome-microbiome axis' emerges. This axis embeds environmentally induced variation, which may influence the adaptive evolution of host-microbe interactions. We furthermore present our perspective on how the epigenome-microbiome axis can be understood and investigated within a holo-omic framework with potential applications in the applied health and food sciences.
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Affiliation(s)
- Michael L Pepke
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark.
| | - Søren B Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen, Denmark.
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4
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Thakur C, Qiu Y, Pawar A, Chen F. Epigenetic regulation of breast cancer metastasis. Cancer Metastasis Rev 2024; 43:597-619. [PMID: 37857941 DOI: 10.1007/s10555-023-10146-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Breast cancer is the most frequently diagnosed malignancy and the second leading cause of cancer-related mortality among women worldwide. Recurrent metastasis is associated with poor patient outcomes and poses a significant challenge in breast cancer therapies. Cancer cells adapting to a new tissue microenvironment is the key event in distant metastasis development, where the disseminating tumor cells are likely to acquire genetic and epigenetic alterations during the process of metastatic colonization. Despite several decades of research in this field, the exact mechanisms governing metastasis are not fully understood. However, emerging body of evidence indicates that in addition to genetic changes, epigenetic reprogramming of cancer cells and the metastatic niche are paramount toward successful metastasis. Here, we review and discuss the latest knowledge about the salient attributes of metastasis and epigenetic regulation in breast cancer and crucial research domains that need further investigation.
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Affiliation(s)
- Chitra Thakur
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA.
| | - Yiran Qiu
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA
| | - Aashna Pawar
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA
| | - Fei Chen
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA.
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Tuminello S, Ashebir YA, Schroff C, Ramaswami S, Durmus N, Chen Y, Snuderl M, Shao Y, Reibman J, Arslan AA. Genome-wide DNA methylation profiles and breast cancer among World Trade Center survivors. Environ Epidemiol 2024; 8:e313. [PMID: 38841706 PMCID: PMC11152787 DOI: 10.1097/ee9.0000000000000313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024] Open
Abstract
Background Increased incidence of cancer has been reported among World Trade Center (WTC)-exposed persons. Aberrant DNA methylation is a hallmark of cancer development. To date, only a few small studies have investigated the relationship between WTC exposure and DNA methylation. The main objective of this study was to assess the DNA methylation profiles of WTC-exposed community members who remained cancer free and those who developed breast cancer. Methods WTC-exposed women were selected from the WTC Environmental Health Center clinic, with peripheral blood collected during routine clinical monitoring visits. The reference group was selected from the NYU Women's Health Study, a prospective cohort study with blood samples collected before 9 November 2001. The Infinium MethylationEPIC array was used for global DNA methylation profiling, with adjustments for cell type composition and other confounders. Annotated probes were used for biological pathway and network analysis. Results A total of 64 WTC-exposed (32 cancer free and 32 with breast cancer) and 32 WTC-unexposed (16 cancer free and 16 with prediagnostic breast cancer) participants were included. Hypermethylated cytosine-phosphate-guanine probe sites (defined as β > 0.8) were more common among WTC-exposed versus unexposed participants (14.3% vs. 4.5%, respectively, among the top 5000 cytosine-phosphate-guanine sites). Cancer-related pathways (e.g., human papillomavirus infection, cGMP-PKG) were overrepresented in WTC-exposed groups (breast cancer patients and cancer-free subjects). Compared to the unexposed breast cancer patients, 47 epigenetically dysregulated genes were identified among WTC-exposed breast cancers. These genes formed a network, including Wnt/β-catenin signaling genes WNT4 and TCF7L2, and dysregulation of these genes contributes to cancer immune evasion. Conclusion WTC exposure likely impacts DNA methylation and may predispose exposed individuals toward cancer development, possibly through an immune-mediated mechanism.
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Affiliation(s)
- Stephanie Tuminello
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
| | - Yibeltal Arega Ashebir
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
| | - Chanel Schroff
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York
| | - Sitharam Ramaswami
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York
| | - Nedim Durmus
- Department of Medicine, NYU Grossman School of Medicine, New York City, New York
| | - Yu Chen
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
- NYU Perlmutter Comprehensive Cancer Center, New York City, New York
| | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York City, New York
| | - Yongzhao Shao
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
- NYU Perlmutter Comprehensive Cancer Center, New York City, New York
| | - Joan Reibman
- Department of Medicine, NYU Grossman School of Medicine, New York City, New York
- Division of Environmental Medicine, Department of Medicine, NYU Grossman School of Medicine, New York City, New York
| | - Alan A. Arslan
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York
- NYU Perlmutter Comprehensive Cancer Center, New York City, New York
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York City, New York
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Vahidi S, Agah S, Mirzajani E, Asghari Gharakhyli E, Norollahi SE, Rahbar Taramsari M, Babaei K, Samadani AA. microRNAs, oxidative stress, and genotoxicity as the main inducers in the pathobiology of cancer development. Horm Mol Biol Clin Investig 2024; 45:55-73. [PMID: 38507551 DOI: 10.1515/hmbci-2023-0012] [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: 02/05/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
Cancer is one of the most serious leading causes of death in the world. Many eclectic factors are involved in cancer progression including genetic and epigenetic alongside environmental ones. In this account, the performance and fluctuations of microRNAs are significant in cancer diagnosis and treatment, particularly as diagnostic biomarkers in oncology. So, microRNAs manage and control the gene expression after transcription by mRNA degradation, or also they can inhibit their translation. Conspicuously, these molecular structures take part in controlling the cellular, physiological and pathological functions, which many of them can accomplish as tumor inhibitors or oncogenes. Relatively, Oxidative stress is defined as the inequality between the creation of reactive oxygen species (ROS) and the body's ability to detoxify the reactive mediators or repair the resulting injury. ROS and microRNAs have been recognized as main cancer promoters and possible treatment targets. Importantly, genotoxicity has been established as the primary reason for many diseases as well as several malignancies. The procedures have no obvious link with mutagenicity and influence the organization, accuracy of the information, or fragmentation of DNA. Conclusively, mutations in these patterns can lead to carcinogenesis. In this review article, we report the impressive and practical roles of microRNAs, oxidative stress, and genotoxicity in the pathobiology of cancer development in conjunction with their importance as reliable cancer biomarkers and their association with circulating miRNA, exosomes and exosomal miRNAs, RNA remodeling, DNA methylation, and other molecular elements in oncology.
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Affiliation(s)
- Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Shahram Agah
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ebrahim Mirzajani
- Department of Biochemistry and Biophysics, School of Medicine, 37554 Guilan University of Medical Sciences , Rasht, Iran
| | | | - Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Morteza Rahbar Taramsari
- Department of Forensic Medicine, School of Medicine, 37554 Guilan University of Medical Sciences , Rasht, Iran
| | - Kosar Babaei
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Trauma Institute, Guilan University of Medical Sciences, Rasht, Iran
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Zhang M, Hu T, Ma T, Huang W, Wang Y. Epigenetics and environmental health. Front Med 2024:10.1007/s11684-023-1038-2. [PMID: 38806988 DOI: 10.1007/s11684-023-1038-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/15/2023] [Indexed: 05/30/2024]
Abstract
Epigenetic modifications including DNA methylation, histone modifications, chromatin remodeling, and RNA modifications complicate gene regulation and heredity and profoundly impact various physiological and pathological processes. In recent years, accumulating evidence indicates that epigenetics is vulnerable to environmental changes and regulates the growth, development, and diseases of individuals by affecting chromatin activity and regulating gene expression. Environmental exposure or induced epigenetic changes can regulate the state of development and lead to developmental disorders, aging, cardiovascular disease, Alzheimer's disease, cancers, and so on. However, epigenetic modifications are reversible. The use of specific epigenetic inhibitors targeting epigenetic changes in response to environmental exposure is useful in disease therapy. Here, we provide an overview of the role of epigenetics in various diseases. Furthermore, we summarize the mechanism of epigenetic alterations induced by different environmental exposures, the influence of different environmental exposures, and the crosstalk between environmental variation epigenetics, and genes that are implicated in the body's health. However, the interaction of multiple factors and epigenetics in regulating the initiation and progression of various diseases complicates clinical treatments. We discuss some commonly used epigenetic drugs targeting epigenetic modifications and methods to prevent or relieve various diseases regulated by environmental exposure and epigenetics through diet.
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Affiliation(s)
- Min Zhang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Ting Hu
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tianyu Ma
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Wei Huang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
| | - Yan Wang
- Key Laboratory of Cancer and Microbiome, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
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Gu W, Wang T, Lin Y, Wang Y, Chen Y, Dai Y, Duan H. Particulate polycyclic aromatic hydrocarbons and metals, DNA methylation and DNA methyltransferase among middle-school students in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172087. [PMID: 38561129 DOI: 10.1016/j.scitotenv.2024.172087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
The main components of particulate matter (PM) had been reported to change DNA methylation levels. However, the mixed effect of PM and its constituents on DNA methylation and the underlying mechanism in children has not been well characterized. To investigate the association between single or mixture exposures and global DNA methylation or DNA methyltransferases (DNMTs), 273 children were recruited (110 in low-exposed area and 163 in high-exposed area) in China. Serum benzo[a]pyridin-7,8-dihydroglycol-9, 10-epoxide (BPDE)-albumin adduct and urinary metals were determined as exposure markers. The global DNA methylation (% 5mC) and the mRNA expression of DNMT1, and DNMT3A were measured. The linear regression, quantile-based g-computation (QGC), and mediation analyses were performed to investigate the effects of individual and mixture exposure. We found that significantly lower levels of % 5mC (P < 0.001) and the mRNA expression of DNMT3A in high-PM exposed group (P = 0.031). After adjustment for age, gender, BMI z-score, detecting status of urinary cotinine, serum folate, and white blood cells, urinary arsenic (As) was negatively correlated with the % 5mC. One IQR increase in urinary As (19.97 μmol/mol creatinine) was associated with a 11.06 % decrease in % 5mC (P = 0.026). Serum BPDE-albumin adduct and urinary cadmium (Cd) were negatively correlated with the levels of DNMT1 and DNMT3A (P < 0.05). Mixture exposure was negatively associated with expression of DNMT3A in QGC analysis (β: -0.19, P < 0.001). Mixture exposure was significantly associated with decreased % 5mC in the children with non-detected cotinine or normal serum folate (P < 0.05), which the most contributors were PAHs and As. The mediated effect of hypomethylation through DNMT1 or DNMT3A pathway was not observed. Our findings indicated that individual and mixture exposure PAHs and metal components had negative associations with global DNA methylation and decreased DNMT3A expression significantly in school-age individuals.
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Affiliation(s)
- Wen Gu
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Ting Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China
| | - Yang Lin
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; Beijing Chaoyang District Center for Disease Prevention and Control, Beijing 100021, China
| | - Yanhua Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; State Key Laboratory of Trauma and Chemical Poisoning, China
| | - Yuanyuan Chen
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Yufei Dai
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Huawei Duan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing 100050, China; State Key Laboratory of Trauma and Chemical Poisoning, China.
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Carswell G, Chamberlin J, Bennett BD, Bushel PR, Chorley BN. Persistent gene expression and DNA methylation alterations linked to carcinogenic effects of dichloroacetic acid. Front Oncol 2024; 14:1389634. [PMID: 38764585 PMCID: PMC11099211 DOI: 10.3389/fonc.2024.1389634] [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: 02/22/2024] [Accepted: 04/18/2024] [Indexed: 05/21/2024] Open
Abstract
Background Mechanistic understanding of transient exposures that lead to adverse health outcomes will enhance our ability to recognize biological signatures of disease. Here, we measured the transcriptomic and epigenomic alterations due to exposure to the metabolic reprogramming agent, dichloroacetic acid (DCA). Previously, we showed that exposure to DCA increased liver tumor incidence in B6C3F1 mice after continuous or early life exposures significantly over background level. Methods Using archived formalin-fixed liver samples, we utilized modern methodologies to measure gene expression and DNA methylation levels to link to previously generated phenotypic measures. Gene expression was measured by targeted RNA sequencing (TempO-seq 1500+ toxicity panel: 2754 total genes) in liver samples collected from 10-, 32-, 57-, and 78-week old mice exposed to deionized water (controls), 3.5 g/L DCA continuously in drinking water ("Direct" group), or DCA for 10-, 32-, or 57-weeks followed by deionized water until sample collection ("Stop" groups). Genome-scaled alterations in DNA methylation were measured by Reduced Representation Bisulfite Sequencing (RRBS) in 78-week liver samples for control, Direct, 10-week Stop DCA exposed mice. Results Transcriptomic changes were most robust with concurrent or adjacent timepoints after exposure was withdrawn. We observed a similar pattern with DNA methylation alterations where we noted attenuated differentially methylated regions (DMRs) in the 10-week Stop DCA exposure groups compared to the Direct group at 78-weeks. Gene pathway analysis indicated cellular effects linked to increased oxidative metabolism, a primary mechanism of action for DCA, closer to exposure windows especially early in life. Conversely, many gene signatures and pathways reversed patterns later in life and reflected more pro-tumorigenic patterns for both current and prior DCA exposures. DNA methylation patterns correlated to early gene pathway perturbations, such as cellular signaling, regulation and metabolism, suggesting persistence in the epigenome and possible regulatory effects. Conclusion Liver metabolic reprogramming effects of DCA interacted with normal age mechanisms, increasing tumor burden with both continuous and prior DCA exposure in the male B6C3F1 rodent model.
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Affiliation(s)
- Gleta Carswell
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - John Chamberlin
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
- Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Brian D. Bennett
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, United States
| | - Pierre R. Bushel
- Massive Genome Informatics Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, United States
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, United States
| | - Brian N. Chorley
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
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10
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Zhang Z, Wang Q, Gao X, Tang X, Xu H, Wang W, Lei X. Reproductive toxicity of cadmium stress in male animals. Toxicology 2024; 504:153787. [PMID: 38522818 DOI: 10.1016/j.tox.2024.153787] [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: 02/05/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 03/26/2024]
Abstract
Cadmium (Cd) is a common heavy metal pollutant in the environment, and the widespread use of products containing Cd compounds in industry has led to excessive levels in the environment, which enter the animal body through the food chain, thus seriously affecting the reproductive development of animals. Related studies have reported that Cd severely affects spermatogonia development and spermatogenesis in animals. In contrast, the reproductive toxicity of Cd in males and its mechanism of action have not been clarified. Therefore, this paper reviewed the toxic effects of Cd on germ cells, spermatogonia somatic cells and hypothalamic-pituitary-gonadal axis (HPG axis) of male animals and its toxic action mechanisms of oxidative stress, apoptosis and autophagy from the perspectives of cytology, genetics and neuroendocrinology. The effects of Cd stress on epigenetic modification of reproductive development in male animals were also analyzed. We hope to provide a reference for the in-depth study of the toxicity of Cd on male animal reproduction.
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Affiliation(s)
- Zikun Zhang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Qi Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Xiaoge Gao
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Xu Tang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Huan Xu
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Wenqiang Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China.
| | - Xin Lei
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China.
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11
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Opare-Addo PA, Sarfo FS, Aikins M, Bediako SA, Ovbiagele B. Epigenetics as a target to mitigate excess stroke risk in people of African ancestry: A scoping review. J Stroke Cerebrovasc Dis 2024; 33:107585. [PMID: 38253246 PMCID: PMC11060795 DOI: 10.1016/j.jstrokecerebrovasdis.2024.107585] [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: 12/09/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Globally, individuals of African ancestry have a relatively greater stroke preponderance compared to other racial/ethnic groups. The higher prevalence of traditional stroke risk factors in this population, however, only partially explains this longstanding disparity. Epigenetic signatures are transgenerational and could be a plausible therapeutic target to further bend the stroke disparities curve for people of African ancestry. There is, however, limited data on epigenetics and stroke risk in this population. PURPOSE To examine existing evidence and knowledge gaps on the potential contribution of epigenetics to excess stroke risk in people of African ancestry and avenues for mitigation. MATERIALS AND METHODS We conducted a scoping review of studies published between January 2003 and July 2023, on epigenetics and stroke risk. We then summarized our findings, highlighting the results for people of African ancestry. RESULTS Of 104 studies, there were only 6 studies that specifically looked at epigenetic mechanisms and stroke risk in people of African ancestry. Results of these studies show how patterns of DNA methylation and non-coding RNA interact with lifestyle choices, xenobiotics, and FVIII levels to raise stroke risk in people of African ancestry. However, no studies evaluated epigenetic patterns as actionable targets for the influence of psychosocial stressors or social context and excess stroke risk in this population (versus others). Also, no studies interrogated the role of established or novel therapeutic agents with the potential to reprogram DNA by adding or removing epigenetic markers in people of African ancestry. CONCLUSION Epigenetics potentially offers a promising target for modifying the effects of lifestyle, environmental exposures, and other factors that differentially affect people of African ancestry and place them at relatively greater stroke risk compared to other populations. Studies that precisely assess the pathways by which epigenetic mechanisms modulate population-specific disparities in the risk of stroke are needed.
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Affiliation(s)
| | - Fred Stephen Sarfo
- Komfo Anokye Teaching Hospital, Kumasi, Ghana; Neurology Division, Kwame Nkrumah University of Science & Technology, P. O. Box 1934, Kumasi, Ghana.
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Kerkhof J, Rastin C, Levy MA, Relator R, McConkey H, Demain L, Dominguez-Garrido E, Kaat LD, Houge SD, DuPont BR, Fee T, Fletcher RS, Gokhale D, Haukanes BI, Henneman P, Hilton S, Hilton BA, Jenkinson S, Lee JA, Louie RJ, Motazacker MM, Rzasa J, Stevenson RE, Plomp A, van der Laan L, van der Smagt J, Walden KK, Banka S, Mannens M, Skinner SA, Friez MJ, Campbell C, Tedder ML, Alders M, Sadikovic B. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases. Genet Med 2024; 26:101075. [PMID: 38251460 DOI: 10.1016/j.gim.2024.101075] [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: 08/29/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
PURPOSE This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSign Clinical Testing Network. METHODS The EpiSign assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSign Knowledge Database, yielding the result that was reported. An international working group, representing distinct EpiSign Clinical Testing Network health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing. RESULTS Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy-number variants (CNVs) of uncertain significance or for assessment of clinical diagnoses without confirmed molecular findings, and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing. CONCLUSION Clinical DNA methylation testing including episignatures, imprinting, and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.
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Affiliation(s)
- Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Cassandra Rastin
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Laura Donker Kaat
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Sofia Douzgou Houge
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | | | | | | | - David Gokhale
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Bjørn Ivar Haukanes
- Haukeland University Hospital, Centre for Medical Genetics and Molecular Medicine, Bergen, Norway
| | - Peter Henneman
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | | | - M Mahdi Motazacker
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | | | - Astrid Plomp
- Department of Clinical Genetics, AMC, Amsterdam, The Netherlands
| | - Liselot van der Laan
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jasper van der Smagt
- Department of Genetics, Utrecht University Medical Center, Utrecht, The Netherlands
| | | | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Marcel Mannens
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | | | | | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | | | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
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13
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024; 16:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [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: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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14
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Pereira S, Apodaca C, Slominski K, Lipsky RK, Coarfa C, Walker CL, McGuire AL, Steele L, Helmer DA. "Holy cow, where do I sign up?" Attitudes of Military Veterans toward Epigenomic Biomarker Toxic Exposure Testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.09.24305554. [PMID: 38699358 PMCID: PMC11065004 DOI: 10.1101/2024.04.09.24305554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Background With the signing of the PACT Act in 2022, there is great interest and investment in studying toxic exposures encountered during military service. One way to address this is through the identification of epigenomic biomarkers associated with exposures. There is increasing evidence suggesting that exposure to toxic substances may result in alterations to DNA methylation and resultant gene expression. These epigenomic changes may lead to adverse health effects for exposed individuals and their offspring. While the development of epigenomic biomarkers for exposures could facilitate understanding of these exposure-related health effects, such testing could also provide unwanted information. Objectives Explore Veterans' attitudes toward epigenomic biomarker research and the potential to test for past exposures that could pose intergenerational risk. Methods Semi-structured interviews with Veterans (n=22) who experienced potentially harmful exposures during their military service. Results Twenty Veterans said they would hypothetically want to receive epigenomic information related to their toxic exposures and potential health impacts as part of a research study. Veterans identified nine potential benefits of this research, including promoting insights concerning intergenerational health, identification of early health interventions to mitigate the impact of exposures, and additional knowledge or explanation for their experiences. At the same time, 16 participants noted potential risks, including psychological distress in response to results, concerns about receiving non-actionable, uncertain, or inaccurate results, and issues related to privacy and discrimination. Ten participants also identified at least one condition in their children that they thought could be related to their exposure and most said they would be interested in receiving research results related to their children's and grandchildren's risk of developing a health condition associated with their exposure. Discussion Results suggest that Veterans might welcome benefits of epigenomic research related to military exposures yet have some concerns about potential negative impacts.
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15
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Baia-da-Silva DC, Mendes PFS, Silva DCBD, Chemelo VS, Bittencourt LO, Padilha PM, Oriá RB, Aschner M, Lima RR. What does scientometry tell us about mercury toxicology and its biological impairments? Heliyon 2024; 10:e27526. [PMID: 38586377 PMCID: PMC10998116 DOI: 10.1016/j.heliyon.2024.e27526] [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: 01/21/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 04/09/2024] Open
Abstract
Mercury is a toxic pollutant that poses risks to both human and environmental health, making it a pressing public health concern. This study aimed to summarize the knowledge on mercury toxicology and the biological impairments caused by exposure to mercury in experimental studies and/or diagnosis in humans. The research was conducted on the main collection of Web of Science, employing as a methodological tool a bibliometric analysis. The selected articles were analyzed, and extracted data such as publication year, journal, author, title, number of citations, corresponding author's country, keywords, and the knowledge mapping was performed about the type of study, chemical form of mercury, exposure period, origin of exposure, tissue/fluid of exposure measurement, mercury concentration, evaluation period (age), mercury effect, model experiments, dose, exposure pathway, and time of exposure. The selected articles were published between 1965 and 2021, with Clarkson TW being the most cited author who has also published the most articles. A total of 38% of the publications were from the USA. These studies assessed the prenatal and postnatal effects of mercury, emphasizing the impact of methylmercury on neurodevelopment, including motor and cognitive evaluations, the association between mercury and autism, and an evaluation of its protective effects against mercury toxicity. In observational studies, the blood, umbilical cord, and hair were the most frequently used for measuring mercury levels. Our data analysis reveals that mercury neurotoxicology has been extensively explored, but the association among the outcomes evaluated in experimental studies has yet to be strengthened. Providing metric evidence on what is unexplored allows for new studies that may help governmental and non-governmental organizations develop guidelines and policies.
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Affiliation(s)
- Daiane Claydes Baia-da-Silva
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Paulo Fernando Santos Mendes
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Diane Cleydes Baia da Silva
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Victória Santos Chemelo
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Leonardo Oliveira Bittencourt
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Pedro Magalhães Padilha
- School of Veterinary Medicine and Animal Science, Institute of Biosciences, São Paulo State University, Botucatu, SP, Brazil
| | - Reinaldo Barreto Oriá
- Laboratory of Tissue Healing, Ontogeny and Nutrition, Department of Morphology, School of Medicine, Institute of Biomedicine, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rafael Rodrigues Lima
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
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16
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Xia Y, Chen K, Yang Q, Chen Z, Jin L, Zhang L, Yu X, Wang L, Xie C, Zhao Y, Shen Y, Tong J. Methylation in cornea and corneal diseases: a systematic review. Cell Death Discov 2024; 10:169. [PMID: 38589350 PMCID: PMC11002037 DOI: 10.1038/s41420-024-01935-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024] Open
Abstract
Corneal diseases are among the primary causes of blindness and vision loss worldwide. However, the pathogenesis of corneal diseases remains elusive, and diagnostic and therapeutic tools are limited. Thus, identifying new targets for the diagnosis and treatment of corneal diseases has gained great interest. Methylation, a type of epigenetic modification, modulates various cellular processes at both nucleic acid and protein levels. Growing evidence shows that methylation is a key regulator in the pathogenesis of corneal diseases, including inflammation, fibrosis, and neovascularization, making it an attractive potential therapeutic target. In this review, we discuss the major alterations of methylation and demethylation at the DNA, RNA, and protein levels in corneal diseases and how these dynamics contribute to the pathogenesis of corneal diseases. Also, we provide insights into identifying potential biomarkers of methylation that may improve the diagnosis and treatment of corneal diseases.
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Affiliation(s)
- Yutong Xia
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Kuangqi Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Qianjie Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Zhitong Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Le Jin
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyue Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Xin Yu
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyin Wang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Chen Xie
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Yuan Zhao
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Ye Shen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
| | - Jianping Tong
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
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17
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Geng H, An Q, Song J, He D, Han H, Wang L. Cadmium-induced global DNA hypermethylation promoting mitochondrial dynamics dysregulation in hippocampal neurons. ENVIRONMENTAL TOXICOLOGY 2024; 39:2043-2051. [PMID: 38095104 DOI: 10.1002/tox.24083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/06/2023] [Accepted: 12/01/2023] [Indexed: 03/09/2024]
Abstract
Environmental cadmium exposure during pregnancy or adolescence can cause neurodevelopmental toxicity, lead to neurological impairment, and reduce cognitive abilities, such as learning and memory. However, the mechanisms by which cadmium causes neurodevelopmental toxicity and cognitive impairment are still not fully elucidated. This study used hippocampal neurons cultured in vitro to observe the impact of cadmium exposure on mitochondrial dynamics and apoptosis. Exposure to 5 μM cadmium causes degradation of hippocampal neuron cell bodies and axons, morphological destruction, low cell viability, and apoptosis increase. Cadmium exposure upregulates the expression of mitochondrial fission proteins Drp1 and Fis1, reduces the expression of mitochondrial fusion-related proteins MFN1, MFN2, and OPA1, as well as reduces the expression of PGC-1a. Mitochondrial morphology detection demonstrated that cadmium exposure changes the morphological structure of mitochondria in hippocampal neurons, increasing the number of punctate and granular mitochondria, reducing the number of tubular and reticular mitochondria, decreasing mitochondrial mass, dissipating mitochondrial membrane potential (ΔΨm), and reducing adenosine triphosphate (ATP) production. Cadmium exposure increases the global methylation level of the genome and upregulates the expression of DNMT1 and DNMT3α in hippocampal neurons. 5-Aza-CdR reduces cadmium-induced genome methylation levels in hippocampal neurons, increases the number of tubular and reticular mitochondria, and promotes cell viability. In conclusion, cadmium regulates the expression of mitochondrial dynamics-related proteins by increasing hippocampal neuron genome methylation, changing mitochondrial morphology and function, and exerting neurotoxic effects.
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Affiliation(s)
- Huixia Geng
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health Sciences, Henan University, Kaifeng, Henan Province, People's Republic of China
| | - Qihang An
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health Sciences, Henan University, Kaifeng, Henan Province, People's Republic of China
| | - Jie Song
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health Sciences, Henan University, Kaifeng, Henan Province, People's Republic of China
| | - Dongling He
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health Sciences, Henan University, Kaifeng, Henan Province, People's Republic of China
| | - Huimin Han
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health Sciences, Henan University, Kaifeng, Henan Province, People's Republic of China
| | - Lai Wang
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health Sciences, Henan University, Kaifeng, Henan Province, People's Republic of China
- School of Life Science, Henan University, Kaifeng, Henan Province, People's Republic of China
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Kiltschewskij DJ, Reay WR, Geaghan MP, Atkins JR, Xavier A, Zhang X, Watkeys OJ, Carr VJ, Scott RJ, Green MJ, Cairns MJ. Alteration of DNA Methylation and Epigenetic Scores Associated With Features of Schizophrenia and Common Variant Genetic Risk. Biol Psychiatry 2024; 95:647-661. [PMID: 37480976 DOI: 10.1016/j.biopsych.2023.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/24/2023]
Abstract
BACKGROUND Unpacking molecular perturbations associated with features of schizophrenia is a critical step toward understanding phenotypic heterogeneity in this disorder. Recent epigenome-wide association studies have uncovered pervasive dysregulation of DNA methylation in schizophrenia; however, clinical features of the disorder that account for a large proportion of phenotypic variability are relatively underexplored. METHODS We comprehensively analyzed patterns of DNA methylation in a cohort of 381 individuals with schizophrenia from the deeply phenotyped Australian Schizophrenia Research Bank. Epigenetic changes were investigated in association with cognitive status, age of onset, treatment resistance, Global Assessment of Functioning scores, and common variant polygenic risk scores for schizophrenia. We subsequently explored alterations within genes previously associated with psychiatric illness, phenome-wide epigenetic covariance, and epigenetic scores. RESULTS Epigenome-wide association studies of the 5 primary traits identified 662 suggestively significant (p < 6.72 × 10-5) differentially methylated probes, with a further 432 revealed after controlling for schizophrenia polygenic risk on the remaining 4 traits. Interestingly, we uncovered many probes within genes associated with a variety of psychiatric conditions as well as significant epigenetic covariance with phenotypes and exposures including acute myocardial infarction, C-reactive protein, and lung cancer. Epigenetic scores for treatment-resistant schizophrenia strikingly exhibited association with clozapine administration, while epigenetic proxies of plasma protein expression, such as CCL17, MMP10, and PRG2, were associated with several features of schizophrenia. CONCLUSIONS Our findings collectively provide novel evidence suggesting that several features of schizophrenia are associated with alteration of DNA methylation, which may contribute to interindividual phenotypic variation in affected individuals.
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Affiliation(s)
- Dylan J Kiltschewskij
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Precision Medicine Program, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - William R Reay
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Precision Medicine Program, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Michael P Geaghan
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Joshua R Atkins
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
| | - Alexandre Xavier
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Centre for Information Based Medicine, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Xiajie Zhang
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Centre for Information Based Medicine, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Oliver J Watkeys
- School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Vaughan J Carr
- School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia; Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Centre for Information Based Medicine, Hunter Medical Research Institute, New Lambton, New South Wales, Australia
| | - Melissa J Green
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia; Precision Medicine Program, Hunter Medical Research Institute, New Lambton, New South Wales, Australia.
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Hatton AA, Cheng FF, Lin T, Shen RJ, Chen J, Zheng Z, Qu J, Lyu F, Harris SE, Cox SR, Jin ZB, Martin NG, Fan D, Montgomery GW, Yang J, Wray NR, Marioni RE, Visscher PM, McRae AF. Genetic control of DNA methylation is largely shared across European and East Asian populations. Nat Commun 2024; 15:2713. [PMID: 38548728 PMCID: PMC10978881 DOI: 10.1038/s41467-024-47005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
DNA methylation is an ideal trait to study the extent of the shared genetic control across ancestries, effectively providing hundreds of thousands of model molecular traits with large QTL effect sizes. We investigate cis DNAm QTLs in three European (n = 3701) and two East Asian (n = 2099) cohorts to quantify the similarities and differences in the genetic architecture across populations. We observe 80,394 associated mQTLs (62.2% of DNAm probes with significant mQTL) to be significant in both ancestries, while 28,925 mQTLs (22.4%) are identified in only a single ancestry. mQTL effect sizes are highly conserved across populations, with differences in mQTL discovery likely due to differences in allele frequency of associated variants and differing linkage disequilibrium between causal variants and assayed SNPs. This study highlights the overall similarity of genetic control across ancestries and the value of ancestral diversity in increasing the power to detect associations and enhancing fine mapping resolution.
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Affiliation(s)
- Alesha A Hatton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Fei-Fei Cheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jie Chen
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jia Qu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fan Lyu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, 4006, Australia
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, 100191, Beijing, China
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Harris KM, Levitt B, Gaydosh L, Martin C, Meyer JM, Mishra AA, Kelly AL, Aiello AE. The Sociodemographic and Lifestyle Correlates of Epigenetic Aging in a Nationally Representative U.S. Study of Younger Adults. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585983. [PMID: 38585956 PMCID: PMC10996523 DOI: 10.1101/2024.03.21.585983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Importance Epigenetic clocks represent molecular evidence of disease risk and aging processes and have been used to identify how social and lifestyle characteristics are associated with accelerated biological aging. However, most of this research is based on older adult samples who already have measurable chronic disease. Objective To investigate whether and how sociodemographic and lifestyle characteristics are related to biological aging in a younger adult sample across a wide array of epigenetic clock measures. Design Nationally representative prospective cohort study. Setting United States (U.S.). Participants Data come from the National Longitudinal Study of Adolescent to Adult Health, a national cohort of adolescents in grades 7-12 in U.S. in 1994 followed for 25 years over five interview waves. Our analytic sample includes participants followed-up through Wave V in 2016-18 who provided blood samples for DNA methylation (DNAm) testing (n=4237) at Wave V. Exposure Sociodemographic (sex, race/ethnicity, immigrant status, socioeconomic status, geographic location) and lifestyle (obesity status, exercise, tobacco, and alcohol use) characteristics. Main Outcome Biological aging assessed from blood DNAm using 16 epigenetic clocks when the cohort was aged 33-44 in Wave V. Results While there is considerable variation in the mean and distribution of epigenetic clock estimates and in the correlations among the clocks, we found sociodemographic and lifestyle factors are more often associated with biological aging in clocks trained to predict current or dynamic phenotypes (e.g., PhenoAge, GrimAge and DunedinPACE) as opposed to clocks trained to predict chronological age alone (e.g., Horvath). Consistent and strong associations of faster biological aging were found for those with lower levels of education and income, and those with severe obesity, no weekly exercise, and tobacco use. Conclusions and Relevance Our study found important social and lifestyle factors associated with biological aging in a nationally representative cohort of younger-aged adults. These findings indicate that molecular processes underlying disease risk can be identified in adults entering midlife before disease is manifest and represent useful targets for interventions to reduce social inequalities in heathy aging and longevity. Key Points Question: Are epigenetic clocks, measures of biological aging developed mainly on older-adult samples, meaningful for younger adults and associated with sociodemographic and lifestyle characteristics in expected patterns found in prior aging research?Findings: Sociodemographic and lifestyle factors were associated with biological aging in clocks trained to predict morbidity and mortality showing accelerated aging among those with lower levels of education and income, and those with severe obesity, no weekly exercise, and tobacco use.Meaning: Age-related molecular processes can be identified in younger-aged adults before disease manifests and represent potential interventions to reduce social inequalities in heathy aging and longevity.
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Ferro dos Santos MR, Giuili E, De Koker A, Everaert C, De Preter K. Computational deconvolution of DNA methylation data from mixed DNA samples. Brief Bioinform 2024; 25:bbae234. [PMID: 38762790 PMCID: PMC11102637 DOI: 10.1093/bib/bbae234] [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: 02/07/2024] [Revised: 03/30/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024] Open
Abstract
In this review, we provide a comprehensive overview of the different computational tools that have been published for the deconvolution of bulk DNA methylation (DNAm) data. Here, deconvolution refers to the estimation of cell-type proportions that constitute a mixed sample. The paper reviews and compares 25 deconvolution methods (supervised, unsupervised or hybrid) developed between 2012 and 2023 and compares the strengths and limitations of each approach. Moreover, in this study, we describe the impact of the platform used for the generation of methylation data (including microarrays and sequencing), the applied data pre-processing steps and the used reference dataset on the deconvolution performance. Next to reference-based methods, we also examine methods that require only partial reference datasets or require no reference set at all. In this review, we provide guidelines for the use of specific methods dependent on the DNA methylation data type and data availability.
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Affiliation(s)
- Maísa R Ferro dos Santos
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Edoardo Giuili
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Andries De Koker
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Celine Everaert
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Katleen De Preter
- VIB-UGent Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Zwijnaarde, Belgium
- Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
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22
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Zwolińska W, Bilska K, Tarhonska K, Reszka E, Skibińska M, Pytlińska N, Słopień A, Dmitrzak-Węglarz M. Biomarkers of Depression among Adolescent Girls: BDNF and Epigenetics. Int J Mol Sci 2024; 25:3281. [PMID: 38542252 PMCID: PMC10970207 DOI: 10.3390/ijms25063281] [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: 02/02/2024] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Alterations in brain-derived neurotrophic factor (BDNF) expression have been suggested to mediate the influence of environmental factors on the emergence of depression through epigenetic modifications. However, research on this subject in the developmental population is lacking and the pathophysiology of adolescent depression remains unclear. We aimed to investigate the alterations in BDNF expression and global DNA methylation in depression among adolescent girls. Thirty female inpatients with the initial diagnosis of depression were assessed before and after the period of antidepressant treatment and compared with thirty age-matched healthy controls. The assessment involved BDNF and proBDNF serum levels, the BDNF gene exon IV promoter methylation, and global DNA methylation. The methylation level in the BDNF gene exon IV promoter was significantly lower in the studied group compared with the control and correlated negatively with the severity of depression. The test distinguished the studied group from the controls with a sensitivity of 37% and specificity of 90%. The differences were no longer present after the period of antidepressant treatment. No differences in the global DNA methylation, BDNF, and proBDNF levels were found. We concluded that decreased methylation in the BDNF exon IV promoter could be considered as a biomarker of a depression state among adolescent girls.
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Affiliation(s)
- Weronika Zwolińska
- Department of Child and Adolescent Psychiatry, Karol Jonscher Clinical Hospital, Poznan University of Medical Sciences, Szpitalna 27/33 St., 60-572 Poznan, Poland; (W.Z.); (N.P.); (A.S.)
| | - Karolina Bilska
- Department of Psychiatric Genetics, Medical Biology Center, Poznan University of Medical Sciences, Rokietnicka St. 8, 60-806 Poznan, Poland; (K.B.); (M.S.)
| | - Kateryna Tarhonska
- Department of Translational Research, Nofer Institute of Occupational Medicine, 91-348 Łódź, Poland; (K.T.); (E.R.)
| | - Edyta Reszka
- Department of Translational Research, Nofer Institute of Occupational Medicine, 91-348 Łódź, Poland; (K.T.); (E.R.)
| | - Maria Skibińska
- Department of Psychiatric Genetics, Medical Biology Center, Poznan University of Medical Sciences, Rokietnicka St. 8, 60-806 Poznan, Poland; (K.B.); (M.S.)
| | - Natalia Pytlińska
- Department of Child and Adolescent Psychiatry, Karol Jonscher Clinical Hospital, Poznan University of Medical Sciences, Szpitalna 27/33 St., 60-572 Poznan, Poland; (W.Z.); (N.P.); (A.S.)
| | - Agnieszka Słopień
- Department of Child and Adolescent Psychiatry, Karol Jonscher Clinical Hospital, Poznan University of Medical Sciences, Szpitalna 27/33 St., 60-572 Poznan, Poland; (W.Z.); (N.P.); (A.S.)
| | - Monika Dmitrzak-Węglarz
- Department of Psychiatric Genetics, Medical Biology Center, Poznan University of Medical Sciences, Rokietnicka St. 8, 60-806 Poznan, Poland; (K.B.); (M.S.)
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23
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Wever BMM, Steenbergen RDM. Unlocking the potential of tumor-derived DNA in urine for cancer detection: methodological challenges and opportunities. Mol Oncol 2024. [PMID: 38462745 DOI: 10.1002/1878-0261.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/20/2023] [Accepted: 01/27/2024] [Indexed: 03/12/2024] Open
Abstract
High cancer mortality rates and the rising cancer burden worldwide drive the development of innovative methods in order to advance cancer diagnostics. Urine contains a viable source of tumor material and allows for self-collection from home. Biomarker testing in this liquid biopsy represents a novel approach that is convenient for patients and can be effective in detecting cancer at a curable stage. Here, we set out to provide a detailed overview of the rationale behind urine-based cancer detection, with a focus on non-urological cancers, and its potential for cancer diagnostics. Moreover, evolving methodological challenges and untapped opportunities for urine biomarker testing are discussed, particularly emphasizing DNA methylation of tumor-derived cell-free DNA. We also provide future recommendations for technical advancements in urine-based cancer detection and elaborate on potential mechanisms involved in the transrenal transport of cell-free DNA.
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Affiliation(s)
- Birgit M M Wever
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
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24
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Cai H, Zheng N, Tang C, Zhang Y, Zuo Z, He C. Tributyltin causes generational neurodevelopmental toxicity and the protective effect of folic acid in zebrafish. J Environ Sci (China) 2024; 137:615-625. [PMID: 37980044 DOI: 10.1016/j.jes.2023.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 11/20/2023]
Abstract
Tributyltin (TBT), a common organotin environmental pollutant, may pose a threat to human development during critical early-life periods. We aimed to assess the neurodevelopmental intergenerational toxicity of early-life exposure to TBT and the protective effect of DNA methyl donor folic acid (FA). Specifically, after early-life exposure (1-21 days post-fertilization, dpf) to TBT (0, 1, 10 and 100 ng/L), zebrafish (Danio rerio) were cultured in clean medium until sexual maturity. The exposed females were mated with unexposed males to produce embryos (F1). The F1 generation were cultured (4-120 hours post-fertilization, hpf) with and without 1 mmol/L FA. The neurotoxic effects of early-life TBT exposure for zebrafish and their offspring (F1) were significantly enhanced anxiety and reduced aggression, decreased gene expression of DNA methyltransferase in the brain and increased serotonin levels in the body. Moreover, the intergenerational neurodevelopmental toxicity, as manifested in the F1 generation, was attenuated by FA supplementation. In summary, early-life TBT exposure led to intergenerational neurodevelopmental deficits in zebrafish, and DNA methyl donors had a protective effect on F1 neurodevelopment, which can inform the prevention and treatment of intergenerational neurotoxicity due to organotin pollutants.
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Affiliation(s)
- Haoxing Cai
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361005, China
| | - Naying Zheng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361005, China
| | - Chen Tang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361005, China
| | - Yuxuan Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361005, China
| | - Zhenghong Zuo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361005, China.
| | - Chengyong He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361005, China.
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25
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García-Giménez JL, Cánovas-Cervera I, Pallardó FV. Oxidative stress and metabolism meet epigenetic modulation in physical exercise. Free Radic Biol Med 2024; 213:123-137. [PMID: 38199289 DOI: 10.1016/j.freeradbiomed.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Physical exercise is established as an important factor of health and generally is recommended for its positive effects on several tissues, organs, and systems. These positive effects come from metabolic adaptations that also include oxidative eustress, in which physical activity increases ROS production and antioxidant mechanisms, although this depends on the intensity of the exercise. Muscle metabolism through mechanisms such as aerobic and anaerobic glycolysis, tricarboxylic acid cycle, and oxidative lipid metabolism can produce metabolites and co-factors which directly impact the epigenetic machinery. In this review, we clearly reinforce the evidence that exercise regulates several epigenetic mechanisms and explain how these mechanisms can be regulated by metabolic products and co-factors produced during exercise. In fact, recent evidence has demonstrated the importance of epigenetics in the gene expression changes implicated in metabolic adaptation after exercise. Importantly, intermediates of the metabolism generated by continuous, acute, moderate, or strenuous exercise control the activity of epigenetic enzymes, therefore turning on or turning off the gene expression of specific programs which can lead to physiological adaptations after exercise.
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Affiliation(s)
- José Luis García-Giménez
- Faculty of Medicine and Dentistry, Department of Physiology, University of Valencia, Av/Blasco Ibañez, 15, Valencia, 46010, Spain; Biomedical Research Institute INCLIVA, Av/Menéndez Pelayo. 4acc, Valencia, 46010, Spain; CIBERER, The Centre for Biomedical Network Research on Rare Diseases, ISCIII, C. de Melchor Fernández Almagro, 3, 28029, Madrid, Spain.
| | - Irene Cánovas-Cervera
- Faculty of Medicine and Dentistry, Department of Physiology, University of Valencia, Av/Blasco Ibañez, 15, Valencia, 46010, Spain; Biomedical Research Institute INCLIVA, Av/Menéndez Pelayo. 4acc, Valencia, 46010, Spain.
| | - Federico V Pallardó
- Faculty of Medicine and Dentistry, Department of Physiology, University of Valencia, Av/Blasco Ibañez, 15, Valencia, 46010, Spain; Biomedical Research Institute INCLIVA, Av/Menéndez Pelayo. 4acc, Valencia, 46010, Spain; CIBERER, The Centre for Biomedical Network Research on Rare Diseases, ISCIII, C. de Melchor Fernández Almagro, 3, 28029, Madrid, Spain.
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26
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Singh S A, Ansari MN, M. Elossaily G, Vellapandian C, Prajapati B. Investigating the Potential Impact of Air Pollution on Alzheimer's Disease and the Utility of Multidimensional Imaging for Early Detection. ACS OMEGA 2024; 9:8615-8631. [PMID: 38434844 PMCID: PMC10905749 DOI: 10.1021/acsomega.3c06328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/25/2023] [Accepted: 01/30/2024] [Indexed: 03/05/2024]
Abstract
Pollution is ubiquitous, and much of it is anthropogenic in nature, which is a severe risk factor not only for respiratory infections or asthma sufferers but also for Alzheimer's disease, which has received a lot of attention recently. This Review aims to investigate the primary environmental risk factors and their profound impact on Alzheimer's disease. It underscores the pivotal role of multidimensional imaging in early disease identification and prevention. Conducting a comprehensive review, we delved into a plethora of literature sources available through esteemed databases, including Science Direct, Google Scholar, Scopus, Cochrane, and PubMed. Our search strategy incorporated keywords such as "Alzheimer Disease", "Alzheimer's", "Dementia", "Oxidative Stress", and "Phytotherapy" in conjunction with "Criteria Pollutants", "Imaging", "Pathology", and "Particulate Matter". Alzheimer's disease is not only a result of complex biological factors but is exacerbated by the infiltration of airborne particles and gases that surreptitiously breach the nasal defenses to traverse the brain, akin to a Trojan horse. Various imaging modalities and noninvasive techniques have been harnessed to identify disease progression in its incipient stages. However, each imaging approach possesses inherent limitations, prompting exploration of a unified technique under a single umbrella. Multidimensional imaging stands as the linchpin for detecting and forestalling the relentless march of Alzheimer's disease. Given the intricate etiology of the condition, identifying a prospective candidate for Alzheimer's disease may take decades, rendering the development of a multimodal imaging technique an imperative. This research underscores the pressing need to recognize the chronic ramifications of invisible particulate matter and to advance our understanding of the insidious environmental factors that contribute to Alzheimer's disease.
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Affiliation(s)
- Ankul Singh S
- Department
of Pharmacology, SRM College of Pharmacy, SRM Institute of Science and Technology (SRMIST), Kattankulathur, Tamil Nadu 603203, India
| | - Mohd Nazam Ansari
- Department
of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Gehan M. Elossaily
- Department
of Basic Medical Sciences, College of Medicine, AlMaarefa University, P.O. Box 71666, Riyadh 13713, Saudi Arabia
| | - Chitra Vellapandian
- Department
of Pharmacology, SRM College of Pharmacy, SRM Institute of Science and Technology (SRMIST), Kattankulathur, Tamil Nadu 603203, India
| | - Bhupendra Prajapati
- Department
of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy,
Shree S.K. Patel College of Pharmaceutical Education and Research, Ganpat University, Gozaria Highway, Mehsana, North Gujarat 384012, India
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27
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Hossain MN, Gao Y, Hatfield MJ, de Avila JM, McClure MC, Du M. Cold exposure impacts DNA methylation patterns in cattle sperm. Front Genet 2024; 15:1346150. [PMID: 38444759 PMCID: PMC10912962 DOI: 10.3389/fgene.2024.1346150] [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: 11/29/2023] [Accepted: 01/23/2024] [Indexed: 03/07/2024] Open
Abstract
DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. Bulls from the Pacific Northwest region of the United States and other northern areas are exposed to extreme cold temperatures during winter. However, the effects of cold exposure on the methylation patterns of bovine sperm remain unclear. To address, DNA methylation profiles of sperm collected during late spring and winter from the same bulls were analyzed using whole genome bisulfite sequencing (WGBS). Bismark (0.22.3) were used for mapping the WGBS reads and R Bioconductor package DSS was used for differential methylation analysis. Cold exposure induced 3,163 differentially methylated cytosines (DMCs) with methylation difference ≥10% and a q-value < 0.05. We identified 438 differentially methylated regions (DMRs) with q-value < 0.05, which overlapped with 186 unique genes. We also identified eight unique differentially methylated genes (DMGs) (Pax6, Macf1, Mest, Ubqln1, Smg9, Ctnnb1, Lsm4, and Peg10) involved in embryonic development, and nine unique DMGs (Prmt6, Nipal1, C21h15orf40, Slc37a3, Fam210a, Raly, Rgs3, Lmbr1, and Gan) involved in osteogenesis. Peg10 and Mest, two paternally expressed imprinted genes, exhibited >50% higher methylation. The differential methylation patterns of six distinct DMRs: Peg10, Smg9 and Mest related to embryonic development and Lmbr1, C21h15orf40 and Prtm6 related to osteogenesis, were assessed by methylation-specific PCR (MS-PCR), which confirmed the existence of variable methylation patterns in those locations across the two seasons. In summary, cold exposure induces differential DNA methylation patterns in genes that appear to affect embryonic development and osteogenesis in the offspring. Our findings suggest the importance of replicating the results of the current study with a larger sample size and exploring the potential of these changes in affecting offspring development.
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Affiliation(s)
- Md Nazmul Hossain
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
- Department of Livestock Production and Management, Faculty of Veterinary, Animal, and Biomedical Sciences, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Yao Gao
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Michael J. Hatfield
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Jeanene M. de Avila
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | | | - Min Du
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
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de Ponthaud C, Abdalla S, Belot MP, Shao X, Penna C, Brouquet A, Bougnères P. Increased CpG methylation at the CDH1 locus in inflamed ileal mucosa of patients with Crohn disease. Clin Epigenetics 2024; 16:28. [PMID: 38355645 PMCID: PMC10865720 DOI: 10.1186/s13148-024-01631-z] [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: 06/20/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND E-cadherin, a major actor of cell adhesion in the intestinal barrier, is encoded by the CDH1 gene associated with susceptibility to Crohn Disease (CD) and colorectal cancer. Since epigenetic mechanisms are suspected to contribute to the multifactorial pathogenesis of CD, we studied CpG methylation at the CDH1 locus. The methylation of the CpG island (CGI) and of the 1st enhancer, two critical regulatory positions, was quantified in surgical specimens of inflamed ileal mucosa and in peripheral blood mononuclear cells (PBMC) of 21 CD patients. Sixteen patients operated on for a non-inflammatory bowel disease, although not normal controls, provided a macroscopically normal ileal mucosa and PBMC for comparison. RESULTS In ileal mucosa, 19/21 (90%) CD patients vs 8/16 control patients (50%) (p < 0.01) had a methylated CDH1 promoter CGI. In PBMC, CD patients with methylated CGI were 11/21 (52%) vs 7/16 controls (44%), respectively. Methylation in the 1st enhancer of CDH1 was also higher in the CD group for each of the studied CpGs and for their average value (45 ± 17% in CD patients vs 36 ± 17% in controls; p < 0.001). Again, methylation was comparable in PBMC. Methylation of CGI and 1st enhancer were not correlated in mucosa or PBMC. CONCLUSIONS Methylation of several CpGs at the CDH1 locus was increased in the inflamed ileal mucosa, not in the PBMC, of CD patients, suggesting the association of CDH1 methylation with ileal inflammation. Longitudinal studies will explore if this increased methylation is a risk marker for colorectal cancer.
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Affiliation(s)
- Charles de Ponthaud
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
- UMR INSERM 1169 and Université Paris Saclay, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Solafah Abdalla
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
- UMR INSERM 1169 and Université Paris Saclay, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Marie-Pierre Belot
- Groupe d'Études sur le Diabète, l'Obésité, la Croissance, GETDOC, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Xiaojian Shao
- Digital Technologies Research Center, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada
| | - Christophe Penna
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Antoine Brouquet
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Pierre Bougnères
- UMR INSERM 1169 and Université Paris Saclay, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France.
- Groupe d'Études sur le Diabète, l'Obésité, la Croissance, GETDOC, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France.
- MIRCEN Institute, CEA Paris-Saclay/site de Fontenay-aux-Roses, Bâtiment 56 PC 103, 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France.
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Vozdova M, Kubickova S, Kopecka V, Pauciullo A, Rubes J. Impact of air pollution from different sources on sperm DNA methylation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-12. [PMID: 38282264 DOI: 10.1080/09603123.2024.2310152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/22/2024] [Indexed: 01/30/2024]
Abstract
Environmental exposure is associated with increased incidence of respiratory and cardiovascular diseases and reduced fertility. Exposure to air pollution can influence gene expression through epigenetic mechanisms. In this study, we analysed gene-specific CpG methylation in spermatozoa of city policemen occupationally exposed to air pollution in two Czech cities differing by sources and composition of the air pollution. In Prague, the pollution is mainly formed by NO2 from heavy traffic. Ostrava is a hotspot of industrial air pollution with high concentrations of particular matter (PM) and benzo[a]pyrene (B[a]P). We performed genome-wide methylation sequencing using the SureSelectXT Human Methyl-Seq system (Agilent Technologies) and next-generation sequencing to reveal differentially methylated CpG sites and regions. We identified differential methylation in the region chr5:662169 - 663376 annotated to genes CEP72 and TPPP. The region was then analysed in sperm DNA from 117 policemen using targeted methylation sequencing, which proved its hypermethylation in sperm of Ostrava policemen.
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Affiliation(s)
- Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Vera Kopecka
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Torino, Italy
| | - Jiri Rubes
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
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Qu Y, Zhang X, Qiao R, Di F, Song Y, Wang J, Ji L, Zhang J, Gu W, Fang Y, Han B, Yang R, Dai L, Ouyang S. Blood FOLR3 methylation dysregulations and heterogeneity in non-small lung cancer highlight its strong associations with lung squamous carcinoma. Respir Res 2024; 25:59. [PMID: 38273401 PMCID: PMC10809478 DOI: 10.1186/s12931-024-02691-8] [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: 09/30/2023] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) accounts for the vast majority of lung cancers. Early detection is crucial to reduce lung cancer-related mortality. Aberrant DNA methylation occurs early during carcinogenesis and can be detected in blood. It is essential to investigate the dysregulated blood methylation markers for early diagnosis of NSCLC. METHODS NSCLC-associated methylation gene folate receptor gamma (FOLR3) was selected from an Illumina 850K array analysis of peripheral blood samples. Mass spectrometry was used for validation in two independent case-control studies (validation I: n = 2548; validation II: n = 3866). Patients with lung squamous carcinoma (LUSC) or lung adenocarcinoma (LUAD), normal controls (NCs) and benign pulmonary nodule (BPN) cases were included. FOLR3 methylations were compared among different populations. Their associations with NSCLC clinical features were investigated. Receiver operating characteristic analyses, Kruskal-Wallis test, Wilcoxon test, logistics regression analysis and nomogram analysis were performed. RESULTS Two CpG sites (CpG_1 and CpG_2) of FOLR3 was significantly lower methylated in NSCLC patients than NCs in the discovery round. In the two validations, both LUSC and LUAD patients presented significant FOLR3 hypomethylations. LUSC patients were highlighted to have significantly lower methylation levels of CpG_1 and CpG_2 than BPN cases and LUAD patients. Both in the two validations, CpG_1 methylation and CpG_2 methylation could discriminate LUSC from NCs well, with areas under the curve (AUCs) of 0.818 and 0.832 in validation I, and 0.789 and 0.780 in validation II. They could also differentiate LUAD from NCs, but with lower efficiency. CpG_1 and CpG_2 methylations could also discriminate LUSC from BPNs well individually in the two validations. With the combined dataset of two validations, the independent associations of age, gender, and FOLR3 methylation with LUSC and LUAD risk were shown and the age-gender-CpG_1 signature could discriminate LUSC and LUAD from NCs and BPNs, with higher efficiency for LUSC. CONCLUSIONS Blood-based FOLR3 hypomethylation was shown in LUSC and LUAD. FOLR3 methylation heterogeneity between LUSC and LUAD highlighted its stronger associations with LUSC. FOLR3 methylation and the age-gender-CpG_1 signature might be novel diagnostic markers for the early detection of NSCLC, especially for LUSC.
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Affiliation(s)
- Yunhui Qu
- Department of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University and the Key Clinical Laboratory of Henan Province, Zhengzhou, 450052, China
| | - Xiuzhi Zhang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, 4500001, China
| | - Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Yakang Song
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Jun Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Longtao Ji
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052, China
| | - Jie Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Yifei Fang
- Department of Respiratory and Sleep Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Rongxi Yang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China.
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, China.
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052, China.
| | - Songyun Ouyang
- Department of Respiratory and Sleep Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Ulschmid CM, Sun MR, Jabbarpour CR, Steward AC, Rivera-González KS, Cao J, Martin AA, Barnes M, Wicklund L, Madrid A, Papale LA, Joseph DB, Vezina CM, Alisch RS, Lipinski RJ. Disruption of DNA methylation-mediated cranial neural crest proliferation and differentiation causes orofacial clefts in mice. Proc Natl Acad Sci U S A 2024; 121:e2317668121. [PMID: 38194455 PMCID: PMC10801837 DOI: 10.1073/pnas.2317668121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/14/2023] [Indexed: 01/11/2024] Open
Abstract
Orofacial clefts of the lip and palate are widely recognized to result from complex gene-environment interactions, but inadequate understanding of environmental risk factors has stymied development of prevention strategies. We interrogated the role of DNA methylation, an environmentally malleable epigenetic mechanism, in orofacial development. Expression of the key DNA methyltransferase enzyme DNMT1 was detected throughout palate morphogenesis in the epithelium and underlying cranial neural crest cell (cNCC) mesenchyme, a highly proliferative multipotent stem cell population that forms orofacial connective tissue. Genetic and pharmacologic manipulations of DNMT activity were then applied to define the tissue- and timing-dependent requirement of DNA methylation in orofacial development. cNCC-specific Dnmt1 inactivation targeting initial palate outgrowth resulted in OFCs, while later targeting during palatal shelf elevation and elongation did not. Conditional Dnmt1 deletion reduced cNCC proliferation and subsequent differentiation trajectory, resulting in attenuated outgrowth of the palatal shelves and altered development of cNCC-derived skeletal elements. Finally, we found that the cellular mechanisms of cleft pathogenesis observed in vivo can be recapitulated by pharmacologically reducing DNA methylation in multipotent cNCCs cultured in vitro. These findings demonstrate that DNA methylation is a crucial epigenetic regulator of cNCC biology, define a critical period of development in which its disruption directly causes OFCs, and provide opportunities to identify environmental influences that contribute to OFC risk.
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Affiliation(s)
- Caden M. Ulschmid
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Miranda R. Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Christopher R. Jabbarpour
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Austin C. Steward
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Kenneth S. Rivera-González
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
- Molecular and Environmental Toxicology Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Jocelyn Cao
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Alexander A. Martin
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Macy Barnes
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Lorena Wicklund
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Andy Madrid
- Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Ligia A. Papale
- Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Diya B. Joseph
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
| | - Chad M. Vezina
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
- Molecular and Environmental Toxicology Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Reid S. Alisch
- Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI53706
- Molecular and Environmental Toxicology Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53706
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Ding Q, Song W, Zhu M, Yu Y, Lin Z, Hu W, Cai J, Zhang Z, Zhang H, Zhou J, Lei W, Zhu YZ. Hydrogen Sulfide and Functional Therapy: Novel Mechanisms from Epigenetics. Antioxid Redox Signal 2024; 40:110-121. [PMID: 37950704 DOI: 10.1089/ars.2023.0425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2023]
Abstract
Hydrogen sulfide (H2S) is a gasotransmitter with significant physiological effects, including anti-inflammatory properties, regulation of oxidative stress, and vasodilation, thus regulating body functions. Functional therapy involves using treatments that target the underlying cause of a disease, rather than simply treating symptoms. Epigenetics refers to changes in gene expression that occur through modifications to DNA, to the proteins that package DNA, or to noncoding RNA mechanisms. Recent research advances suggest that H2S may play a role in epigenetic regulation by altering DNA methylation patterns and regulating histone deacetylases, enzymes that modify histone proteins, or modulating microRNA mechanisms. These critical findings suggest that H2S may be a promising molecule for functional therapy in various diseases where epigenetic modifications are dysregulated. We reviewed the relevant research progress in this area, hoping to provide new insights into the epigenetic mechanisms of H2S. Despite the challenges of clinical use of H2S, future research may lead to the progress of new therapeutic approaches. Antioxid. Redox Signal. 40, 110-121.
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Affiliation(s)
- Qian Ding
- University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wu Song
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China
| | - Menglin Zhu
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China
| | - Yue Yu
- School of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Zhongxiao Lin
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China
| | - Wei Hu
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China
| | - Jianghong Cai
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China
| | - Zhongyi Zhang
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China
| | - Hao Zhang
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China
| | - Junyang Zhou
- Biomedical Science, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Wei Lei
- University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention of Cardiovascular Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yi Zhun Zhu
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau SAR, China
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China
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Zhu L, Zhu C, Jin J, Wang J, Zhao X, Yang R. Identification of an association between coronary heart disease and ITGB2 methylation in peripheral blood by a case-control study. Clin Chim Acta 2024; 552:117627. [PMID: 37923103 DOI: 10.1016/j.cca.2023.117627] [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: 05/11/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Blood DNA methylation was associated with coronary heart disease (CHD) risk in Caucasians. We investigated the association between DNA methylation in peripheral blood at the reported loci and CHD in the Chinese population. METHODS The integrin subunit beta 2 (ITGB2) gene was identified in 196 CHD cases and 184 controls, and its methylation level was determined by mass spectrometry. Logistic regression was used to assess the association. RESULTS Hypomethylation of ITGB2 was significantly associated with heart failure CHD and NYHA Ⅰ&Ⅱ CHD patients with minor to medium cardiac function impairment (ITGB2_CpG_11/cg08422803, OR per -10 % methylation = 1.15 and 1.16; p = 0.012 and 0.018 by Bonferroni correction, respectively). Hypomethylation of ITGB2_CpG_11/cg08422803 was a risk factor for CHD in people < 65 years and males (p < 0.05 after Bonferroni correction). The combination of ITGB2 methylation and conventional CHD risk factors could efficiently discriminate CHD, heart failure CHD, NYHA I&II CHD, and myocardial infarction CHD patients from controls (AUC = 0.78, 0.81, 0.80, and 0.81, respectively). CONCLUSION Blood-based ITGB2 methylation has the potential as a biomarker for CHD. The combination of ITGB2 methylation and conventional CHD risk factors may improve the risk assessment and detection of CHD.
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Affiliation(s)
- Liya Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Kunshan Center for Disease Control and Prevention, Kunshan, 215300, China
| | - Chao Zhu
- Department of Cardiology, Beijing Friendship Hospital, Capital Medical University, 95 Yong'an Road, West District, Beijing, 100050, China
| | - Jialie Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jinxin Wang
- Department of Cardiology, the Second Medical Center, Chinese PLA General Hospital, 100853 Beijing, China
| | - Xiaojing Zhao
- Military translational medicine lab, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100853, China; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China.
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Wang PW, Huang YF, Wang CH, Fang LJ, Chen ML. Prenatal to preschool exposure of nonylphenol and bisphenol A exposure and neurodevelopment in young children. Pediatr Neonatol 2024; 65:76-84. [PMID: 37679260 DOI: 10.1016/j.pedneo.2023.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Nonylphenol (NP) and bisphenol A (BPA) are produced in large quantities worldwide as multipurpose agents. However, studies on relations between NP and BPA exposure and childhood neurodevelopment are few, and the results are inconsistent. This study aimed to investigate associations between prenatal and early childhood NP and BPA exposure and neurodevelopment in mother-child pairs. METHODS Pregnant women at 27-38 weeks' gestation were recruited, as were children 2-3 years of age (n = 94) and 4-6 years of age (n = 56) years. Urine was collected to assess NP and BPA exposure. Bayley Scales of Infant and Toddler Development (3rd edition; Bayley-III), Wechsler Preschool and Primary Scale of Intelligence (4th edition), and the Full Scale Intelligence Quotient (WPPSI-IV-FSIQ) were used to assess the neurodevelopment of the children. RESULTS The detection rate and concentration of NP and BPA in the urine of children 4-6 years old were higher than in those 2-3 years old. Children were divided into a high concentration group (3rd tertile) and a reference group (1st and 2nd tertiles) based on natural log-transformed urine concentration of NP and BPA. Girls' Bayley-III motor scores in the high concentration group were higher than those of the BPA reference group of urine of mothers (β = 6.85, 95% confidence interval [CI]: 1.58-12.13). Boys' FSIQ in the higher concentration group were significantly lower than those in children 2-3 years old in the NP reference group (β = -11.29, 95% CI: -18.62 to -3.96) (all, p < 0.05). CONCLUSIONS Prenatal and childhood exposure to NP and BPA may have different effects on the neurodevelopment of young children, and there are no consistent effects between boys and girls.
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Affiliation(s)
- Pei-Wei Wang
- Institute of Environmental and Occupational Health Sciences, School of Medicine, Yangming Campus, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Pediatrics, Heping Fuyou Branch, Taipei City Hospital, Taipei, Taiwan
| | - Yu-Fang Huang
- Institute of Environmental and Occupational Health Sciences, School of Medicine, Yangming Campus, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Chung-Hao Wang
- Department of Pediatrics, Heping Fuyou Branch, Taipei City Hospital, Taipei, Taiwan
| | - Li-Jung Fang
- Department of Pediatrics, Heping Fuyou Branch, Taipei City Hospital, Taipei, Taiwan
| | - Mei-Lien Chen
- Institute of Environmental and Occupational Health Sciences, School of Medicine, Yangming Campus, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Arai K, Qi H, Inoue-Murayama M. Age estimation of captive Asian elephants (Elephas maximus) based on DNA methylation: An exploratory analysis using methylation-sensitive high-resolution melting (MS-HRM). PLoS One 2023; 18:e0294994. [PMID: 38079426 PMCID: PMC10712859 DOI: 10.1371/journal.pone.0294994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Age is an important parameter for bettering the understanding of biodemographic trends-development, survival, reproduction and environmental effects-critical for conservation. However, current age estimation methods are challenging to apply to many species, and no standardised technique has been adopted yet. This study examined the potential use of methylation-sensitive high-resolution melting (MS-HRM), a labour-, time-, and cost-effective method to estimate chronological age from DNA methylation in Asian elephants (Elephas maximus). The objective of this study was to investigate the accuracy and validation of MS-HRM use for age determination in long-lived species, such as Asian elephants. The average lifespan of Asian elephants is between 50-70 years but some have been known to survive for more than 80 years. DNA was extracted from 53 blood samples of captive Asian elephants across 11 zoos in Japan, with known ages ranging from a few months to 65 years. Methylation rates of two candidate age-related epigenetic genes, RALYL and TET2, were significantly correlated with chronological age. Finally, we established a linear, unisex age estimation model with a mean absolute error (MAE) of 7.36 years. This exploratory study suggests an avenue to further explore MS-HRM as an alternative method to estimate the chronological age of Asian elephants.
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Affiliation(s)
- Kana Arai
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
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Tuminello S, Nguyen E, Durmus N, Alptekin R, Yilmaz M, Crisanti MC, Snuderl M, Chen Y, Shao Y, Reibman J, Taioli E, Arslan AA. World Trade Center Exposure, DNA Methylation Changes, and Cancer: A Review of Current Evidence. EPIGENOMES 2023; 7:31. [PMID: 38131903 PMCID: PMC10742700 DOI: 10.3390/epigenomes7040031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/22/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction: Known carcinogens in the dust and fumes from the destruction of the World Trade Center (WTC) towers on 9 November 2001 included metals, asbestos, and organic pollutants, which have been shown to modify epigenetic status. Epigenome-wide association analyses (EWAS) using uniform (Illumina) methodology have identified novel epigenetic profiles of WTC exposure. Methods: We reviewed all published data, comparing differentially methylated gene profiles identified in the prior EWAS studies of WTC exposure. This included DNA methylation changes in blood-derived DNA from cases of cancer-free "Survivors" and those with breast cancer, as well as tissue-derived DNA from "Responders" with prostate cancer. Emerging molecular pathways related to the observed DNA methylation changes in WTC-exposed groups were explored and summarized. Results: WTC dust exposure appears to be associated with DNA methylation changes across the genome. Notably, WTC dust exposure appears to be associated with increased global DNA methylation; direct dysregulation of cancer genes and pathways, including inflammation and immune system dysregulation; and endocrine system disruption, as well as disruption of cholesterol homeostasis and lipid metabolism. Conclusion: WTC dust exposure appears to be associated with biologically meaningful DNA methylation changes, with implications for carcinogenesis and development of other chronic diseases.
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Affiliation(s)
- Stephanie Tuminello
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
| | - Emelie Nguyen
- Institute for Translational Epidemiology, Icahn School of Medicine at Mount Sinai, New York, NY 10016, USA
| | - Nedim Durmus
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ramazan Alptekin
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Muhammed Yilmaz
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Yu Chen
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Yongzhao Shao
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Joan Reibman
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
- Division of Environmental Medicine, Department of Medicine, NYU Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Emanuela Taioli
- Institute for Translational Epidemiology, Icahn School of Medicine at Mount Sinai, New York, NY 10016, USA
| | - Alan A. Arslan
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY 10016, USA
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Watkins SH, Testa C, Simpkin AJ, Smith GD, Coull B, De Vivo I, Tilling K, Waterman PD, Chen JT, Diez-Roux AV, Krieger N, Suderman M, Relton C. An epigenome-wide analysis of DNA methylation, racialized and economic inequities, and air pollution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570610. [PMID: 38105971 PMCID: PMC10723401 DOI: 10.1101/2023.12.07.570610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Importance DNA methylation (DNAm) provides a plausible mechanism by which adverse exposures become embodied and contribute to health inequities, due to its role in genome regulation and responsiveness to social and biophysical exposures tied to societal context. However, scant epigenome-wide association studies (EWAS) have included structural and lifecourse measures of exposure, especially in relation to structural discrimination. Objective Our study tests the hypothesis that DNAm is a mechanism by which racial discrimination, economic adversity, and air pollution become biologically embodied. Design A series of cross-sectional EWAS, conducted in My Body My Story (MBMS, biological specimens collected 2008-2010, DNAm assayed in 2021); and the Multi Ethnic Study of Atherosclerosis (MESA; biological specimens collected 2010-2012, DNAm assayed in 2012-2013); using new georeferenced social exposure data for both studies (generated in 2022). Setting MBMS was recruited from four community health centers in Boston; MESA was recruited from four field sites in: Baltimore, MD; Forsyth County, NC; New York City, NY; and St. Paul, MN. Participants Two population-based samples of US-born Black non-Hispanic (Black NH), white non-Hispanic (white NH), and Hispanic individuals (MBMS; n=224 Black NH and 69 white NH) and (MESA; n=229 Black NH, n=555 white NH and n=191 Hispanic). Exposures Eight social exposures encompassing racial discrimination, economic adversity, and air pollution. Main outcome Genome-wide changes in DNAm, as measured using the Illumina EPIC BeadChip (MBMS; using frozen blood spots) and Illumina 450k BeadChip (MESA; using purified monocytes). Our hypothesis was formulated after data collection. Results We observed the strongest associations with traffic-related air pollution (measured via black carbon and nitrogen oxides exposure), with evidence from both studies suggesting that air pollution exposure may induce epigenetic changes related to inflammatory processes. We also found suggestive associations of DNAm variation with measures of structural racial discrimination (e.g., for Black NH participants, born in a Jim Crow state; adult exposure to racialized economic residential segregation) situated in genes with plausible links to effects on health. Conclusions and Relevance Overall, this work suggests that DNAm is a biological mechanism through which structural racism and air pollution become embodied and may lead to health inequities.
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Affiliation(s)
- Sarah Holmes Watkins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christian Testa
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Andrew J. Simpkin
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
| | - George Davey Smith
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Brent Coull
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Immaculata De Vivo
- Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kate Tilling
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Pamela D. Waterman
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Jarvis T. Chen
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Ana V. Diez-Roux
- Department of Epidemiology and Biostatistics and Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, USA
| | - Nancy Krieger
- Department of Social and Behavioral Sciences, Harvard T H Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Matthew Suderman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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Dou JF, Schmidt RJ, Volk HE, Nitta MM, Feinberg JI, Newschaffer CJ, Croen LA, Hertz-Picciotto I, Fallin MD, Bakulski KM. Exposure to heavy metals in utero and autism spectrum disorder at age 3: A meta-analysis of two longitudinal cohorts of siblings of children with autism. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.21.23298827. [PMID: 38045240 PMCID: PMC10690342 DOI: 10.1101/2023.11.21.23298827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Background Autism spectrum disorder (ASD) is a prevalent and heterogeneous neurodevelopmental disorder. Risk is attributed to genetic and prenatal environmental factors, though the environmental agents are incompletely characterized. Methods In Early Autism Risk Longitudinal Investigation (EARLI) and Markers of Autism Risk in Babies Learning Early Signs (MARBLES), two pregnancy cohorts of siblings of children with ASD, maternal urinary metals concentrations at two time points during pregnancy were measured using inductively coupled plasma mass spectrometry. At age three, clinicians assessed ASD with DSM-5 criteria. Using multivariable log binomial regression, we examined each metal for association with ASD status, adjusting for gestational age at urine sampling, child sex, maternal age, and maternal education, and meta-analyzed across the two cohorts. Results In EARLI (n=170) 17.6% of children were diagnosed with ASD, and an additional 43.5% were classified as having other non-neurotypical development (Non-TD). In MARBLES (n=156), 22.7% were diagnosed with ASD, while an additional 11.5% had Non-TD. In earlier pregnancy metals measures, having cadmium concentration over the level of detection was associated with 1.78 (1.19, 2.67) times higher risk of ASD, and 1.43 (1.06, 1.92) times higher risk of Non-TD. A doubling of early pregnancy cesium concentration was marginally associated with 1.81 (0.95, 3.42) times higher risk of ASD, and 1.58 (0.95, 2.63) times higher risk of Non-TD. Conclusion Exposure in utero to elevated levels of cadmium and cesium, as measured in maternal urine collected during pregnancy, was associated with increased risk of developing ASD.
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Affiliation(s)
- John F. Dou
- University of Michigan, Ann Arbor, Michigan, USA
| | | | | | | | | | | | - Lisa A. Croen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
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Bakulski KM, Blostein F, London SJ. Linking Prenatal Environmental Exposures to Lifetime Health with Epigenome-Wide Association Studies: State-of-the-Science Review and Future Recommendations. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:126001. [PMID: 38048101 PMCID: PMC10695268 DOI: 10.1289/ehp12956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND The prenatal environment influences lifetime health; epigenetic mechanisms likely predominate. In 2016, the first international consortium paper on cigarette smoking during pregnancy and offspring DNA methylation identified extensive, reproducible exposure signals. This finding raised expectations for epigenome-wide association studies (EWAS) of other exposures. OBJECTIVE We review the current state-of-the-science for DNA methylation associations across prenatal exposures in humans and provide future recommendations. METHODS We reviewed 134 prenatal environmental EWAS of DNA methylation in newborns, focusing on 51 epidemiological studies with meta-analysis or replication testing. Exposures spanned cigarette smoking, alcohol consumption, air pollution, dietary factors, psychosocial stress, metals, other chemicals, and other exogenous factors. Of the reproducible DNA methylation signatures, we examined implementation as exposure biomarkers. RESULTS Only 19 (14%) of these prenatal EWAS were conducted in cohorts of 1,000 or more individuals, reflecting the still early stage of the field. To date, the largest perinatal EWAS sample size was 6,685 participants. For comparison, the most recent genome-wide association study for birth weight included more than 300,000 individuals. Replication, at some level, was successful with exposures to cigarette smoking, folate, dietary glycemic index, particulate matter with aerodynamic diameter < 10 μ m and < 2.5 μ m , nitrogen dioxide, mercury, cadmium, arsenic, electronic waste, PFAS, and DDT. Reproducible effects of a more limited set of prenatal exposures (smoking, folate) enabled robust methylation biomarker creation. DISCUSSION Current evidence demonstrates the scientific premise for reproducible DNA methylation exposure signatures. Better powered EWAS could identify signatures across many exposures and enable comprehensive biomarker development. Whether methylation biomarkers of exposures themselves cause health effects remains unclear. We expect that larger EWAS with enhanced coverage of epigenome and exposome, along with improved single-cell technologies and evolving methods for integrative multi-omics analyses and causal inference, will expand mechanistic understanding of causal links between environmental exposures, the epigenome, and health outcomes throughout the life course. https://doi.org/10.1289/EHP12956.
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Affiliation(s)
| | - Freida Blostein
- University of Michigan, Ann Arbor, Michigan, USA
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephanie J. London
- National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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Jackson P, Kempf MC, Goodin BR, A. Hidalgo B, Aroke EN. Neighborhood Environment and Epigenetic Age: A Scoping Review. West J Nurs Res 2023; 45:1139-1149. [PMID: 37902222 PMCID: PMC10748459 DOI: 10.1177/01939459231208304] [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] [Indexed: 10/31/2023]
Abstract
BACKGROUND Interest in how the neighborhood environment impacts age-related health conditions has been increasing for decades. Epigenetic changes are environmentally derived modifications to the genome that alter the way genes function-thus altering health status. Epigenetic age, a biomarker for biological age, has been shown to be a useful predictor of several age-related health conditions. Consequently, its relation to the neighborhood environment has been the focus of a growing body of literature. OBJECTIVE We aimed to describe the scope of the evidence on the relationship between neighborhood environmental characteristics and epigenetic age. METHODS Using scoping review following methods established by Arksey and O'Malley, we first defined our research questions and searched the literature in PubMed, PsycINFO, and EMBASE. Next, we selected the literature to be included, and finally, we analyzed and summarized the information. RESULTS Nine articles met the inclusion criteria. Most studies examined deprivation as the neighborhood characteristic of interest. While all studies were observational in design, the articles included diverse participants, including men and women, adults and children, and multiple ethnicities. Results demonstrated a relationship between the neighborhood environment and epigenetic age, whether the characteristic of interest is socioeconomic or physical. CONCLUSIONS Overall, studies concluded there was a relationship between neighborhood characteristics and epigenetic age, whether the characteristic of interest was socioeconomic or physical. However, findings varied based on how the neighborhood characteristic and/or epigenetic age was measured. Furthermore, a paucity of investigations on physical characteristics was noticeable and warrants increased attention.
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Affiliation(s)
- Pamela Jackson
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Burel R. Goodin
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Bertha A. Hidalgo
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Edwin N. Aroke
- School of Nursing, University of Alabama at Birmingham, Birmingham, AL, USA
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Chen J, Gatev E, Everson T, Conneely KN, Koen N, Epstein MP, Kobor MS, Zar HJ, Stein DJ, Hüls A. Pruning and thresholding approach for methylation risk scores in multi-ancestry populations. Epigenetics 2023; 18:2187172. [PMID: 36908043 PMCID: PMC10026878 DOI: 10.1080/15592294.2023.2187172] [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] [Indexed: 03/14/2023] Open
Abstract
Recent efforts have focused on developing methylation risk scores (MRS), a weighted sum of the individual's DNA methylation (DNAm) values of pre-selected CpG sites. Most of the current MRS approaches that utilize Epigenome-wide association studies (EWAS) summary statistics only include genome-wide significant CpG sites and do not consider co-methylation. New methods that relax the p-value threshold to include more CpG sites and account for the inter-correlation of DNAm might improve the predictive performance of MRS. We paired informed co-methylation pruning with P-value thresholding to generate pruning and thresholding (P+T) MRS and evaluated its performance among multi-ancestry populations. Through simulation studies and real data analyses, we demonstrated that pruning provides an improvement over simple thresholding methods for prediction of phenotypes. We demonstrated that European-derived summary statistics can be used to develop P+T MRS among other populations such as African populations. However, the prediction accuracy of P+T MRS may differ across multi-ancestry population due to environmental/cultural/social differences.
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Affiliation(s)
- Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA USA
| | - Evan Gatev
- Institute of Molecular Biology "Acad. Roumen Tsanev", Sofia, Bulgaria
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Todd Everson
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA USA
| | - Nastassja Koen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Michael P Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA USA
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Heather J Zar
- Department of Pediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
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Serdarevic F, Luo M, Karabegović I, Binter AC, Alemany S, Mutzel R, Guxens M, Bustamante M, Hajdarpasic A, White T, Felix JF, Cecil CAM, Tiemeier H. DNA methylation at birth and fine motor ability in childhood: an epigenome-wide association study with replication. Epigenetics 2023; 18:2207253. [PMID: 37139702 PMCID: PMC10161945 DOI: 10.1080/15592294.2023.2207253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Lower fine motor performance in childhood has been associated with poorer cognitive development and neurodevelopmental conditions such as autism spectrum disorder, yet, biological underpinnings remain unclear. DNA methylation (DNAm), an essential process for healthy neurodevelopment, is a key molecular system of interest. In this study, we conducted the first epigenome-wide association study of neonatal DNAm with childhood fine motor ability and further examined the replicability of epigenetic markers in an independent cohort. The discovery study was embedded in Generation R, a large population-based prospective cohort, including a subsample of 924 ~ 1026 European-ancestry singletons with available data on DNAm in cord blood and fine motor ability at a mean (SD) age of 9.8 (0.4) years. Fine motor ability was measured using a finger-tapping test (3 subtests including left-, right-hand and bimanual), one of the most frequently used neuropsychological instruments of fine motor function. The replication study comprised 326 children with a mean (SD) age of 6.8 (0.4) years from an independent cohort, the INfancia Medio Ambiente (INMA) study. Four CpG sites at birth were prospectively associated with childhood fine motor ability after genome-wide correction. Of these, one CpG (cg07783800 in GNG4) was replicated in INMA, showing that lower levels of methylation at this site were associated with lower fine motor performance in both cohorts. GNG4 is highly expressed in the brain and has been implicated in cognitive decline. Our findings support a prospective, reproducible association between DNAm at birth and fine motor ability in childhood, pointing to GNG4 methylation at birth as a potential biomarker of fine motor ability.
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Affiliation(s)
- Fadila Serdarevic
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Centre, Rotterdam, the Netherlands
- Department of Social and Behavioral Science, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Sarajevo Medical School, Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
| | - Mannan Luo
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Centre, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, the Netherlands
| | - Irma Karabegović
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Anne-Claire Binter
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Alemany
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Centre, Rotterdam, the Netherlands
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
| | - Ryan Mutzel
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Centre, Rotterdam, the Netherlands
| | - Monica Guxens
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Centre, Rotterdam, the Netherlands
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Aida Hajdarpasic
- Department of Medical Biology, and Genetics, Sarajevo Medical School, Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
| | - Tonya White
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Centre, Rotterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Centre, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Centre, Rotterdam, the Netherlands
- Department of Social and Behavioral Science, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Kim S, Qin Y, Park HJ, Yue M, Xu Z, Forno E, Chen W, Celedón JC. Methyl-TWAS: A powerful method for in silico transcriptome-wide association studies (TWAS) using long-range DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566586. [PMID: 38014125 PMCID: PMC10680683 DOI: 10.1101/2023.11.10.566586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
In silico transcriptome-wide association studies (TWAS) are commonly used to test whether expression of specific genes is linked to a complex trait. However, genotype-based in silico TWAS such as PrediXcan, exhibit low prediction accuracy for a majority of genes because genotypic data lack tissue- and disease-specificity and are not affected by the environment. Because methylation is tissue-specific and, like gene expression, can be modified by environment or disease status, methylation should predict gene expression with more accuracy than SNPs. Therefore, we propose Methyl-TWAS, the first approach that utilizes long-range methylation markers to impute gene expression for in silico TWAS through penalized regression. Methyl-TWAS 1) predicts epigenetically regulated/associated expression (eGReX), which incorporates tissue-specific expression and both genetically- (GReX) and environmentally-regulated expression to identify differentially expressed genes (DEGs) that could not be identified by genotype-based methods; and 2) incorporates both cis- and trans- CpGs, including various regulatory regions to identify DEGs that would be missed using cis- methylation only. Methyl-TWAS outperforms PrediXcan and two other methods in imputing gene expression in the nasal epithelium, particularly for immunity-related genes and DEGs in atopic asthma. Methyl-TWAS identified 3,681 (85.2%) of the 4,316 DEGs identified in a previous TWAS of atopic asthma using measured expression, while PrediXcan could not identify any gene. Methyl-TWAS also outperforms PrediXcan for expression imputation as well as in silico TWAS in white blood cells. Methyl-TWAS is a valuable tool for in silico TWAS, leveraging a growing body of publicly available genome-wide DNA methylation data for a variety of human tissues.
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Affiliation(s)
- Soyeon Kim
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yidi Qin
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hyun Jung Park
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Molin Yue
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhongli Xu
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juan C. Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
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Ho PJ, Khng AJ, Tan BKT, Lim GH, Tan SM, Tan VKM, Tan RSYC, Lim EH, Iau PTC, Chew YJ, Lim YY, Hartman M, Tan EY, Li J. Alterations to DNA methylation patterns induced by chemotherapy treatment are associated with negative impacts on the olfactory pathway. Breast Cancer Res 2023; 25:136. [PMID: 37932858 PMCID: PMC10626732 DOI: 10.1186/s13058-023-01730-4] [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: 06/05/2023] [Accepted: 10/15/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Exposure to cytotoxic chemotherapy treatment may alter DNA methylation (DNAm) in breast cancer patients. METHODS We performed DNAm analysis in 125 breast cancer patients with blood drawn before and after chemotherapy, using the Illumina MethylationEPIC array. DNAm changes of 588,798 individual CpGs (including 41,207 promoter regions) were evaluated using linear regression models adjusted for monocyte proportion. Gene set enrichment analyses (GSEA) were conducted to identify key Gene Ontology (GO) biological processes or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with chemotherapy. Results were validated in a separate cohort of breast cancer patients who were treated (n = 1273) and not treated (n = 872) by chemotherapy (1808 blood, 337 saliva). RESULTS A total of 141 differentially methylated CpGs and 11 promoters were significantly associated with chemotherapy after multiple testing corrections in both the paired sample and single time point analyses. GSEA of promoter regions (pre-ranked by test statistics) identified six suppressed biological processes (p < 4.67e-8) related to sensory perception and detection of chemical stimuli, including smell perception (GO:0007606, GO:0007608, GO:0009593, GO:0050906, GO:0050907, and GO:0050911). The same six biological processes were significantly suppressed in the validation dataset (p < 9.02e-14). The KEGG pathway olfactory transduction (hsa04740) was also found to be significantly suppressed (ppaired-samples = 1.72e-9, psingle-timepoint-blood = 2.03e-15 and psingle-timepoint-saliva = 7.52e-56). CONCLUSION The enrichment of imprinted genes within biological processes and pathways suggests a biological mechanism by which chemotherapy could affect the perception of smell.
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Affiliation(s)
- Peh Joo Ho
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Republic of Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Republic of Singapore
| | - Alexis Jiaying Khng
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Benita Kiat-Tee Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore, Republic of Singapore
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
- Department of General Surgery, Sengkang General Hospital, Singapore, Republic of Singapore
| | - Geok Hoon Lim
- KK Breast Department, KK Women's and Children's Hospital, Singapore, 229899, Republic of Singapore
| | - Su-Ming Tan
- Division of Breast Surgery, Changi General Hospital, Singapore, Republic of Singapore
| | - Veronique Kiak Mien Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore, Republic of Singapore
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Ryan Shea Ying Cong Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
- Oncology Academic Programme, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Elaine Hsuen Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Philip Tsau-Choong Iau
- Department of Surgery, University Surgical Cluster, National University Health System, Singapore, 119228, Singapore
- Department of General Surgery, Ng Teng Fong General Hospital, 1 Jurong East St 21, Singapore, 609606, Republic of Singapore
| | - Ying Jia Chew
- Department of Surgery, University Surgical Cluster, National University Health System, Singapore, 119228, Singapore
- Department of General Surgery, Ng Teng Fong General Hospital, 1 Jurong East St 21, Singapore, 609606, Republic of Singapore
| | - Yi Ying Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Republic of Singapore
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Republic of Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Republic of Singapore
- Department of Surgery, University Surgical Cluster, National University Health System, Singapore, 119228, Singapore
| | - Ern Yu Tan
- Department of General Surgery, Tan Tock Seng Hospital, Singapore, 308433, Republic of Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore
| | - Jingmei Li
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore.
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Republic of Singapore.
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Fleckhaus J, Bugert P, Al-Rashedi NAM, Rothschild MA. Investigation of the impact of biogeographic ancestry on DNA methylation based age predictions comparing a Middle East and a Central European population. Forensic Sci Int Genet 2023; 67:102923. [PMID: 37598451 DOI: 10.1016/j.fsigen.2023.102923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/10/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023]
Abstract
DNA methylation based age prediction is a new method in the toolbox of forensic genetics. Typically, the method is applied in the course of police investigation e.g. to predict the age of an unknown person that has left a biological trace at a crime scene. The method can also be used to answer other forensic questions, for example to estimate the age of unknown human bodies in the course of the identification process. In the present study, we tested for a potential impact of biogeographic ancestry (BGA) on age predictions using five age dependent methylated CpG sites within the genetic regions of ELOVL2, MIR29B2CHG, FHL2, KLF14 and TRIM59. We collected 102 blood samples each from donors living in Iraq, Middle East (ME) and Germany, Central Europe (EU). Both sample sets were matched in sex and age ranging from 18 to 68 years with exactly one male and female sample per year of age. All samples were analyzed by bisulfite pyrosequencing applying a multiplex pre-amplification strategy based on a single input of 35 ng converted DNA in the PCR. For the CpGs in MIR29B2CHG, FHL2 and KLF14, we observed significantly different methylation levels between the two populations. While we were able to train two highly accurate prediction models for the respective population with mean absolute deviations between predicted and actual ages (MAD) of 3.34 years for the ME model, and 2.72 years for the EU model, we found an absolute prediction difference between the two population specific models of more than 4 years. A combined model for both populations compensated the methylation difference between the two populations, providing MADs of prediction of only 3.81 years for ME and 3.31 years for EU samples. In total, the results of the present study strongly support the benefit of BGA information for more reliable methylation based age predictions.
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Affiliation(s)
- J Fleckhaus
- Institute of Legal Medicine, Medical Faculty, University Hospital and University of Cologne, Melatenguertel 60-62, D-50823 Cologne, Germany.
| | - P Bugert
- Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service of Baden-Württemberg - Hessen gGmbH, Mannheim, Germany
| | - N A M Al-Rashedi
- Department of Biology, College of Science, Al Muthanna University, Samawah, Iraq
| | - M A Rothschild
- Institute of Legal Medicine, Medical Faculty, University Hospital and University of Cologne, Melatenguertel 60-62, D-50823 Cologne, Germany
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Gryzinska M, Kot B, Dudzinska E, Biernasiuk A, Jakubczak A, Malm A, Andraszek K. Changes in the Level of DNA Methylation in Candida albicans under the Influence of Physical and Chemical Factors. Int J Mol Sci 2023; 24:15873. [PMID: 37958861 PMCID: PMC10647513 DOI: 10.3390/ijms242115873] [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: 09/13/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
The effects of physical factors such as radiation (electromagnetic, microwave, infrared, laser, UVC, and X-ray) and high temperature, as well as chemical factors (controlled atmosphere) on the level of global DNA cytosine methylation in C. albicans ATCC 10231 cells were investigated. Prolonged exposure to each type of radiation significantly increased the DNA methylation level. In addition, the global methylation level in C. albicans cells increased with the incubation temperature. An increase in the percentage of methylated DNA was also noted in C. albicans cells cultured in an atmosphere with reduced O2. In contrast, in an atmosphere containing more than 3% CO2 and in anaerobic conditions, the DNA methylation level decreased relative to the control. This study showed that prolonged exposure to various types of radiation and high temperature as well as reduced O2 in the atmosphere caused a significant increase in the global DNA methylation level. This is most likely a response protecting DNA against damage, which at the same time can lead to epigenetic disorders, and in consequence can adversely affect the functioning of the organism.
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Affiliation(s)
- Magdalena Gryzinska
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland;
| | - Barbara Kot
- Institute of Biological Sciences, University of Siedlce, 08-110 Siedlce, Poland
| | - Ewa Dudzinska
- Department of Dietetics and Nutrition Education, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Anna Biernasiuk
- Chair and Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.M.)
| | - Andrzej Jakubczak
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland;
| | - Anna Malm
- Chair and Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.B.); (A.M.)
| | - Katarzyna Andraszek
- Institute of Animal Science and Fisheries, University of Siedlce, 08–110 Siedlce, Poland;
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47
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Harvey J, Pishva E, Chouliaras L, Lunnon K. Elucidating distinct molecular signatures of Lewy body dementias. Neurobiol Dis 2023; 188:106337. [PMID: 37918758 DOI: 10.1016/j.nbd.2023.106337] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/15/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023] Open
Abstract
Dementia with Lewy bodies and Parkinson's disease dementia are common neurodegenerative diseases that share similar neuropathological profiles and spectra of clinical symptoms but are primarily differentiated by the order in which symptoms manifest. The question of whether a distinct molecular pathological profile could distinguish these disorders is yet to be answered. However, in recent years, studies have begun to investigate genomic, epigenomic, transcriptomic and proteomic differences that may differentiate these disorders, providing novel insights in to disease etiology. In this review, we present an overview of the clinical and pathological hallmarks of Lewy body dementias before summarizing relevant research into genetic, epigenetic, transcriptional and protein signatures in these diseases, with a particular interest in those resolving "omic" level changes. We conclude by suggesting future research directions to address current gaps and questions present within the field.
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Affiliation(s)
- Joshua Harvey
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - Leonidas Chouliaras
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, UK; Specialist Dementia and Frailty Service, Essex Partnership University NHS Foundation Trust, Epping, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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48
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Marson F, Zampieri M, Verdone L, Bacalini MG, Ravaioli F, Morandi L, Chiarella SG, Vetriani V, Venditti S, Caserta M, Raffone A, Dotan Ben-Soussan T, Reale A. Quadrato Motor Training (QMT) is associated with DNA methylation changes at DNA repeats: A pilot study. PLoS One 2023; 18:e0293199. [PMID: 37878626 PMCID: PMC10599555 DOI: 10.1371/journal.pone.0293199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/07/2023] [Indexed: 10/27/2023] Open
Abstract
The control of non-coding repeated DNA by DNA methylation plays an important role in genomic stability, contributing to health and healthy aging. Mind-body practices can elicit psychophysical wellbeing via epigenetic mechanisms, including DNA methylation. However, in this context the effects of movement meditations have rarely been examined. Consequently, the current study investigates the effects of a specifically structured movement meditation, called the Quadrato Motor Training (QMT) on psychophysical wellbeing and on the methylation level of repeated sequences. An 8-week daily QMT program was administered to healthy women aged 40-60 years and compared with a passive control group matched for gender and age. Psychological well-being was assessed within both groups by using self-reporting scales, including the Meaning in Life Questionnaire [MLQ] and Psychological Wellbeing Scale [PWB]). DNA methylation profiles of repeated sequences (ribosomal DNA, LINE-1 and Alu) were determined in saliva samples by deep-sequencing. In contrast to controls, the QMT group exhibited increased Search for Meaning, decreased Presence of Meaning and increased Positive Relations, suggesting that QMT may lessen the automatic patterns of thinking. In the QMT group, we also found site-specific significant methylation variations in ribosomal DNA and LINE-1 repeats, consistent with increased genome stability. Finally, the correlations found between changes in methylation and psychometric indices (MLQ and PWB) suggest that the observed epigenetic and psychological changes are interrelated. Collectively, the current results indicate that QMT may improve psychophysical health trajectories by influencing the DNA methylation of specific repetitive sequences.
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Affiliation(s)
- Fabio Marson
- Research Institute for Neuroscience, Education and Didactics, Fondazione Patrizio Paoletti, Assisi, Italy
- Neuroimaging Laboratory, Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Loredana Verdone
- CNR Institute of Molecular Biology and Pathology, National Council of Research (CNR), Rome, Italy
| | - Maria Giulia Bacalini
- Brain Aging Laboratory, IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Francesco Ravaioli
- Dep. of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Luca Morandi
- Dep. of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- Functional and Molecular Neuroimaging Unit, IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Salvatore Gaetano Chiarella
- Institute of Sciences and Technologies of Cognition (ISTC), National Council of Research (CNR), Rome, Italy
- Department of Psychology, Sapienza University of Rome, Rome, Italy
| | - Valerio Vetriani
- Dept. of Biology and biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Sabrina Venditti
- Dept. of Biology and biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Micaela Caserta
- CNR Institute of Molecular Biology and Pathology, National Council of Research (CNR), Rome, Italy
| | - Antonino Raffone
- Department of Psychology, Sapienza University of Rome, Rome, Italy
| | - Tal Dotan Ben-Soussan
- Research Institute for Neuroscience, Education and Didactics, Fondazione Patrizio Paoletti, Assisi, Italy
| | - Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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49
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Mirisola MG. The Nutriepigenome. Genes (Basel) 2023; 14:1997. [PMID: 38002940 PMCID: PMC10671240 DOI: 10.3390/genes14111997] [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: 07/31/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Unlike genetic changes, epigenetics modulates gene expression without stable modification of the genome. Even though all cells, including sperm and egg, have an epigenome pattern, most of these modifications occur during lifetime and interestingly, some of them, are reversible. Lifestyle and especially nutrients as well as diet regimens are presently gaining importance due to their ability to affect the epigenome. On the other hand, since the epigenome profoundly affects gene expression profile it can be speculated that the epigenome could modulate individual response to nutrients. Recent years have thus seen growing interest on nutrients, macronutrients ratio and diet regimens capable to affect the epigenetic pattern. In fact, while genetic alterations are mostly detrimental at the individual level, reshaping the epigenome may be a feasible strategy to positively counteract the detrimental effect of aging. Here, I review nutrient consumption and diet regimens as a possible strategy to counteract aging-driven epigenome derangement.
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Affiliation(s)
- Mario G Mirisola
- STeBiCeF Department, Università di Palermo, Building 16, Viale delle Scienze, 90128 Palermo, Italy
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50
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Filipowicz G, Wajda A, Stypińska B, Kmiołek T, Felis-Giemza A, Stańczyk S, Czuszyńska Z, Walczyk M, Olesińska M, Paradowska-Gorycka A. Mixed Connective Tissue Disease as Different Entity: Global Methylation Aspect. Int J Mol Sci 2023; 24:15495. [PMID: 37895173 PMCID: PMC10607312 DOI: 10.3390/ijms242015495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Mixed connective tissue disease (MCTD) is a very rare disorder that belongs in the rare and clinically multifactorial groups of diseases. The pathogenesis of MCTD is still unclear. The best understood epigenetic alteration is DNA methylation whose role is to regulate gene expression. In the literature, there are ever-increasing assumptions that DNA methylation can be one of the possible reasons for the development of Autoimmune Connective Tissue Diseases (ACTDs) such as systemic sclerosis (SSc) and systemic lupus erythematosus (SLE). The aim of this study was to define the global DNA methylation changes between MCTD and other ACTDs patients in whole blood samples. The study included 54 MCTD patients, 43 SSc patients, 45 SLE patients, and 43 healthy donors (HC). The global DNA methylation level was measured by ELISA. Although the global DNA methylation was not significantly different between MCTD and control, we observed that hypomethylation distinguishes the MCTD patients from the SSc and SLE patients. The present analysis revealed a statistically significant difference of global methylation between SLE and MCTD (p < 0.001), SLE and HC (p = 0.008), SSc and MCTD (p ≤ 0.001), and SSc and HC (p < 0.001), but neither between MCTD and HC (p = 0.09) nor SSc and SLE (p = 0.08). The highest % of global methylation (median, IQR) has been observed in the group of patients with SLE [0.73 (0.43, 1.22] and SSc [0,91 (0.59, 1.50)], whereas in the MCTD [0.29 (0.20, 0.54)], patients and healthy subjects [0.51 (0.24, 0.70)] were comparable. In addition, our study provided evidence of different levels of global DNA methylation between the SSc subtypes (p = 0.01). Our study showed that patients with limited SSc had a significantly higher global methylation level when compared to diffuse SSc. Our data has shown that the level of global DNA methylation may not be a good diagnostic marker to distinguish MCTD from other ACTDs. Our research provides the groundwork for a more detailed examination of the significance of global DNA methylation as a distinguishing factor in patients with MCTD compared to other ACTDs patients.
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Affiliation(s)
- Gabriela Filipowicz
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Barbara Stypińska
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Tomasz Kmiołek
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Anna Felis-Giemza
- Biologic Therapy Center, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland (S.S.)
| | - Sandra Stańczyk
- Biologic Therapy Center, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland (S.S.)
| | - Zenobia Czuszyńska
- Department of Rheumatology, Clinical Immunology, Geriatrics and Internal Medicine, Medical University of Gdansk, Smulochowskiego 17, 80-214 Gdansk, Poland
| | - Marcela Walczyk
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland
| | - Marzena Olesińska
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
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