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Shirai T, Okazaki S, Otsuka I, Miyachi M, Tanifuji T, Shindo R, Okada S, Minami H, Horai T, Mouri K, Hishimoto A. Accelerated epigenetic aging in alcohol dependence. J Psychiatr Res 2024; 173:175-182. [PMID: 38547739 DOI: 10.1016/j.jpsychires.2024.03.025] [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: 12/06/2023] [Revised: 03/12/2024] [Accepted: 03/21/2024] [Indexed: 04/17/2024]
Abstract
Alcohol dependence poses a global health threat associated with aging and reduced life expectancy. Recently, aging research through deoxyribonucleic acid (DNA) methylation has gained attention. New epigenetic clocks have been developed; however, no study has investigated GrimAge components, GrimAge2 components and DunedinPACE in patients with alcohol dependence. In this study, we aimed to perform epigenetic clock analysis to evaluate epigenetic age acceleration and DNA methylation-based age-predictive components in patients with alcohol dependence and controls. We utilized publicly available DNA methylation data (GSE98876) for our analysis. Additionally, we compared the values of the same items before and after the patients underwent a treatment program. The dataset comprised 23 controls and 24 patients. We observed that DunedinPACE accelerated more in patients with alcohol dependence. AgeAccelGrim and AgeAccelGrim2 decelerated more after the treatment program than before, and beta-2-microglobulin and Cystatin C decreased after the treatment program than before. These findings are crucial as they affect the cranial nerve area, potentially contributing to cognitive dysfunction and psychiatric symptoms in patients with alcohol dependence.
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Affiliation(s)
- Toshiyuki Shirai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masao Miyachi
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takaki Tanifuji
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ryota Shindo
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shohei Okada
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Haruka Minami
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tadasu Horai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kentaro Mouri
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
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Terracina S, Tarani L, Ceccanti M, Vitali M, Francati S, Lucarelli M, Venditti S, Verdone L, Ferraguti G, Fiore M. The Impact of Oxidative Stress on the Epigenetics of Fetal Alcohol Spectrum Disorders. Antioxidants (Basel) 2024; 13:410. [PMID: 38671857 PMCID: PMC11047541 DOI: 10.3390/antiox13040410] [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: 03/06/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Fetal alcohol spectrum disorders (FASD) represent a continuum of lifelong impairments resulting from prenatal exposure to alcohol, with significant global impact. The "spectrum" of disorders includes a continuum of physical, cognitive, behavioral, and developmental impairments which can have profound and lasting effects on individuals throughout their lives, impacting their health, social interactions, psychological well-being, and every aspect of their lives. This narrative paper explores the intricate relationship between oxidative stress and epigenetics in FASD pathogenesis and its therapeutic implications. Oxidative stress, induced by alcohol metabolism, disrupts cellular components, particularly in the vulnerable fetal brain, leading to aberrant development. Furthermore, oxidative stress is implicated in epigenetic changes, including alterations in DNA methylation, histone modifications, and microRNA expression, which influence gene regulation in FASD patients. Moreover, mitochondrial dysfunction and neuroinflammation contribute to epigenetic changes associated with FASD. Understanding these mechanisms holds promise for targeted therapeutic interventions. This includes antioxidant supplementation and lifestyle modifications to mitigate FASD-related impairments. While preclinical studies show promise, further clinical trials are needed to validate these interventions' efficacy in improving clinical outcomes for individuals affected by FASD. This comprehensive understanding of the role of oxidative stress in epigenetics in FASD underscores the importance of multidisciplinary approaches for diagnosis, management, and prevention strategies. Continued research in this field is crucial for advancing our knowledge and developing effective interventions to address this significant public health concern.
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Affiliation(s)
- Sergio Terracina
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy (M.L.)
| | - Luigi Tarani
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, 00185 Roma, Italy
| | - Mauro Ceccanti
- SITAC, Società Italiana per il Trattamento dell’Alcolismo e le sue Complicanze, 00185 Rome, Italy;
| | | | - Silvia Francati
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy (M.L.)
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy (M.L.)
- Pasteur Institute Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
| | - Sabrina Venditti
- Department of Biology and Biotechnologies Charles Darwin, Sapienza University, 00185 Rome, Italy
| | - Loredana Verdone
- Institute of Molecular Biology and Pathology (IBPM-CNR), 00185 Rome, Italy
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, 00185 Rome, Italy (M.L.)
| | - Marco Fiore
- Institute of Biochemistry and Cell Biology (IBBC-CNR), Department of Sensory Organs, Sapienza University of Rome, 00185 Roma, Italy
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Tanifuji T, Okazaki S, Otsuka I, Mouri K, Horai T, Shindo R, Shirai T, Hishimoto A. Epigenetic clock analysis reveals increased plasma cystatin C levels based on DNA methylation in major depressive disorder. Psychiatry Res 2023; 322:115103. [PMID: 36803907 DOI: 10.1016/j.psychres.2023.115103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/01/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Major depressive disorder (MDD) is a common mental illness and a major public health concern worldwide. Depression is associated with epigenetic changes that regulate gene expression, and analyzing these changes may help elucidate the pathophysiology of MDD. Genome-wide DNA methylation (DNAm) profiles can function as 'epigenetic clocks' that can help estimate biological aging. Here, we assessed biological aging in patients with MDD using various DNAm-based indicators of epigenetic aging. We used a publicly available dataset containing data obtained from the whole blood samples of MDD patients (n = 489) and controls (n = 210). We analyzed five epigenetic clocks (HorvathAge, HannumAge, SkinBloodAge, PhenoAge, and GrimAge) and DNAm-based telomere length (DNAmTL). We also investigated seven DNAm-based age-predictive plasma proteins (including cystatin C) and smoking status, which are components of GrimAge. Following adjustment for confounding factors such as age and sex, patients with MDD showed no significant difference in epigenetic clocks and DNAmTL. However, DNAm-based plasma cystatin C levels were significantly higher in patients with MDD than controls. Our findings revealed specific DNAm changes predicting plasma cystatin C levels in MDD. These findings may help elucidate the pathophysiology of MDD, leading to the development of new biomarkers and medications.
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Affiliation(s)
- Takaki Tanifuji
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Kentaro Mouri
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Tadasu Horai
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Ryota Shindo
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Toshiyuki Shirai
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; Department of Psychiatry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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Dos Santos Oliveira NC, Katrinli S, de Assis SG, Smith AK, Serpeloni F. Community and domestic violence are associated with DNA methylation GrimAge acceleration and heart rate variability in adolescents. Eur J Psychotraumatol 2023; 14:2202054. [PMID: 37144662 PMCID: PMC10165931 DOI: 10.1080/20008066.2023.2202054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Background: Cumulative exposure to violence can change the regulation of epigenetic and physiological markers. Although violence has been associated with accelerated cellular aging, little is known about associations with cardiac autonomic activity.Objective: The current study aimed to investigate the relationship of exposure to community and domestic violence (CDV) with vagal activity and epigenetic aging acceleration.Methods: A total of 86 adolescents (57% female) were evaluated and interviewed at two time-points in São Gonçalo (2014-2019), a Brazilian city with high levels of violence. Exposure to CDV was assessed in both time-points. GrimAge acceleration was calculated from saliva DNA methylation using Infinium HumanMethylation450K (Illumina) collected in the first assessment. Heart rate variability (HRV) was collected during two stress tasks at the second assessment.Results: The exposure to violence witnessed or directly experienced at home and in the community increased significantly (t = 4.87, p < .01) across two-time points, and males had reported higher violence exposure (t = 2.06, p = .043). Violence at 1st assessment was significantly associated with GrimAge acceleration (B = .039, p value = .043). Violence at both assessments were associated with HRV measured during the narration of the worst trauma (traumaHRV) (B = .009, p value = .039, and B = .007, p value = .024, 1st and 2nd assessment respectively). GrimAge acceleration was significantly associated with traumaHRV (B = .043, p value = .049), and HRV measured during a 3D roller coaster video (B = .061, p value = .024).Conclusions: We found relevant evidence that experiencing violence during adolescence is associated with epigenetic aging and stress-related vagal activity. Understanding these factors during this period could contribute to the development of early interventions for health promotion.HIGHLIGHTS Higher exposure to Community and domestic violence is associated with increased GrimAge acceleration.Higher GrimAge acceleration is associated with increased stress-related vagal activity.Exposure to community and domestic violence increased significantly over time.
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Affiliation(s)
- Nayara Cristina Dos Santos Oliveira
- National Institute of Woman, Child, and Adolescence Health Fernandes Figueira, Rio de Janeiro, Brazil
- Department of Violence and Health Studies Jorge Careli, National School of Public Health, Fiocruz, Rio de Janeiro, Brazil
| | - Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Simone Gonçalves de Assis
- National Institute of Woman, Child, and Adolescence Health Fernandes Figueira, Rio de Janeiro, Brazil
- Department of Violence and Health Studies Jorge Careli, National School of Public Health, Fiocruz, Rio de Janeiro, Brazil
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Fernanda Serpeloni
- Department of Violence and Health Studies Jorge Careli, National School of Public Health, Fiocruz, Rio de Janeiro, Brazil
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Okazaki S, Kimura R, Otsuka I, Tomiwa K, Funabiki Y, Hagiwara M, Murai T, Hishimoto A. Epigenetic aging in Williams syndrome. J Child Psychol Psychiatry 2022; 63:1553-1562. [PMID: 35416284 DOI: 10.1111/jcpp.13613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/16/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Williams syndrome (WS) is a rare genetic disorder caused by a microdeletion at the 7q11.23 region and is characterized by diverse symptoms encompassing physical and cognitive features. WS was reported to be associated to altered DNA methylation (DNAm) patterns. However, due to the limited information from long-term studies, it remains unclear whether WS accelerates aging. Genome-wide DNAm profiles can serve as "epigenetic clocks" to help estimate biological aging along with age-related markers, such as plasma proteins and telomere length. METHODS We investigated GrimAge, DNAm-based telomere length (DNAmTL), and other epigenetic clocks in blood samples of 32 patients with WS and 32 healthy controls. RESULTS We observed a significant acceleration in GrimAge, DNAmTL, and other epigenetic clocks in patients with WS as compared with those of controls. In addition, several GrimAge components, such as adrenomedullin, growth differentiation factor-15, leptin and plasminogen activator inhibitor-1, were altered in patients with WS. CONCLUSIONS This study provides novel evidence supporting the hypothesis that WS may be associated to accelerated biological aging. A better understanding of the overall underlying biological effects of WS can provide new foundations for improved patient care; thus, long-term follow-up studies are still warranted.
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Affiliation(s)
- Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - Yasuko Funabiki
- Department of Cognitive and Behavioral Science, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan.,Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Psychiatry, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Child and Adolescent Psychiatry, Yokohama City University Hospital, Yokohama, Japan
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6
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Blostein FA, Fisher J, Dou J, Schneper L, Ware EB, Notterman DA, Mitchell C, Bakulski KM. Polymethylation scores for prenatal maternal smoke exposure persist until age 15 and are detected in saliva in the Fragile Families and Child Wellbeing cohort. Epigenetics 2022; 17:2223-2240. [PMID: 35980258 PMCID: PMC9665138 DOI: 10.1080/15592294.2022.2112815] [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: 05/05/2022] [Accepted: 08/05/2022] [Indexed: 01/18/2023] Open
Abstract
Prenatal maternal smoking is associated with low birthweight, neurological disorders, and asthma in exposed children. DNA methylation signatures can function as biomarkers of prenatal smoke exposure. However, the robustness of DNA methylation signatures across child ages, genetic ancestry groups, or tissues is not clear. Using coefficients from a meta-analysis of prenatal smoke exposure and DNA methylation in newborn cord blood, we created polymethylation scores of saliva DNA methylation from children at ages 9 and 15 in the Fragile Families and Child Wellbeing study. In the full sample at age 9 (n = 753), prenatal smoke exposure was associated with a 0.51 (95%CI: 0.35, 0.66) standard deviation higher polymethylation score. The direction and magnitude of the association was consistent in European and African genetic ancestry samples. In the full sample at age 15 (n = 747), prenatal smoke exposure was associated with a 0.48 (95%CI: 0.32, 0.63) standard deviation higher polymethylation score, and the association was attenuated among the European and Admixed-Latin genetic ancestry samples. The polymethylation score classified prenatal smoke exposure accurately (AUC age 9 = 0.77, age 15 = 0.76). Including the polymethylation score increased the AUC of base model covariates by 5 (95% CI: (2.1, 7.2)) percentage points, while including a single candidate site in the AHRR gene did not (P-value = 0.19). Polymethylation scores for prenatal smoking were portable across genetic ancestries and more accurate than an individual DNA methylation site. Polymethylation scores from saliva samples could serve as robust and practical biomarkers of prenatal smoke exposure.
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Affiliation(s)
- Freida A. Blostein
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - John Dou
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Erin B. Ware
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Kelly M. Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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Di Lena P, Sala C, Nardini C. Evaluation of different computational methods for DNA methylation-based biological age. Brief Bioinform 2022; 23:6632619. [PMID: 35794713 DOI: 10.1093/bib/bbac274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/27/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
In recent years there has been a widespread interest in researching biomarkers of aging that could predict physiological vulnerability better than chronological age. Aging, in fact, is one of the most relevant risk factors for a wide range of maladies, and molecular surrogates of this phenotype could enable better patients stratification. Among the most promising of such biomarkers is DNA methylation-based biological age. Given the potential and variety of computational implementations (epigenetic clocks), we here present a systematic review of such clocks. Furthermore, we provide a large-scale performance comparison across different tissues and diseases in terms of age prediction accuracy and age acceleration, a measure of deviance from physiology. Our analysis offers both a state-of-the-art overview of the computational techniques developed so far and a heterogeneous picture of performances, which can be helpful in orienting future research.
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Affiliation(s)
- Pietro Di Lena
- Department of Computer Science and Engineering, University of Bologna, Mura Anteo Zamboni 7, 40126 Bologna, Italy
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
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Liang X, Sinha R, Justice AC, Cohen MH, Aouizerat BE, Xu K. A new monocyte epigenetic clock reveals nonlinear effects of alcohol consumption on biological aging in three independent cohorts (N = 2242). Alcohol Clin Exp Res 2022; 46:736-748. [PMID: 35257385 PMCID: PMC9117474 DOI: 10.1111/acer.14803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND Assessing the effect of alcohol consumption on biological age is essential for understanding alcohol use-related comorbidities and mortality. Previously developed epigenetic clocks are mainly based on DNA methylation in heterogeneous cell types, which provide limited knowledge on the impacts of alcohol consumption at the individual cellular level. Evidence shows that monocytes play an important role in both alcohol-induced pathophysiology and the aging process. In this study, we developed a novel monocyte-based DNA methylation clock (MonoDNAmAge) to assess the impact of alcohol consumption on monocyte age. METHODS A machine learning method was applied to select a set of chronological age-associated DNA methylation CpG sites from 1202 monocyte methylomes. Pearson correlation was tested between MonoDNAmAge and chronological age in three independent cohorts (Ntotal = 2242). Using the MonoDNAmAge clock and four established clocks (i.e., HorvathDNAmAge, HannumDNAmAge, PhenoDNAmAge, GrimDNAmAge), we then evaluated the effect of alcohol consumption on epigenetic aging in the three cohorts [i.e., Yale Stress Center Community Study (YSCCS), Veteran Aging Cohort Study (VACS), Women's Interagency HIV Study (WIHS)] using linear and quadratic models. RESULTS The MonoDNAmAge, comprised of 186 CpG sites, was moderately to strongly correlated with chronological age in the three cohorts (r = 0.90, p = 3.12E-181 in YSCCS; r = 0.54, p = 1.75E-96 in VACS; r = 0.66, p = 1.50E-60 in WIHS). More importantly, we found a nonlinear association between MonoDNAmAge and alcohol consumption (pmodel = 4.55E-08, px2 = 7.80E-08 in YSCCS; pmodel = 1.85E-02, px2 = 3.46E-02 in VACS). Heavy alcohol consumption increased EAAMonoDNAmAge up to 1.60 years while light alcohol consumption decreased EAAMonoDNAmAge up to 2.66 years. These results were corroborated by the four established epigenetic clocks (i.e., HorvathDNAmAge, HannumDNAmAge, PhenoDNAmAge, GrimDNAmAge). CONCLUSIONS The results suggest a nonlinear relationship between alcohol consumption and its effects on epigenetic age. Considering adverse effects of alcohol consumption on health, nonlinear effects of alcohol use should be interpreted with caution. The findings, for the first time, highlight the complex effects of alcohol consumption on biological aging.
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Affiliation(s)
- Xiaoyu Liang
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA,VA Connecticut Healthcare SystemWest HavenConnecticutUSA,Department of Preventive MedicineUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Rajita Sinha
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA,Child Study CenterYale School of MedicineNew HavenConnecticutUSA,Department of NeuroscienceYale School of MedicineNew HavenConnecticutUSA
| | - Amy C. Justice
- VA Connecticut Healthcare SystemWest HavenConnecticutUSA,Yale University School of MedicineNew Haven Veterans Affairs Connecticut Healthcare SystemNew HavenConnecticutUSA
| | - Mardge H. Cohen
- Department of MedicineStroger Hospital of Cook CountyChicagoIllinoisUSA
| | - Bradley E. Aouizerat
- Bluestone Center for Clinical ResearchCollege of DentistryNew York UniversityNew YorkNew YorkUSA,Department of Oral and Maxillofacial SurgeryCollege of DentistryNew York UniversityNew YorkNew YorkUSA
| | - Ke Xu
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA,VA Connecticut Healthcare SystemWest HavenConnecticutUSA
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Okazaki S, Kimura R, Otsuka I, Funabiki Y, Murai T, Hishimoto A. Epigenetic clock analysis and increased plasminogen activator inhibitor-1 in high-functioning autism spectrum disorder. PLoS One 2022; 17:e0263478. [PMID: 35113965 PMCID: PMC8812940 DOI: 10.1371/journal.pone.0263478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is characterized by impaired social communication and behavioral problems. An increased risk of premature mortality has been observed in individuals with ASD. Therefore, we hypothesized that biological aging is accelerated in individuals with ASD. Recently, several studies have established genome-wide DNA methylation (DNAm) profiles as ‘epigenetic clocks’ that can estimate biological aging. In addition, ASD has been associated with differential DNAm patterns. Methods We used two independent datasets from blood samples consisting of adult patients with high-functioning ASD and controls: the 1st cohort (38 ASD cases and 31 controls) and the 2nd cohort (6 ASD cases and 10 controls). We explored well-studied epigenetic clocks such as HorvathAge, HannumAge, SkinBloodAge, PhenoAge, GrimAge, and DNAm-based telomere length (DNAmTL). In addition, we investigated seven DNAm-based age-related plasma proteins, including plasminogen activator inhibitor-1 (PAI-1), and smoking status, which are the components of GrimAge. Results Compared to controls, individuals with ASD in the 1st cohort, but not in the 2nd cohort, exhibited a trend for increased GrimAge acceleration and a significant increase of PAI-1 levels. A meta-analysis showed significantly increased PAI-1 levels in individuals with ASD compared to controls. Conclusion Our findings suggest there is no epigenetic age acceleration in the blood of individuals with ASD. However, this study provides novel evidence regarding increased plasma PAI-1 levels in individuals with high-functioning ASD. These findings suggest PAI-1 may be a biomarker for high-functioning ASD, however, larger studies based on epigenetic clocks and PAI-1 will be necessary to confirm these findings.
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Affiliation(s)
- Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yasuko Funabiki
- Department of Cognitive and Behavioral Science, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Psychiatry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- * E-mail:
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10
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Shinko Y, Okazaki S, Otsuka I, Horai T, Kim S, Tanifuji T, Hishimoto A. Accelerated epigenetic age and shortened telomere length based on DNA methylation in Nicolaides-Baraitser syndrome. Mol Genet Genomic Med 2022; 10:e1876. [PMID: 35092358 PMCID: PMC8922957 DOI: 10.1002/mgg3.1876] [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: 04/07/2021] [Revised: 07/06/2021] [Accepted: 01/06/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Nicolaides-Baraitser syndrome (NCBRS) is a rare disorder characterized by neurodevelopmental delays, seizures, and diverse physical characteristics. The DNA methylation (DNAm) profile in NCBRS is significantly different. DNAm is linked to the biological aging of cells and the health risks associated with biological aging. In this study, we examined changes in biological ages in NCBRS to provide insights into the prognosis and health risks of NCBRS. METHODS We used a publicly available dataset to examine biological aging in NCBRS using DNAm-based epigenetic ages, such as PhenoAge and GrimAge, as well as DNAm-based estimator of telomere length (DNAmTL). We investigated 12 cases, clinically diagnosed as NCBRS, and 27 controls. RESULTS Compared to controls, NCBRS cases exhibited significantly accelerated PhenoAge and GrimAge as well as significantly shortened DNAmTL. CONCLUSION These results suggest an acceleration of biological aging in NCBRS and provide insights into the prognosis and health risks of NCBRS.
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Affiliation(s)
- Yutaka Shinko
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tadasu Horai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Saehyeon Kim
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takaki Tanifuji
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Psychiatry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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Association of prenatal alcohol exposure with offspring DNA methylation in mammals: a systematic review of the evidence. Clin Epigenetics 2022; 14:12. [PMID: 35073992 PMCID: PMC8785586 DOI: 10.1186/s13148-022-01231-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/06/2022] [Indexed: 12/18/2022] Open
Abstract
Abstract
Background
Prenatal alcohol exposure (PAE) is associated with a range of adverse offspring neurodevelopmental outcomes. Several studies suggest that PAE modifies DNA methylation in offspring cells and tissues, providing evidence for a potential mechanistic link to Fetal Alcohol Spectrum Disorder (FASD). We systematically reviewed existing evidence on the extent to which maternal alcohol use during pregnancy is associated with offspring DNA methylation.
Methods
A systematic literature search was conducted across five online databases according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. PubMed, Web of Science, EMBASE, Google Scholar and CINAHL Databases were searched for articles relating to PAE in placental mammals. Data were extracted from each study and the Risk of Bias in Non-Randomized Studies of Interventions (ROBINS-I) was used to assess the potential for bias in human studies.
Results
Forty-three articles were identified for inclusion. Twenty-six animal studies and 16 human studies measured offspring DNA methylation in various tissues using candidate gene analysis, methylome-wide association studies (MWAS), or total nuclear DNA methylation content. PAE dose and timing varied between studies. Risk of bias was deemed high in nearly all human studies. There was insufficient evidence in human and animal studies to support global disruption of DNA methylation from PAE. Inconclusive evidence was found for hypomethylation at IGF2/H19 regions within somatic tissues. MWAS assessing PAE effects on offspring DNA methylation showed inconsistent evidence. There was some consistency in the relatively small number of MWAS conducted in populations with FASD. Meta-analyses could not be conducted due to significant heterogeneity between studies.
Conclusion
Considering heterogeneity in study design and potential for bias, evidence for an association between PAE and offspring DNA methylation was inconclusive. Some reproducible associations were observed in populations with FASD although the limited number of these studies warrants further research.
Trail Registration: This review is registered with PROSPERO (registration number: CRD42020167686).
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Loke YJ, Muggli E, Saffery R, Ryan J, Lewis S, Elliott EJ, Halliday J, Craig JM. Sex- and tissue-specific effects of binge-level prenatal alcohol consumption on DNA methylation at birth. Epigenomics 2021; 13:1921-1938. [PMID: 34841896 DOI: 10.2217/epi-2021-0285] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background: Binge-level prenatal alcohol exposure (PAE) causes developmental abnormalities, which may be mediated in part by epigenetic mechanisms. Despite this, few studies have characterised the association of binge PAE with DNA methylation in offspring. Methods: We investigated the association between binge PAE and genome-wide DNA methylation profiles in a sex-specific manner in neonatal buccal and placental samples. Results: We identified no differentially methylated CpGs or differentially methylated regions (DMRs) at false discovery rate <0.05. However, using a sum-of-ranks approach, we identified a DMR in each tissue of female offspring. The DMR identified in buccal samples is located near regions with previously-reported associations to fetal alcohol spectrum disorder (FASD) and binge PAE. Conclusion: Our findings warrant further replication and highlight a potential epigenetic link between binge PAE and FASD.
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Affiliation(s)
- Yuk Jing Loke
- Molecular Immunity, Murdoch Children's Research Institute, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Victoria, 3010, Australia
| | - Evelyne Muggli
- Department of Paediatrics, University of Melbourne, Victoria, 3010, Australia.,Victorian Infant Brain Studies, Murdoch Children's Research Institute, Victoria, 3052, Australia.,Reproductive Epidemiology, Murdoch Children's Research Institute, Victoria, 3052, Australia
| | - Richard Saffery
- Molecular Immunity, Murdoch Children's Research Institute, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Victoria, 3010, Australia
| | - Joanne Ryan
- Molecular Immunity, Murdoch Children's Research Institute, Victoria, 3052, Australia.,Biological Neuropsychiatry & Dementia Unit, School of Public Health, Monash University, Victoria, 3004, Australia
| | - Sharon Lewis
- Department of Paediatrics, University of Melbourne, Victoria, 3010, Australia.,Reproductive Epidemiology, Murdoch Children's Research Institute, Victoria, 3052, Australia
| | - Elizabeth J Elliott
- Specialty of Child & Adolescent Health, Faculty of Medicine & Health, University of Sydney, NSW, 2050, Australia.,The Australian Paediatric Surveillance Unit, Sydney Children's Hospital Network, NSW, 2045, Australia
| | - Jane Halliday
- Department of Paediatrics, University of Melbourne, Victoria, 3010, Australia.,Reproductive Epidemiology, Murdoch Children's Research Institute, Victoria, 3052, Australia
| | - Jeffrey M Craig
- Molecular Immunity, Murdoch Children's Research Institute, Victoria, 3052, Australia.,Department of Paediatrics, University of Melbourne, Victoria, 3010, Australia.,The Institute of Mental & Physical Health & Clinical Translation, Deakin University, Victoria, 3220, Australia
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Alberry B, Laufer BI, Chater-Diehl E, Singh SM. Epigenetic Impacts of Early Life Stress in Fetal Alcohol Spectrum Disorders Shape the Neurodevelopmental Continuum. Front Mol Neurosci 2021; 14:671891. [PMID: 34149355 PMCID: PMC8209299 DOI: 10.3389/fnmol.2021.671891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
Neurodevelopment in humans is a long, elaborate, and highly coordinated process involving three trimesters of prenatal development followed by decades of postnatal development and maturation. Throughout this period, the brain is highly sensitive and responsive to the external environment, which may provide a range of inputs leading to positive or negative outcomes. Fetal alcohol spectrum disorders (FASD) result from prenatal alcohol exposure (PAE). Although the molecular mechanisms of FASD are not fully characterized, they involve alterations to the regulation of gene expression via epigenetic marks. As in the prenatal stages, the postnatal period of neurodevelopment is also sensitive to environmental inputs. Often this sensitivity is reflected in children facing adverse conditions, such as maternal separation. This exposure to early life stress (ELS) is implicated in the manifestation of various behavioral abnormalities. Most FASD research has focused exclusively on the effect of prenatal ethanol exposure in isolation. Here, we review the research into the effect of prenatal ethanol exposure and ELS, with a focus on the continuum of epigenomic and transcriptomic alterations. Interestingly, a select few experiments have assessed the cumulative effect of prenatal alcohol and postnatal maternal separation stress. Regulatory regions of different sets of genes are affected by both treatments independently, and a unique set of genes are affected by the combination of treatments. Notably, epigenetic and gene expression changes converge at the clustered protocadherin locus and oxidative stress pathway. Functional studies using epigenetic editing may elucidate individual contributions of regulatory regions for hub genes and further profiling efforts may lead to the development of non-invasive methods to identify children at risk. Taken together, the results favor the potential to improve neurodevelopmental outcomes by epigenetic management of children born with FASD using favorable postnatal conditions with or without therapeutic interventions.
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Affiliation(s)
- Bonnie Alberry
- Department of Biology, Faculty of Science, The University of Western Ontario, London, ON, Canada
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA, United States.,Genome Center, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis, Davis, CA, United States
| | - Eric Chater-Diehl
- Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Shiva M Singh
- Department of Biology, Faculty of Science, The University of Western Ontario, London, ON, Canada
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