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Cuyvers B, Ein-Dor T, Houbrechts M, Freson K, Goossens L, Van Den Noortgate W, van Leeuwen K, Bijttebier P, Claes S, Turner J, Chubar V, Bakermans-Kranenburg MJ, Bosmans G. Exploring the role of OXTR gene methylation in attachment development: A longitudinal study. Dev Psychobiol 2024; 66:e22496. [PMID: 38689124 DOI: 10.1002/dev.22496] [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: 04/03/2023] [Revised: 03/26/2024] [Accepted: 04/07/2024] [Indexed: 05/02/2024]
Abstract
The current study explored longitudinally whether oxytocin receptor gene methylation (OXTRm) changes moderated the association between parental sensitivity changes and children's attachment changes over three waves. Six hundred six Flemish children (10-12 years, 42.8%-44.8% boys) completed attachment measures and provided salivary OXTRm data on seven CpG sites. Their parents reported their sensitive parenting. Results suggest that OXTRm changes hardly link to attachment (in)security changes after the age of 10. Some support was found for interaction effects between parental sensitivity changes and OXTRm changes on attachment changes over time. Effects suggest that for children with increased OXTRm in the promotor region and decreased methylation in the inhibitor region over time, increased parental sensitivity was associated with increased secure attachment and decreased insecure attachment over time.
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Affiliation(s)
- Bien Cuyvers
- Clinical Psychology, KU Leuven University, Leuven, Belgium
| | - Tsachi Ein-Dor
- Social Sciences, School of Psychology, Reichman University Herzliya, Herzliya, Israel
| | | | - Kathleen Freson
- Centre for Molecular and Vascular Biology, KU Leuven University, Leuven, Belgium
| | - Luc Goossens
- School Psychology and Development in Context, KU Leuven University, Leuven, Belgium
| | | | - Karla van Leeuwen
- Family and Educational Sciences, KU Leuven University, Leuven, Belgium
| | - Patricia Bijttebier
- School Psychology and Development in Context, KU Leuven University, Leuven, Belgium
| | - Stephan Claes
- Research Group Psychiatry, UZ Leuven-KU Leuven University, Leuven, Belgium
| | - Jonathan Turner
- Immune Endocrine Epigenetics Research Group, Luxembourg Institute of Health, Esch sur Alzette, Luxembourg, Luxembourg
| | - Viktoria Chubar
- Research Group Psychiatry, UZ Leuven-KU Leuven University, Leuven, Belgium
| | - Marian J Bakermans-Kranenburg
- William James Center for Research, ISPA University Institute of sychological, Social and Life Sciences, Lisbon, Portugal
- Centre for Attachment Research, the New School for Social Research, New York, USA
| | - Guy Bosmans
- Clinical Psychology, KU Leuven University, Leuven, Belgium
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2
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Shokhirev MN, Torosin NS, Kramer DJ, Johnson AA, Cuellar TL. CheekAge: a next-generation buccal epigenetic aging clock associated with lifestyle and health. GeroScience 2024; 46:3429-3443. [PMID: 38441802 PMCID: PMC11009193 DOI: 10.1007/s11357-024-01094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/05/2024] [Indexed: 04/13/2024] Open
Abstract
Epigenetic aging clocks are computational models that predict age using DNA methylation information. Initially, first-generation clocks were developed to make predictions using CpGs that change with age. Over time, next-generation clocks were created using CpGs that relate to both age and health. Since existing next-generation clocks were constructed in blood, we sought to develop a next-generation clock optimized for prediction in cheek swabs, which are non-invasive and easy to collect. To do this, we collected MethylationEPIC data as well as lifestyle and health information from 8045 diverse adults. Using a novel simulated annealing approach that allowed us to incorporate lifestyle and health factors into training as well as a combination of CpG filtering, CpG clustering, and clock ensembling, we constructed CheekAge, an epigenetic aging clock that has a strong correlation with age, displays high test-retest reproducibility across replicates, and significantly associates with a plethora of lifestyle and health factors, such as BMI, smoking status, and alcohol intake. We validated CheekAge in an internal dataset and multiple publicly available datasets, including samples from patients with progeria or meningioma. In addition to exploring the underlying biology of the data and clock, we provide a free online tool that allows users to mine our methylomic data and predict epigenetic age.
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Gerra MC, Dallabona C, Cecchi R. Epigenetic analyses in forensic medicine: future and challenges. Int J Legal Med 2024; 138:701-719. [PMID: 38242965 PMCID: PMC11003920 DOI: 10.1007/s00414-024-03165-8] [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: 04/20/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
The possibility of using epigenetics in forensic investigation has gradually risen over the last few years. Epigenetic changes with their dynamic nature can either be inherited or accumulated throughout a lifetime and be reversible, prompting investigation of their use across various fields. In forensic sciences, multiple applications have been proposed, such as the discrimination of monozygotic twins, identifying the source of a biological trace left at a crime scene, age prediction, determination of body fluids and tissues, human behavior association, wound healing progression, and determination of the post-mortem interval (PMI). Despite all these applications, not all the studies considered the impact of PMI and post-sampling effects on the epigenetic modifications and the tissue-specificity of the epigenetic marks.This review aims to highlight the substantial forensic significance that epigenetics could support in various forensic investigations. First, basic concepts in epigenetics, describing the main epigenetic modifications and their functions, in particular, DNA methylation, histone modifications, and non-coding RNA, with a particular focus on forensic applications, were covered. For each epigenetic marker, post-mortem stability and tissue-specificity, factors that should be carefully considered in the study of epigenetic biomarkers in the forensic context, have been discussed. The advantages and limitations of using post-mortem tissues have been also addressed, proposing directions for these innovative strategies to analyze forensic specimens.
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Affiliation(s)
- Maria Carla Gerra
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 11a, Viale Delle Scienze 11a, 43124, Parma, PR, Italy.
| | - Rossana Cecchi
- Department of Medicine and Surgery, University of Parma, Via Antonio Gramsci 14, 43126, Parma, PR, Italy
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Creasey N, Beijers R, O'Donnell KJ, de Weerth C, Tollenaar MS. Maternal sensitivity and child internalizing and externalizing behavior: a mediating role for glucocorticoid receptor gene ( NR3C1) methylation? Dev Psychopathol 2024; 36:967-978. [PMID: 36896668 DOI: 10.1017/s0954579423000226] [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] [Indexed: 03/11/2023]
Abstract
The early caregiving environment can have lasting effects on child mental health. Animal models suggest that glucocorticoid receptor gene (NR3C1) DNA methylation plays a mediating role in linking more responsive caregiving to improved behavioral outcomes by its impact on the stress regulatory system. In this longitudinal study, we examined whether children's NR3C1 methylation levels mediate an effect of maternal sensitivity in infancy on levels of child internalizing and externalizing behavior in a community sample. Maternal sensitivity of 145 mothers was rated at infant age 5 weeks, 12 months, and 30 months by observing mother-infant interactions. Buccal DNA methylation was assessed in the same children at age 6 years and maternal-reported internalizing and externalizing behavior was assessed at age 6 and 10 years. Higher sensitivity at age 5 weeks significantly predicted lower DNA methylation levels at two NR3C1 CpG loci, although methylation levels at these loci did not mediate an effect of maternal sensitivity on levels of child internalizing and externalizing behavior. Overall, the study provides evidence that maternal sensitivity in early infancy is associated with DNA methylation levels at loci involved in stress regulation, but the significance of this finding for child mental health remains unclear.
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Affiliation(s)
- Nicole Creasey
- Preventive Youth Care, Research Institute of Child Development and Education, University of Amsterdam, the Netherlands
| | - Roseriet Beijers
- Department of Social Development, Behavioral Science Institute, Radboud University, the Netherlands, and Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, the Netherlands
| | - Kieran J O'Donnell
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, McGill University, QC, Canada; Canadian Institute for Advanced Research, Child and Brain Development Program, Canada; and Yale Child Study Center & Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, USA
| | - Carolina de Weerth
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, the Netherlands
| | - Marieke S Tollenaar
- Institute of Psychology and Leiden Institute for Brain and Cognition, Leiden University, the Netherlands
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5
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Yang T, Li C, Wei Q, Pang D, Cheng Y, Huang J, Lin J, Xiao Y, Jiang Q, Wang S, Shang H. Genome-wide DNA methylation analysis related to ALS patient progression and survival. J Neurol 2024; 271:2672-2683. [PMID: 38372747 DOI: 10.1007/s00415-024-12222-6] [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: 10/31/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND Epigenetics contributes to the pathogenesis of amyotrophic lateral sclerosis (ALS). We aimed to characterize the DNA methylation profiles associated with clinical heterogeneity in disease progression and survival among patients. METHODS We included a cohort of 41 patients with sporadic ALS, with a median follow-up of 86.9 months, and 27 rigorously matched healthy controls. Blood-based genome-wide DNA methylation analysis was conducted. RESULTS A total of 948 progression rate-associated differentially methylated positions, 298 progression rate-associated differentially methylated regions (R-DMRs), 590 survival time-associated DMPs, and 197 survival time-associated DMRs (S-DMRs) were identified, using complementary grouping strategies. Enrichment analysis of differentially methylated genes highlighted the involvement of synapses and axons in ALS progression and survival. Clinical analysis revealed a positive correlation between the average methylation levels of the R-DMR in PRDM8 and disease progression rate (r = 0.479, p = 0.002). Conversely, there was an inverse correlation between the average methylation levels of the R-DMR in ANKRD33 and disease progression rate (r = - 0.476, p = 0.002). In addition, patients with higher methylation levels within the S-DMR of ZNF696 experienced longer survival (p = 0.016), while those with elevated methylation levels in the S-DMR of RAI1 had shorter survival (p = 0.006). CONCLUSION DNA methylation holds promise as a potential biomarker for tracking disease progression and predicting survival outcome and also offers targets for precision medicine.
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Affiliation(s)
- Tianmi Yang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yangfan Cheng
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Junyu Lin
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yi Xiao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Qirui Jiang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Shichan Wang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China.
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6
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Pett L, Li Z, Abrishamcar S, Hodge K, Everson T, Christensen G, Gearing M, Kobor MS, Konwar C, MacIsaac JL, Dever K, Wingo AP, Levey A, Lah JJ, Wingo TS, Hüls A. The association between neighborhood deprivation and DNA methylation in an autopsy cohort. Aging (Albany NY) 2024; 16:6694-6716. [PMID: 38663907 PMCID: PMC11087100 DOI: 10.18632/aging.205764] [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: 09/01/2023] [Accepted: 03/18/2024] [Indexed: 05/08/2024]
Abstract
Previous research has found that living in a disadvantaged neighborhood is associated with poor health outcomes. Living in disadvantaged neighborhoods may alter inflammation and immune response in the body, which could be reflected in epigenetic mechanisms such as DNA methylation (DNAm). We used robust linear regression models to conduct an epigenome-wide association study examining the association between neighborhood deprivation (Area Deprivation Index; ADI), and DNAm in brain tissue from 159 donors enrolled in the Emory Goizueta Alzheimer's Disease Research Center (Georgia, USA). We found one CpG site (cg26514961, gene PLXNC1) significantly associated with ADI after controlling for covariates and multiple testing (p-value=5.0e-8). Effect modification by APOE ε4 was statistically significant for the top ten CpG sites from the EWAS of ADI, indicating that the observed associations between ADI and DNAm were mainly driven by donors who carried at least one APOE ε4 allele. Four of the top ten CpG sites showed a significant concordance between brain tissue and tissues that are easily accessible in living individuals (blood, buccal cells, saliva), including DNAm in cg26514961 (PLXNC1). Our study identified one CpG site (cg26514961, PLXNC1 gene) that was significantly associated with neighborhood deprivation in brain tissue. PLXNC1 is related to immune response, which may be one biological pathway how neighborhood conditions affect health. The concordance between brain and other tissues for our top CpG sites could make them potential candidates for biomarkers in living individuals.
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Affiliation(s)
- Lindsay Pett
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Zhenjiang Li
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Sarina Abrishamcar
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Kenyaita Hodge
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Todd Everson
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Grace Christensen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael S. Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Chaini Konwar
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Julia L. MacIsaac
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Kristy Dever
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada
| | - Aliza P. Wingo
- Division of Mental Health, Atlanta VA Medical Center, Decatur, GA 30033, USA
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Allan Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James J. Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Thomas S. Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
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7
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Fernández-Pérez I, Jiménez-Balado J, Macias-Gómez A, Suárez-Pérez A, Vallverdú-Prats M, Pérez-Giraldo A, Viles-García M, Peris-Subiza J, Vidal-Notari S, Giralt-Steinhauer E, Guisado-Alonso D, Esteller M, Rodriguez-Campello A, Jiménez-Conde J, Ois A, Cuadrado-Godia E. Blood DNA Methylation Analysis Reveals a Distinctive Epigenetic Signature of Vasospasm in Aneurysmal Subarachnoid Hemorrhage. Transl Stroke Res 2024:10.1007/s12975-024-01252-x. [PMID: 38649590 DOI: 10.1007/s12975-024-01252-x] [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: 02/27/2024] [Revised: 03/28/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
Vasospasm is a potentially preventable cause of poor prognosis in patients with aneurysmal subarachnoid hemorrhage (aSAH). Epigenetics might provide insight on its molecular mechanisms. We aimed to analyze the association between differential DNA methylation (DNAm) and development of vasospasm. We conducted an epigenome-wide association study in 282 patients with aSAH admitted to our hospital. DNAm was assessed with the EPIC Illumina chip (> 850 K CpG sites) in whole-blood samples collected at hospital admission. We identified differentially methylated positions (DMPs) at the CpG level using Cox regression models adjusted for potential confounders, and then we used the DMP results to find differentially methylated regions (DMRs) and enriched biological pathways. A total of 145 patients (51%) experienced vasospasm. In the DMP analysis, we identified 31 CpGs associated with vasospasm at p-value < 10-5. One of them (cg26189827) was significant at the genome-wide level (p-value < 10-8), being hypermethylated in patients with vasospasm and annotated to SUGCT gene, mainly expressed in arteries. Region analysis revealed 13 DMRs, some of them annotated to interesting genes such as POU5F1, HLA-DPA1, RUFY1, and CYP1A1. Functional enrichment analysis showed the involvement of biological processes related to immunity, inflammatory response, oxidative stress, endothelial nitric oxide, and apoptosis. Our findings show, for the first time, a distinctive epigenetic signature of vasospasm in aSAH, establishing novel links with essential biological pathways, including inflammation, immune responses, and oxidative stress. Although further validation is required, our results provide a foundation for future research into the complex pathophysiology of vasospasm.
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Affiliation(s)
- Isabel Fernández-Pérez
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Joan Jiménez-Balado
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain.
| | - Adrià Macias-Gómez
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Antoni Suárez-Pérez
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Marta Vallverdú-Prats
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | | | - Marc Viles-García
- Neuroradiology Department, Hospital del Mar, Barcelona, Catalunya, Spain
| | | | | | - Eva Giralt-Steinhauer
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Daniel Guisado-Alonso
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Research Institute Against Leukemia Josep Carreras, Badalona, Catalunya, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalunya, Spain
| | - Ana Rodriguez-Campello
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Jordi Jiménez-Conde
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Angel Ois
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Elisa Cuadrado-Godia
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
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8
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Dahrendorff J, Currier G, Uddin M. Leveraging DNA methylation to predict treatment response in major depressive disorder: A critical review. Am J Med Genet B Neuropsychiatr Genet 2024:e32985. [PMID: 38650309 DOI: 10.1002/ajmg.b.32985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/18/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024]
Abstract
Major depressive disorder (MDD) is a debilitating and prevalent mental disorder with a high disease burden. Despite a wide array of different treatment options, many patients do not respond to initial treatment attempts. Selection of the most appropriate treatment remains a significant clinical challenge in psychiatry, highlighting the need for the development of biomarkers with predictive utility. Recently, the epigenetic modification DNA methylation (DNAm) has emerged to be of great interest as a potential predictor of MDD treatment outcomes. Here, we review efforts to date that seek to identify DNAm signatures associated with treatment response in individuals with MDD. Searches were conducted in the databases PubMed, Scopus, and Web of Science with the concepts and keywords MDD, DNAm, antidepressants, psychotherapy, cognitive behavior therapy, electroconvulsive therapy, transcranial magnetic stimulation, and brain stimulation therapies. We identified 32 studies implicating DNAm patterns associated with MDD treatment outcomes. The majority of studies (N = 25) are focused on selected target genes exploring treatment outcomes in pharmacological treatments (N = 22) with a few studies assessing treatment response to electroconvulsive therapy (N = 3). Additionally, there are few genome-scale efforts (N = 7) to characterize DNAm patterns associated with treatment outcomes. There is a relative dearth of studies investigating DNAm patterns in relation to psychotherapy, electroconvulsive therapy, or transcranial magnetic stimulation; importantly, most existing studies have limited sample sizes. Given the heterogeneity in both methods and results of studies to date, there is a need for additional studies before existing findings can inform clinical decisions.
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Affiliation(s)
- Jan Dahrendorff
- Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Glenn Currier
- Department of Psychiatry and Behavioral Neurosciences, University of South Florida, Tampa, Florida, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
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9
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Marra PS, Seki T, Nishizawa Y, Chang G, Yamanishi K, Nishiguchi T, Shibata K, Braun P, Shinozaki G. Genome-wide DNA methylation analysis in female veterans with military sexual trauma and comorbid PTSD/MDD. J Affect Disord 2024; 351:624-630. [PMID: 38309478 PMCID: PMC11107447 DOI: 10.1016/j.jad.2024.01.241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND Military sexual trauma (MST) is a prevalent issue within the U.S. military. Victims are more likely to develop comorbid diseases such as posttraumatic stress disorder (PTSD) and major depressive disorder (MDD). Nonetheless, not everyone who suffers from MST develops PTSD and/or MDD. DNA methylation, which can regulate gene expression, might give us insight into the molecular mechanisms behind this discrepancy. Therefore, we sought to identify genomic loci and enriched biological pathways that differ between patients with and without MST, PTSD, and MDD. METHODS Saliva samples were collected from 113 female veterans. Following DNA extraction and processing, DNA methylation levels were measured through the Infinium HumanMethylationEPIC BeadChip array. We used limma and bump hunting methods to generate the differentially methylated positions and differentially methylated regions (DMRs), respectively. Concurrently, we used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome to find enriched pathways. RESULTS A DMR close to the transcription start site of ZFP57 was differentially methylated between subjects with and without PTSD, replicating previous findings and emphasizing the potential role of ZFP57 in PTSD susceptibility. In the pathway analyses, none survived multiple correction, although top GO terms included some potentially relevant to MST, PTSD, and MDD etiology. CONCLUSION We conducted one of the first DNA methylation analyses investigating MST along with PTSD and MDD. In addition, we found one DMR near ZFP57 to be associated with PTSD. The replication of this finding indicates further investigation of ZFP57 in PTSD may be warranted.
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Affiliation(s)
- Pedro S Marra
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA; University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Tomoteru Seki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, Tokyo Medical University, Shinjuku, Tokyo, Japan
| | - Yoshitaka Nishizawa
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Neuropsychiatry, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Gloria Chang
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA; Developmental Psychology Graduate Program, Department of Psychological Sciences, University of Missouri, Columbia, MO, USA
| | - Kyosuke Yamanishi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Neuropsychiatry, Hyogo Medical University, Nishinomiya, Hyogo, Japan
| | - Tsuyoshi Nishiguchi
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Neuropsychiatry, Tottori University Faculty of Medicine, Yonago, Tottori, Japan
| | - Kazuki Shibata
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Sumitomo Pharma Co. Ltd, Osaka, Osaka, Japan
| | - Patricia Braun
- Department of Biology, Clarke University, Dubuque, IA, USA
| | - Gen Shinozaki
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA, USA; Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.
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10
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Taylor JY, Jones-Patten A, Prescott L, Potts-Thompson S, Joyce C, Tayo B, Saban K. The race-based stress reduction intervention (RiSE) study on African American women in NYC and Chicago: Design and methods for complex genomic analysis. PLoS One 2024; 19:e0295293. [PMID: 38598554 PMCID: PMC11006145 DOI: 10.1371/journal.pone.0295293] [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: 05/24/2023] [Accepted: 11/19/2023] [Indexed: 04/12/2024] Open
Abstract
RiSE study aims to evaluate a race-based stress-reduction intervention as an effective strategy to improve coping and decrease stress-related symptoms, inflammatory burden, and modify DNA methylation of stress response-related genes in older AA women. This article will describe genomic analytic methods to be utilized in this longitudinal, randomized clinical trial of older adult AA women in Chicago and NYC that examines the effect of the RiSE intervention on DNAm pre- and post-intervention, and its overall influence on inflammatory burden. Salivary DNAm will be measured at baseline and 6 months following the intervention, using the Oragene-DNA kit. Measures of perceived stress, depressive symptoms, fatigue, sleep, inflammatory burden, and coping strategies will be assessed at 4 time points including at baseline, 4 weeks, 8 weeks, and 6 months. Genomic data analysis will include the use of pre-processed and quality-controlled methylation data expressed as beta (β) values. Association analyses will be performed to detect differentially methylated sites on the targeted candidate genes between the intervention and non-intervention groups using the Δβ (changes in methylation) with adjustment for age, health behaviors, early life adversity, hybridization batch, and top principal components of the probes as covariates. To account for multiple testing, we will use FDR adjustment with a corrected p-value of <0.05 regarded as statistically significant. To assess the relationship between inflammatory burden and Δβ among the study samples, we will repeat association analyses with the inclusion of individual inflammation protein measures. ANCOVA will be used because it is more statistically powerful to detect differences.
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Affiliation(s)
- Jacquelyn Y. Taylor
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Alexandria Jones-Patten
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Laura Prescott
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Stephanie Potts-Thompson
- Center for Research on People of Color, Columbia University School of Nursing, New York, New York, United States of America
| | - Cara Joyce
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Bamidele Tayo
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Karen Saban
- Marcella Niehoff School of Nursing, Center for Translational Research and Education, Loyola University Chicago, Maywood, Illinois, United States of America
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11
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Martz CD, Benner AD, Goosby BJ, Mitchell C, Gaydosh L. Structural racism in primary schools and changes in epigenetic age acceleration among Black and White youth. Soc Sci Med 2024; 347:116724. [PMID: 38458127 PMCID: PMC11134904 DOI: 10.1016/j.socscimed.2024.116724] [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: 08/24/2023] [Revised: 11/14/2023] [Accepted: 02/23/2024] [Indexed: 03/10/2024]
Abstract
Structural racism generates racial inequities in U.S. primary education, including segregated schools, inequitable funding and resources, racial disparities in discipline and achievement, and hostile racial climates, which are risk factors for adverse youth health and development. Black youth are disproportionately exposed to adverse school contexts that may become biologically embedded via stress-mediated epigenetic pathways. This study examined whether childhood exposure to adverse school contexts is associated with changes in epigenetic aging during adolescent development. DNA methylation-based epigenetic clocks were calculated from saliva samples at ages 9 and 15 among Black (n = 774) and White (n = 287) youth in the Future of Families and Child Wellbeing Study (2009-2015). We performed latent class analyses to identify race-specific primary school contexts using administrative data on segregation, discipline, achievement, resources, economic disadvantage, and racial harassment. We then estimated change in epigenetic age acceleration from childhood to adolescence across school typologies using GrimAge, PhenoAge, and DunedinPACE epigenetic clocks. Three distinct school contexts were identified for Black youth: segregated and highly-disadvantaged (17.0%), segregated and moderately-disadvantaged (52.1%), and integrated and moderately-disadvantaged (30.8%). Two school contexts emerged for White youth: integrated and unequal (46.5%) and predominantly White & advantaged (53.5%). At age 15, Black youth who attended segregated and highly-disadvantaged primary schools experienced increases in their speed of epigenetic aging with GrimAge and DunedinPACE. Slowed epigenetic aging with GrimAge was observed for Black youth who attended integrated and moderately-disadvantaged schools. School contexts were not associated with changes in epigenetic age acceleration for White youth. Our findings suggest that manifestations of structural racism in primary school contexts are associated with early-life epigenetic age acceleration and may forecast future health inequities.
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Affiliation(s)
- Connor D Martz
- Population Research Center, The University of Texas at Austin, United States.
| | - Aprile D Benner
- Population Research Center, The University of Texas at Austin, United States; Department of Human Development and Family Sciences, The University of Texas at Austin, United States
| | - Bridget J Goosby
- Population Research Center, The University of Texas at Austin, United States; Department of Sociology, The University of Texas at Austin, United States
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, United States
| | - Lauren Gaydosh
- Population Research Center, The University of Texas at Austin, United States; Department of Sociology, The University of Texas at Austin, United States
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12
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Tomoda A, Nishitani S, Takiguchi S, Fujisawa TX, Sugiyama T, Teicher MH. The neurobiological effects of childhood maltreatment on brain structure, function, and attachment. Eur Arch Psychiatry Clin Neurosci 2024:10.1007/s00406-024-01779-y. [PMID: 38466395 DOI: 10.1007/s00406-024-01779-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/16/2024] [Indexed: 03/13/2024]
Abstract
Childhood maltreatment is a risk factor for psychopathologies, and influences brain development at specific periods, particularly during early childhood and adolescence. This narrative review addresses phenotypic alterations in sensory systems associated with specific types of childhood maltreatment exposure, periods of vulnerability to the neurobiological effects of maltreatment, and the relationships between childhood maltreatment and brain structure, function, connectivity, and network architecture; psychopathology; and resilience. It also addresses neurobiological alterations associated with maternal communication and attachment disturbances, and uses laboratory-based measures during infancy and case-control studies to elucidate neurobiological alterations in reactive attachment disorders in children with maltreatment histories. Moreover, we review studies on the acute effects of oxytocin on reactive attachment disorder and maltreatment and methylation of oxytocin regulatory genes. Epigenetic changes may play a critical role in initiating or producing the atypical structural and functional brain alterations associated with childhood maltreatment. However, these changes could be reversed through psychological and pharmacological interventions, and by anticipating or preventing the emergence of brain alterations and subsequent psychopathological risks.
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Affiliation(s)
- Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, 23-3 Matsuoka-Shimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan.
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Fukui, Japan.
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan.
| | - Shota Nishitani
- Research Center for Child Mental Development, University of Fukui, 23-3 Matsuoka-Shimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Fukui, Japan
| | - Shinichiro Takiguchi
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Fukui, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Takashi X Fujisawa
- Research Center for Child Mental Development, University of Fukui, 23-3 Matsuoka-Shimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Fukui, Japan
| | - Toshiro Sugiyama
- Research Center for Child Mental Development, University of Fukui, 23-3 Matsuoka-Shimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Fukui, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Martin H Teicher
- Developmental Biopsychiatry Research Program, McLean Hospital, Belmont, USA
- Department of Psychiatry, Harvard Medical School, Boston, USA
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13
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Carver AJ, Hing B, Elser BA, Lussier SJ, Yamanashi T, Howard MA, Kawasaki H, Shinozaki G, Stevens HE. Correlation of telomere length in brain tissue with peripheral tissues in living human subjects. Front Mol Neurosci 2024; 17:1303974. [PMID: 38516039 PMCID: PMC10954899 DOI: 10.3389/fnmol.2024.1303974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
Telomeres are important to chromosomal stability, and changes in their length correlate with disease, potentially relevant to brain disorders. Assessing telomere length in human brain is invasive, but whether peripheral tissue telomere length correlates with that in brain is not known. Saliva, buccal, blood, and brain samples were collected at time points before, during, and after subjects undergoing neurosurgery (n = 35) for intractable epilepsy. DNA was isolated from samples and average telomere length assessed by qPCR. Correlations of telomere length between tissue samples were calculated across subjects. When data were stratified by sex, saliva telomere length correlated with brain telomere length in males only. Buccal telomere length correlated with brain telomere length when males and females were combined. These findings indicate that in living subjects, telomere length in peripheral tissues variably correlates with that in brain and may be dependent on sex. Peripheral tissue telomere length may provide insight into brain telomere length, relevant to assessment of brain disorder pathophysiology.
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Affiliation(s)
- Annemarie J. Carver
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, United States
| | - Benjamin Hing
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Benjamin A. Elser
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA, United States
| | - Stephanie J. Lussier
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Biostatistics Graduate Program, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Takehiko Yamanashi
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Standford University, Stanford, CA, United States
- Division of Neuropsychiatry, Tottori University, Tottori, Japan
| | - Matthew A. Howard
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Department of Neurosurgery, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Hiroto Kawasaki
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Department of Neurosurgery, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Gen Shinozaki
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Standford University, Stanford, CA, United States
| | - Hanna E. Stevens
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, United States
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, IA, United States
- Hawk-Intellectual and Developmental Disabilities Research Center, University of Iowa, Iowa City, IA, United States
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14
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Donmez HG, Celik HT, Kayki G, Tanacan A, Cagan M, Yigit S, Yurdakok M, Cakar AN, Beksac MS. Impact of Prematurity on the Buccal Epithelial Cells of the Neonates via Wnt/Beta-Catenin Signaling Pathway and Apoptosis. Am J Perinatol 2024; 41:445-451. [PMID: 34891194 DOI: 10.1055/s-0041-1740348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Understanding the reflections of prematurity is necessary for the management of neonatal complications. We focused on the impact of prematurity and related "maternal risk factors/obstetric complications" on buccal cells of the neonates via evaluation of the Wnt/β-catenin signaling pathway and apoptosis. STUDY DESIGN This study consisted of "early preterm neonates (EPN) (≤34th gestational week [gw]) (n = 36)," "late preterm neonates (LPN) (34th- < 37th gw) (n = 46)," and "term neonates (control) (≥37th gw) (n = 56)." Cohort was also subclassified according to the presence of maternal risk factors, obstetric complications, and neonatal complications. Wnt/β-catenin signaling and caspase-3 activation pathways were studied immunocytochemically. RESULTS Wnt/β-catenin signaling positivity was statistically more frequent at buccal smears of the EPN and LPN groups compared with controls (p < 0.001). The cutoff for gestational age at delivery in receiver operating characteristic curve with the best balance of sensitivity (67.4%) and specificity (67.3%) was 35.8th gw for determining the reduction of Wnt/β-catenin signaling positivity (p < 0.001). The study demonstrated that obstetric complications significantly affected the activity of signaling, while maternal risk factors do not have any effect on Wnt/β-catenin signaling pathway (p = 0.003 and p = 0.828, respectively). This study also demonstrated a significant relationship between Wnt/β-catenin signaling pathway and the presence of neonatal complications (p = 0.015). CONCLUSION Dynamic characteristics of buccal cells are influenced by prematurity and related obstetric and neonatal problems. Buccal smear is a good tool to investigate the impact of prematurity and obstetric problems on perinatal outcome. KEY POINTS · Neonatal buccal cells are affected by prematurity and related obstetric/neonatal problems.. · 35.8th gw is critical for determining the reduction of Wnt/β-catenin signaling positivity.. · Obstetric and neonatal complications significantly related to Wnt/β-catenin signaling activity..
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Affiliation(s)
- Hanife Guler Donmez
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Hasan Tolga Celik
- Division of Neonatology, Department of Pediatrics, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Gozdem Kayki
- Division of Neonatology, Department of Pediatrics, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Atakan Tanacan
- Division of Perinatology, Department of Obstetrics and Gynecology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
- Department of Obstetrics and Gynecology, Turkish Ministry of Health Ankara City Hospital, Ankara, Turkey
| | - Murat Cagan
- Division of Perinatology, Department of Obstetrics and Gynecology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Sule Yigit
- Division of Neonatology, Department of Pediatrics, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Murat Yurdakok
- Division of Neonatology, Department of Pediatrics, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Ayse Nur Cakar
- Department of Histology, Faculty of Medicine, TOBB University, Ankara, Turkey
| | - Mehmet Sinan Beksac
- Division of Perinatology, Department of Obstetrics and Gynecology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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15
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Wang Z, Fu G, Ma G, Wang C, Wang Q, Lu C, Fu L, Zhang X, Cong B, Li S. The association between DNA methylation and human height and a prospective model of DNA methylation-based height prediction. Hum Genet 2024; 143:401-421. [PMID: 38507014 DOI: 10.1007/s00439-024-02659-0] [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: 09/12/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024]
Abstract
As a vital anthropometric characteristic, human height information not only helps to understand overall developmental status and genetic risk factors, but is also important for forensic DNA phenotyping. We utilized linear regression analysis to test the association between each CpG probe and the height phenotype. Next, we designed a methylation sequencing panel targeting 959 CpGs and subsequent height inference models were constructed for the Chinese population. A total of 11,730 height-associated sites were identified. By employing KPCA and deep neural networks, a prediction model was developed, of which the cross-validation RMSE, MAE and R2 were 5.62 cm, 4.45 cm and 0.64, respectively. Genetic factors could explain 39.4% of the methylation level variance of sites used in the height inference models. Collectively, we demonstrated an association between height and DNA methylation status through an EWAS analysis. Targeted methylation sequencing of only 959 CpGs combined with deep learning techniques could provide a model to estimate human height with higher accuracy than SNP-based prediction models.
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Affiliation(s)
- Zhonghua Wang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Guangping Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Guanju Ma
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Chunyan Wang
- Physical Examination Center of Shijiazhuang People's Hospital, Shijiazhuang, 050011, Hebei, China
| | - Qian Wang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Chaolong Lu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Lihong Fu
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Xiaojing Zhang
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China
| | - Shujin Li
- College of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Hebei Medical University, Chinese Academy of Medical Sciences, Shijiazhuang, 050017, Hebei, China.
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16
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Kwok AJ, Lu J, Huang J, Ip BY, Mok VCT, Lai HM, Ko H. High-resolution omics of vascular ageing and inflammatory pathways in neurodegeneration. Semin Cell Dev Biol 2024; 155:30-49. [PMID: 37380595 DOI: 10.1016/j.semcdb.2023.06.005] [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: 04/29/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
High-resolution omics, particularly single-cell and spatial transcriptomic profiling, are rapidly enhancing our comprehension of the normal molecular diversity of gliovascular cells, as well as their age-related changes that contribute to neurodegeneration. With more omic profiling studies being conducted, it is becoming increasingly essential to synthesise valuable information from the rapidly accumulating findings. In this review, we present an overview of the molecular features of neurovascular and glial cells that have been recently discovered through omic profiling, with a focus on those that have potentially significant functional implications and/or show cross-species differences between human and mouse, and that are linked to vascular deficits and inflammatory pathways in ageing and neurodegenerative disorders. Additionally, we highlight the translational applications of omic profiling, and discuss omic-based strategies to accelerate biomarker discovery and facilitate disease course-modifying therapeutics development for neurodegenerative conditions.
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Affiliation(s)
- Andrew J Kwok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jianning Lu
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junzhe Huang
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bonaventure Y Ip
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hei Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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17
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Camerota M, Lester BM, Castellanos FX, Carter BS, Check J, Helderman J, Hofheimer JA, McGowan EC, Neal CR, Pastyrnak SL, Smith LM, O'Shea TM, Marsit CJ, Everson TM. Epigenome-wide association study identifies neonatal DNA methylation associated with two-year attention problems in children born very preterm. Transl Psychiatry 2024; 14:126. [PMID: 38418845 PMCID: PMC10902402 DOI: 10.1038/s41398-024-02841-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Prior research has identified epigenetic predictors of attention problems in school-aged children but has not yet investigated these in young children, or children at elevated risk of attention problems due to preterm birth. The current study evaluated epigenome-wide associations between neonatal DNA methylation and attention problems at age 2 years in children born very preterm. Participants included 441 children from the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study, a multi-site study of infants born < 30 weeks gestational age. DNA methylation was measured from buccal swabs collected at NICU discharge using the Illumina MethylationEPIC Bead Array. Attention problems were assessed at 2 years of adjusted age using the attention problems subscale of the Child Behavior Checklist (CBCL). After adjustment for multiple testing, DNA methylation at 33 CpG sites was associated with child attention problems. Differentially methylated CpG sites were located in genes previously linked to physical and mental health, including several genes associated with ADHD in prior epigenome-wide and genome-wide association studies. Several CpG sites were located in genes previously linked to exposure to prenatal risk factors in the NOVI sample. Neonatal epigenetics measured at NICU discharge could be useful in identifying preterm children at risk for long-term attention problems and related psychiatric disorders, who could benefit from early prevention and intervention efforts.
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Affiliation(s)
- Marie Camerota
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA.
- Brown Center for the Study of Children at Risk, Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA.
| | - Barry M Lester
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
- Brown Center for the Study of Children at Risk, Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA
- Department of Pediatrics, Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA
| | - Francisco Xavier Castellanos
- Department of Child and Adolescent Psychiatry, NYU Grossman School of Medicine, New York, NY, USA
- Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - Brian S Carter
- Department of Pediatrics-Neonatology, Children's Mercy Hospital, Kansas City, MO, USA
| | - Jennifer Check
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer Helderman
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Julie A Hofheimer
- Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Elisabeth C McGowan
- Department of Pediatrics, Alpert Medical School of Brown University and Women and Infants Hospital, Providence, RI, USA
| | - Charles R Neal
- Department of Pediatrics, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Steven L Pastyrnak
- Department of Pediatrics, Spectrum Health-Helen DeVos Hospital, Grand Rapids, MI, USA
| | - Lynne M Smith
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Thomas Michael O'Shea
- Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Todd M Everson
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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18
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Luqman A, He M, Hassan A, Ullah M, Zhang L, Rashid Khan M, Din AU, Ullah K, Wang W, Wang G. Mood and microbes: a comprehensive review of intestinal microbiota's impact on depression. Front Psychiatry 2024; 15:1295766. [PMID: 38404464 PMCID: PMC10884216 DOI: 10.3389/fpsyt.2024.1295766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/22/2024] [Indexed: 02/27/2024] Open
Abstract
Depression is considered a multifaceted and intricate mental disorder of growing concern due to its significant impact on global health issues. The human gut microbiota, also known as the "second brain," has an important role in the CNS by regulating it through chemical, immunological, hormonal, and neurological processes. Various studies have found a significant bidirectional link between the brain and the gut, emphasizing the onset of depression therapies. The biological and molecular processes underlying depression and microbiota are required, as the bidirectional association may represent a novel study. However, profound insights into the stratification and diversity of the gut microbiota are still uncommon. This article investigates the emerging evidence of a bacterial relationship between the gut and the brain's neurological system and its potential pathogenicity and relevance. The interplay of microbiota, immune system, nervous system neurotransmitter synthesis, and neuroplasticity transitions is also widely studied. The consequences of stress, dietary fibers, probiotics, prebiotics, and antibiotics on the GB axis are being studied. Multiple studies revealed the processes underlying this axis and led to the development of effective microbiota-based drugs for both prevention and treatment. Therefore, the results support the hypothesis that gut microbiota influences depression and provide a promising area of research for an improved knowledge of the etiology of the disease and future therapies.
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Affiliation(s)
- Ameer Luqman
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, National and Local Joint Engineering Laboratory for Vascular Implant, Bioengineering College of Chongqing University, Chongqing, China
| | - Mei He
- Chongqing University Cancer Hospital, Chongqing, China
| | - Adil Hassan
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, National and Local Joint Engineering Laboratory for Vascular Implant, Bioengineering College of Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Nano/Micro Composite Materials and Devices, Chongqing University of Science and Technology, Chongqing, China
- JinFeng Laboratory, Chongqing, China
| | - Mehtab Ullah
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, National and Local Joint Engineering Laboratory for Vascular Implant, Bioengineering College of Chongqing University, Chongqing, China
| | | | - Muhammad Rashid Khan
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, National and Local Joint Engineering Laboratory for Vascular Implant, Bioengineering College of Chongqing University, Chongqing, China
| | - Ahmad Ud Din
- Plants for Human Health Institute, Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Kannapolis, NC, United States
| | - Kamran Ullah
- Department of Biology, The University of Haripur, Haripur, Pakistan
| | - Wei Wang
- Chongqing University Cancer Hospital, Chongqing, China
| | - Guixue Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, National and Local Joint Engineering Laboratory for Vascular Implant, Bioengineering College of Chongqing University, Chongqing, China
- JinFeng Laboratory, Chongqing, China
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19
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Noel ES, Chen A, Peña YA, Honeycutt JA. Early life adversity drives sex-dependent changes in 5-mC DNA methylation of parvalbumin cells in the prefrontal cortex in rats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578313. [PMID: 38352518 PMCID: PMC10862911 DOI: 10.1101/2024.01.31.578313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Early life adversity (ELA) can result in increased risk for developing affective disorders, such as anxiety or depression, later in life, with women showing increased risk. Interactions between an individual's genes and their environment play key roles in producing, as well as mitigating, later life neuropathology. Our current understanding of the underlying epigenomic drivers of ELA associated anxiety and depression are limited, and this stems in part from the complexity of underlying biochemical processes associated with how early experiences shapes later life behavior. Epigenetic alterations, or experience-driven modifications to DNA, can be leveraged to understand the interplay between genes and the environment. The present study characterized DNA methylation patterning, assessed via evaluation of 5-methylcytosine (5-mC), following ELA in a Sprague Dawley rat model of ELA induced by early caregiver deprivation. This study utilized maternal separation to investigate sex- and age-specific outcomes of ELA on epigenetic patterning in parvalbumin (PV)-containing interneurons in the prefrontal cortex (PFC), a subpopulation of inhibitory neurons which are associated with ELA and affective dysfunction. While global analysis of 5-mC methylation and CpG site specific pyrosequencing of the PV promoter, Pvalb, showed no obvious effects of ELA, when analyses were restricted to assessing 5-mC intensity in colocalized PV cells, there were significant sex and age dependent effects. We found that ELA leads sex-specific changes in PV cell counts, and that cell counts can be predicted by 5-mC intensity, with males and females showing distinct patterns of methylation and PV outcomes. ELA also produced sex-specific effects in corticosterone reactivity, with juvenile females showing a blunted stress hormone response compared to controls. Overall, ELA led to a sex-specific developmental shift in PV profile, which is comparable to profiles that are seen at a later developmental timepoint, and this shift may be mediated in part by epigenomic alterations driven by altered DNA methylation.
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Affiliation(s)
- Emma S Noel
- Program in Biochemistry, Brunswick, ME 04011 USA
| | - Alissa Chen
- Program in Neuroscience, Brunswick, ME 04011 USA
| | | | - Jennifer A Honeycutt
- Program in Neuroscience, Brunswick, ME 04011 USA
- Department of Psychology Bowdoin College, Brunswick, ME 04011 USA
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20
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Mirza S, Lima CNC, Del Favero-Campbell A, Rubinstein A, Topolski N, Cabrera-Mendoza B, Kovács EHC, Blumberg HP, Richards JG, Williams AJ, Wemmie JA, Magnotta VA, Fiedorowicz JG, Gaine ME, Walss-Bass C, Quevedo J, Soares JC, Fries GR. Blood epigenome-wide association studies of suicide attempt in adults with bipolar disorder. Transl Psychiatry 2024; 14:70. [PMID: 38296944 PMCID: PMC10831084 DOI: 10.1038/s41398-024-02760-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Suicide attempt (SA) risk is elevated in individuals with bipolar disorder (BD), and DNA methylation patterns may serve as possible biomarkers of SA. We conducted epigenome-wide association studies (EWAS) of blood DNA methylation associated with BD and SA. DNA methylation was measured at >700,000 positions in a discovery cohort of n = 84 adults with BD with a history of SA (BD/SA), n = 79 adults with BD without history of SA (BD/non-SA), and n = 76 non-psychiatric controls (CON). EWAS revealed six differentially methylated positions (DMPs) and seven differentially methylated regions (DMRs) between BD/SA and BD/non-SA, with multiple immune-related genes implicated. There were no epigenome-wide significant differences when BD/SA and BD/non-SA were each compared to CON, and patterns suggested that epigenetics differentiating BD/SA from BD/non-SA do not differentiate BD/non-SA from CON. Weighted gene co-methylation network analysis and trait enrichment analysis of the BD/SA vs. BD/non-SA contrast further corroborated immune system involvement, while gene ontology analysis implicated calcium signalling. In an independent replication cohort of n = 48 BD/SA and n = 47 BD/non-SA, fold changes at the discovery cohort's significant sites showed moderate correlation across cohorts and agreement on direction. In both cohorts, classification accuracy for SA history among individuals with BD was highest when methylation at the significant CpG sites as well as information from clinical interviews were combined, with an AUC of 88.8% (CI = 83.8-93.8%) and 82.1% (CI = 73.6-90.5%) for the combined epigenetic-clinical classifier in the discovery and replication cohorts, respectively. Our results provide novel insight to the role of immune system functioning in SA and BD and also suggest that integrating information from multiple levels of analysis holds promise to improve risk assessment for SA in adults with BD.
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Affiliation(s)
- Salahudeen Mirza
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Institute of Child Development, University of Minnesota, 55455, Minneapolis, MN, USA
- Department of Psychiatry, Yale School of Medicine, 06510, New Haven, CT, USA
| | - Camila N C Lima
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
| | - Alexandra Del Favero-Campbell
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
| | - Alexandre Rubinstein
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
| | - Natasha Topolski
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
| | | | - Emese H C Kovács
- Department of Neuroscience and Pharmacology, The University of Iowa, 51 Newton Rd, 52242, Iowa City, IA, USA
| | - Hilary P Blumberg
- Department of Psychiatry, Yale School of Medicine, 06510, New Haven, CT, USA
| | - Jenny Gringer Richards
- Department of Radiology, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
| | - Aislinn J Williams
- Department of Psychiatry, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
- Iowa Neuroscience Institute, The University of Iowa, 169 Newton Rd, 52242, Iowa City, IA, USA
| | - John A Wemmie
- Department of Psychiatry, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
- Iowa Neuroscience Institute, The University of Iowa, 169 Newton Rd, 52242, Iowa City, IA, USA
- Department of Veterans Affairs Medical Center, Iowa City, IA, USA
| | - Vincent A Magnotta
- Department of Radiology, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
- Department of Psychiatry, The University of Iowa, 200 Hawkins Dr, 52242, Iowa City, IA, USA
| | - Jess G Fiedorowicz
- University of Ottawa Brain and Mind Research Institute, Ottawa Hospital Research Institute, 501 Smyth, K1H 8L6, Ottawa, ON, Canada
| | - Marie E Gaine
- Iowa Neuroscience Institute, The University of Iowa, 169 Newton Rd, 52242, Iowa City, IA, USA
- Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, 180 South Grand Ave, 52242, Iowa City, IA, USA
| | - Consuelo Walss-Bass
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
- Center for Interventional Psychiatry, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, 1941 East Rd, 77054, Houston, TX, USA
| | - Jair C Soares
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA
| | - Gabriel R Fries
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054, Houston, TX, USA.
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054, Houston, TX, USA.
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, TX, USA.
- Center for Interventional Psychiatry, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, 1941 East Rd, 77054, Houston, TX, USA.
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21
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Großmann NL, Weihs A, Kühn L, Sauer S, Röh S, Wiechmann T, Rex-Haffner M, Völzke H, Völker U, Binder EB, Teumer A, Homuth G, Klinger-König J, Grabe HJ. Methylation Patterns of the FKBP5 Gene in Association with Childhood Maltreatment and Depressive Disorders. Int J Mol Sci 2024; 25:1485. [PMID: 38338761 PMCID: PMC10855893 DOI: 10.3390/ijms25031485] [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: 12/22/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Childhood maltreatment is an important risk factor for adult depression and has been associated with changes in the hypothalamic pituitary adrenal (HPA) axis, including cortisol secretion and methylation of the FKBP5 gene. Furthermore, associations between depression and HPA changes have been reported. This study investigated the associations of whole-blood FKBP5 mRNA levels, serum cortisol levels, childhood maltreatment, and depressive symptoms with the whole-blood methylation status (assessed via target bisulfite sequencing) of 105 CpGs at the FKBP5 locus using data from the general population-based Study of Health in Pomerania (SHIP) (N = 203). Both direct and interaction effects with the rs1360780 single-nucleotide polymorphism were investigated. Nominally significant associations of main effects on methylation of a single CpG site were observed at intron 3, intron 7, and the 3'-end of the gene. Additionally, methylation at two clusters at the 3'-end and intron 7 were nominally associated with childhood maltreatment × rs1360780 and depressive symptoms × rs1360780, respectively. The results add to the understanding of molecular mechanisms underlying the emergence of depression and could aid the development of personalised depression therapy and drug development.
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Affiliation(s)
- Nora L Großmann
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Antoine Weihs
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17489 Greifswald, Germany
| | - Luise Kühn
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Susann Sauer
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Simone Röh
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Tobias Wiechmann
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Monika Rex-Haffner
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, University Medicine Greifswald, 17475 Greifswald, Germany
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Elisabeth B Binder
- Department Genes and Environment, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alexander Teumer
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Johanna Klinger-König
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17489 Greifswald, Germany
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22
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Smirnova L, Modafferi S, Schlett C, Osborne LM, Payne JL, Sabunciyan S. Blood extracellular vesicles carrying brain-specific mRNAs are potential biomarkers for detecting gene expression changes in the female brain. Mol Psychiatry 2024:10.1038/s41380-023-02384-6. [PMID: 38212371 DOI: 10.1038/s41380-023-02384-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 01/13/2024]
Abstract
The absence of non-invasive tests that can monitor the status of the brain is a major obstacle for psychiatric care. In order to address this need, we assessed the feasibility of using tissue-specific gene expression to determine the origin of extracellular vesicle (EV) mRNAs in peripheral blood. Using the placenta as a model, we discovered that 26 messenger RNAs that are specifically expressed in the placenta are present in EVs circulating in maternal blood. Twenty-three of these transcripts were either exclusively or highly expressed in maternal blood during pregnancy only and not in the postpartum period, verifying the feasibility of using tissue-specific gene expression to infer the tissue of origin for EV mRNAs. Using the same bioinformatic approach, which provides better specificity than isolating L1 cell-adhesion molecule containing EVs, we discovered that 181 mRNAs that are specifically expressed in the female brain are also present in EVs circulating in maternal blood. Gene set enrichment analysis revealed that these transcripts, which are involved in synaptic functions and myelination, are enriched for genes implicated in mood disorders, schizophrenia, and substance use disorders. The EV mRNA levels of 13 of these female brain-specific transcripts are associated with postpartum depression (adjusted p-vals = 3 × 10-5 to 0.08), raising the possibility that they can be used to infer the state of the brain. In order to determine the extent to which EV mRNAs reflect transcription in the brain, we compared mRNAs isolated from cells and EVs in an iPSC-derived brain microphysiological system differentiated for 3 and 9 weeks. We discovered that, although cellular and extracellular mRNA levels are not identical, they do correlate, and it is possible to extrapolate cellular RNA expression changes in the brain via EV mRNA levels. Our findings bring EV mRNAs to the forefront of peripheral biomarker development efforts in psychiatric diseases by demonstrating the feasibility of inferring transcriptional changes in the brain via blood EV mRNA levels.
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Affiliation(s)
- Lena Smirnova
- Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Sergio Modafferi
- Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Charlotte Schlett
- Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Lauren M Osborne
- Departments of Obstetrics & Gynecology and of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - Jennifer L Payne
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sarven Sabunciyan
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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23
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Zheng J, Womer FY, Tang L, Guo H, Zhang X, Tang Y, Wang F. Integrative omics analysis reveals epigenomic and transcriptomic signatures underlying brain structural deficits in major depressive disorder. Transl Psychiatry 2024; 14:17. [PMID: 38195555 PMCID: PMC10776753 DOI: 10.1038/s41398-023-02724-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
Several lines of evidence support the involvement of transcriptomic and epigenetic mechanisms in the brain structural deficits of major depressive disorder (MDD) separately. However, research in these two areas has remained isolated. In this study, we proposed an integrative strategy that combined neuroimaging, brain-wide gene expression, and peripheral DNA methylation data to investigate the genetic basis of gray matter abnormalities in MDD. The MRI T1-weighted images and Illumina 850 K DNA methylation microarrays were obtained from 269 patients and 416 healthy controls, and brain-wide transcriptomic data were collected from Allen Human Brain Atlas. The between-group differences in gray matter volume (GMV) and differentially methylated CpG positions (DMPs) were examined. The genes with their expression patterns spatially related to GMV changes and genes with DMPs were overlapped and selected. Using principal component regression, the associations between DMPs in overlapped genes and GMV across individual patients were investigated, and the region-specific correlations between methylation status and gene expression were examined. We found significant associations between the decreased GMV and DMPs methylation status in the anterior cingulate cortex, inferior frontal cortex, and fusiform face cortex regions. These DMPs genes were primarily enriched in the neurodevelopmental and synaptic transmission process. There was a significant negative correlation between DNA methylation and gene expression in genes associated with GMV changes of the frontal cortex in MDD. Our findings suggest that GMV abnormalities in MDD may have a transcriptomic and epigenetic basis. This imaging-transcriptomic-epigenetic integrative analysis provides spatial and biological links between cortical morphological deficits and peripheral epigenetic signatures in MDD.
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Affiliation(s)
- Junjie Zheng
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China
| | - Fay Y Womer
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lili Tang
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China
| | - Huiling Guo
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
- Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Xizhe Zhang
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Yanqing Tang
- Department of Psychiatry, The First Hospital of China Medical University, Shenyang, China.
- Brain Function Research Section, The First Hospital of China Medical University, Shenyang, China.
- Department of Gerontology, The First Hospital of China Medical University, Shenyang, China.
- Shengjing Hospital of China Medical University, Shenyang, China.
| | - Fei Wang
- Early Intervention Unit, Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China.
- Functional Brain Imaging Institute of Nanjing Medical University, Nanjing, China.
- Department of Mental Health, School of Public Health, Nanjing Medical University, Nanjing, China.
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24
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Schuch JB, Bandeira CE, Junior JLS, Müller D, Charão MF, da Silva BS, Grevet EH, Kessler FHP, von Diemen L, Rovaris DL, Bau CHD. Global DNA methylation patterns in Alcohol Use Disorder. Genet Mol Biol 2024; 46:e20230139. [PMID: 38197733 PMCID: PMC10778554 DOI: 10.1590/1678-4685-gmb-2023-0139] [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: 05/03/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024] Open
Abstract
Alcohol Use Disorder (AUD) is a highly prevalent condition worldwide that produces a wide range of pathophysiological consequences, with a critical impact on health and social issues. Alcohol influences gene expression through epigenetic changes mainly through DNA methylation. In this sense, levels of 5-methylcytosine (5-mC), namely Global DNA methylation (GMe), which can be influenced by environmental and hormonal effects, represent a putative biological mechanism underlying alcohol effects. Our aim was to investigate the influence of AUD diagnosis and alcohol patterns (i.e., years of addiction, use in the last 30 days, and alcohol severity) on GMe levels. The sample consisted of 256 men diagnosed with AUD and 361 men without AUD. DNA samples from peripheral blood were used to assess GMe levels, measured through the levels of 5-mC using high-performance liquid chromatography. Results from multiple linear regression analysis indicated that the presence of AUD was associated with lower GMe levels (beta=-0.155, p=0.011). Other alcohol-related outcomes were not associated with DNA methylation. Our findings are consistent with the hypothesis that the impact of chronic and heavy alcohol use in GMe could be a potential mechanism mediating the multiple organ damages related to AUD.
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Affiliation(s)
- Jaqueline B. Schuch
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa em Álcool e Drogas, Porto Alegre, RS, Brazil
| | - Cibele E. Bandeira
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Fisiologia e Biofísica, São Paulo, SP, Brazil
| | - Jorge L. S. Junior
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Diana Müller
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
| | - Mariele F. Charão
- Universidade Feevale, Programa de Pós-Graduação em Toxicologia e Análises Toxicológicas, Novo Hamburgo, RS, Brazil
| | - Bruna S. da Silva
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Fisiologia e Biofísica, São Paulo, SP, Brazil
| | - Eugenio H. Grevet
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
| | - Felix H. P. Kessler
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa em Álcool e Drogas, Porto Alegre, RS, Brazil
| | - Lisia von Diemen
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa em Álcool e Drogas, Porto Alegre, RS, Brazil
| | - Diego L. Rovaris
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Fisiologia e Biofísica, São Paulo, SP, Brazil
| | - Claiton H. D. Bau
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
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25
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Wortinger LA, Stavrum AK, Shadrin AA, Szabo A, Rukke SH, Nerland S, Smelror RE, Jørgensen KN, Barth C, Andreou D, Weibell MA, Djurovic S, Andreassen OA, Thoresen M, Ursini G, Agartz I, Le Hellard S. Divergent epigenetic responses to perinatal asphyxia in severe mental disorders. Transl Psychiatry 2024; 14:16. [PMID: 38191519 PMCID: PMC10774425 DOI: 10.1038/s41398-023-02709-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/10/2024] Open
Abstract
Epigenetic modifications influenced by environmental exposures are molecular sources of phenotypic heterogeneity found in schizophrenia and bipolar disorder and may contribute to shared etiopathogenetic mechanisms of these two disorders. Newborns who experienced perinatal asphyxia have suffered reduced oxygen delivery to the brain around the time of birth, which increases the risk of later psychiatric diagnosis. This study aimed to investigate DNA methylation in blood cells for associations with a history of perinatal asphyxia, a neurologically harmful condition occurring within the biological environment of birth. We utilized prospective data from the Medical Birth Registry of Norway to identify incidents of perinatal asphyxia in 643 individuals with schizophrenia or bipolar disorder and 676 healthy controls. We performed an epigenome wide association study to distinguish differentially methylated positions associated with perinatal asphyxia. We found an interaction between methylation and exposure to perinatal asphyxia on case-control status, wherein having a history of perinatal asphyxia was associated with an increase of methylation in healthy controls and a decrease of methylation in patients on 4 regions of DNA important for brain development and function. The differentially methylated regions were observed in genes involved in oligodendrocyte survival and axonal myelination and functional recovery (LINGO3); assembly, maturation and maintenance of the brain (BLCAP;NNAT and NANOS2) and axonal transport processes and neural plasticity (SLC2A14). These findings are consistent with the notion that an opposite epigenetic response to perinatal asphyxia, in patients compared with controls, may contribute to molecular mechanisms of risk for schizophrenia and bipolar disorder.
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Affiliation(s)
- Laura A Wortinger
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway.
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Anne-Kristin Stavrum
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Alexey A Shadrin
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Attila Szabo
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | | | - Stener Nerland
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Runar Elle Smelror
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kjetil Nordbø Jørgensen
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychiatry, Telemark Hospital, Skien, Norway
| | - Claudia Barth
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dimitrios Andreou
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Melissa A Weibell
- TIPS-Network for Clinical Research in Psychosis, Department of Psychiatry, Stavanger University Hospital, Stavanger, Norway
- Faculty of Health, Network for Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Srdjan Djurovic
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ole A Andreassen
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Marianne Thoresen
- Department of Physiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Neonatal Neuroscience, Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Gianluca Ursini
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ingrid Agartz
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- Centre for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet and Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Stephanie Le Hellard
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
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26
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Farrell C, Hu C, Lapborisuth K, Pu K, Snir S, Pellegrini M. Identifying epigenetic aging moderators using the epigenetic pacemaker. FRONTIERS IN BIOINFORMATICS 2024; 3:1308680. [PMID: 38235295 PMCID: PMC10791860 DOI: 10.3389/fbinf.2023.1308680] [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: 10/06/2023] [Accepted: 12/04/2023] [Indexed: 01/19/2024] Open
Abstract
Epigenetic clocks are DNA methylation-based chronological age prediction models that are commonly employed to study age-related biology. The difference between the predicted and observed age is often interpreted as a form of biological age acceleration, and many studies have measured the impact of environmental and disease-associated factors on epigenetic age. Most epigenetic clocks are fit using approaches that minimize the error between the predicted and observed chronological age, and as a result, they may not accurately model the impact of factors that moderate the relationship between the actual and epigenetic age. Here, we compare epigenetic clocks that are constructed using penalized regression methods to an evolutionary framework of epigenetic aging with the epigenetic pacemaker (EPM), which directly models DNA methylation as a function of a time-dependent epigenetic state. In simulations, we show that the value of the epigenetic state is impacted by factors such as age, sex, and cell-type composition. Next, in a dataset aggregated from previous studies, we show that the epigenetic state is also moderated by sex and the cell type. Finally, we demonstrate that the epigenetic state is also moderated by toxins in a study on polybrominated biphenyl exposure. Thus, we find that the pacemaker provides a robust framework for the study of factors that impact epigenetic age acceleration and that the effect of these factors may be obscured in traditional clocks based on linear regression models.
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Affiliation(s)
- Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Chanyue Hu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kalsuda Lapborisuth
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kyle Pu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sagi Snir
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
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27
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Ell MA, Schiele MA, Iovino N, Domschke K. Epigenetics of Fear, Anxiety and Stress - Focus on Histone Modifications. Curr Neuropharmacol 2024; 22:843-865. [PMID: 36946487 PMCID: PMC10845084 DOI: 10.2174/1570159x21666230322154158] [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: 09/30/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 03/23/2023] Open
Abstract
Fear-, anxiety- and stress-related disorders are among the most frequent mental disorders. Given substantial rates of insufficient treatment response and often a chronic course, a better understanding of the pathomechanisms of fear-, anxiety- and stress-related disorders is urgently warranted. Epigenetic mechanisms such as histone modifications - positioned at the interface between the biological and the environmental level in the complex pathogenesis of mental disorders - might be highly informative in this context. The current state of knowledge on histone modifications, chromatin-related pharmacology and animal models modified for genes involved in the histone-related epigenetic machinery will be reviewed with respect to fear-, anxiety- and stress-related states. Relevant studies, published until 30th June 2022, were identified using a multi-step systematic literature search of the Pub- Med and Web of Science databases. Animal studies point towards histone modifications (e.g., H3K4me3, H3K9me1/2/3, H3K27me2/3, H3K9ac, H3K14ac and H4K5ac) to be dynamically and mostly brain region-, task- and time-dependently altered on a genome-wide level or gene-specifically (e.g., Bdnf) in models of fear conditioning, retrieval and extinction, acute and (sub-)chronic stress. Singular and underpowered studies on histone modifications in human fear-, anxiety- or stress-related phenotypes are currently restricted to the phenotype of PTSD. Provided consistent validation in human phenotypes, epigenetic biomarkers might ultimately inform indicated preventive interventions as well as personalized treatment approaches, and could inspire future innovative pharmacological treatment options targeting the epigenetic machinery improving treatment response in fear-, anxiety- and stressrelated disorders.
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Affiliation(s)
- Marco A. Ell
- Department of Psychiatry and Psychotherapy, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Miriam A. Schiele
- Department of Psychiatry and Psychotherapy, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Nicola Iovino
- Department of Chromation Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Katharina Domschke
- Department of Psychiatry and Psychotherapy, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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28
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Van Assche E, Hohoff C, Zang J, Knight MJ, Baune BT. Epigenetic modification related to cognitive changes during a cognitive training intervention in depression. Prog Neuropsychopharmacol Biol Psychiatry 2023; 127:110835. [PMID: 37516234 DOI: 10.1016/j.pnpbp.2023.110835] [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: 05/01/2023] [Revised: 07/17/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND DNA methylation as a biomarker is well suited to investigate dynamic processes, such as symptom improvement. For this study we focus on epigenomic state or trait markers as early signatures of cognitive improvement in individuals receiving a cognitive intervention. We performed a first epigenome-wide association study (EWAS) on patients with cognitive dysfunction in depression comparing those with vs without cognitive dysfunction and those cognitively improving vs non-improving following a cognitive intervention. METHOD Data from a randomized controlled trial (RCT) were used for this analysis, where cognitive function of 112 patients randomly assigned to a personalized cognitive intervention was compared to standard cognitive treatment. Cognition was measured for this study using the four cognitive tasks from the THINC-it battery. We compared individuals with cognitive impairment with individuals without cognitive impairment at baseline and after a cognitive intervention of 8 weeks. Blood for DNA methylation analysis (Illumina Infinium MethylationEPIC 850 k BeadChip) was collected at baseline and 8 weeks into the treatment. For the baseline analysis, after quality control, the final sample comprised 90 individuals, and analyses at week 8 were performed on 84 individuals. Data cleaning, quality control, and differential methylation analysis of DNA methylation data was performed using the RnBeads package (R). Analyses were corrected for gender, age, depression score (MADRS), reported years of education, height and weight, as well as surrogate variables estimated by the pipeline used. The within-individual paired longitudinal analysis was performed using Welch's t-test. RESULTS Analyses at baseline and at week 8 did not show any genome-wide significant CpGs (p < 5 × 10-8) comparing patients with and without cognitive impairment. The most significant result in the baseline analysis comparing the groups with and without cognitive impairment at baseline is located in an open Sea region with predominantly regulatory qualities (cg10962945; 6.61 × 10-7). The most significant CpG at 8 weeks was also located in open sea, though in exon 13 of the NTRK2-gene, linked to the BDNF pathway (cg13620631, 5.56 × 10-7). Finally, a within-individual paired longitudinal analysis with only patients that show improved cognitive function over time was performed, showing 65 CpGs that overlapped between the 1% most significant of this analysis and the 1% most significant CpGs from the cross-sectional analysis at 8 weeks. CONCLUSION Our result suggest that DNA methylation can be suitable to capture early signs of treatment response of a cognitive intervention in depression. In our layered approach we could capture dynamics that can help differentiate between biological trait and state markers of cognitive function in depression. Despite not being genome-wide significant, the CpG locations returned by our analysis comparing patients with and without cognitive impairment, are in line with prior knowledge on pathways and genes relevant for depression treatment and cognition.
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Affiliation(s)
| | - Christa Hohoff
- Department of Psychiatry, University of Münster, Münster, Germany.
| | - Johannes Zang
- Department of Psychiatry, University of Münster, Münster, Germany.
| | - Matthew J Knight
- Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Bernhard T Baune
- Department of Psychiatry, University of Münster, Münster, Germany; Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia.
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29
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Wieting J, Jahn K, Bleich S, Frieling H, Deest M. A targeted long-read sequencing approach questions the association of OXTR methylation with high-functioning autism. Clin Epigenetics 2023; 15:195. [PMID: 38124130 PMCID: PMC10734107 DOI: 10.1186/s13148-023-01616-4] [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: 08/21/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND DNA sequence variation and altered epigenetic regulation of the oxytocin receptor gene (OXTR) have been implicated in autism and autistic-like behaviors. While previous studies have examined subsegments of OXTR, nanopore Cas9-targeted sequencing (nCATS) allows deep characterization of entire genes with simultaneous assessment of epigenetic 5-methylcytosine (5mC) modification and without the need for prior DNA amplification or bisulfite conversion. This pilot study uses an nCATS approach to sequence the entire OXTR gene and its regulatory construct and screen for 5mC modification to compare results between individuals with high-functioning autism (HFA) and neurotypical controls (NC). METHODS Using DNA extracted from peripheral blood, OXTR (Hg38, chr3: 8750381-8770434, 20,054 base pairs) was analyzed by nCATS. 5mC modification probabilities were calculated and visualized across the gene and differential methylation analysis was performed. RESULTS Twenty adults with HFA (10 males, 10 females) and 20 age- and sex-matched NC (± 5 years) were included. There were no apparent group differences in the entire OXTR gene sequence, except for the intron variant rs918316, which was clustered in the HFA group. However, differential methylation analysis did not reveal a single significant group-dependent differentially methylated site among the 412 CpG sites captured. LIMITATIONS Limitations of this study include the small number of samples due to the pilot nature of the study, which particularly limits the relevance of the sequence variants found. It should also be noted that the use of peripheral blood material limits the ability to draw conclusions about central processes. CONCLUSIONS Previous findings of autism-associated OXTR epigenetic alterations were not reproducible with our method. In our opinion, this may lead to a reconsideration of the relevance of altered methylation at individual OXTR CpG positions in autism research. However, given the pilot nature of the study, these results need to be replicated in independent cohorts and with larger sample sizes.
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Affiliation(s)
- Jelte Wieting
- Hannover Medical School, Department of Psychiatry, Social Psychiatry and Psychotherapy, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- Laboratory for Molecular Neuroscience, Feodor-Lynen-Str. 35, 30625, Hannover, Germany.
| | - Kirsten Jahn
- Laboratory for Molecular Neuroscience, Feodor-Lynen-Str. 35, 30625, Hannover, Germany
| | - Stefan Bleich
- Hannover Medical School, Department of Psychiatry, Social Psychiatry and Psychotherapy, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Laboratory for Molecular Neuroscience, Feodor-Lynen-Str. 35, 30625, Hannover, Germany
| | - Helge Frieling
- Hannover Medical School, Department of Psychiatry, Social Psychiatry and Psychotherapy, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Laboratory for Molecular Neuroscience, Feodor-Lynen-Str. 35, 30625, Hannover, Germany
| | - Maximilian Deest
- Hannover Medical School, Department of Psychiatry, Social Psychiatry and Psychotherapy, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Laboratory for Molecular Neuroscience, Feodor-Lynen-Str. 35, 30625, Hannover, Germany
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30
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Strawn M, Safranski TJ, Behura SK. Does DNA methylation in the fetal brain leave an epigenetic memory in the blood? Gene 2023; 887:147788. [PMID: 37696423 DOI: 10.1016/j.gene.2023.147788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023]
Abstract
Epigenetic memory is an emerging concept that refers to the process in which epigenetic changes occurring early-in life can lead to long-term programs of gene regulation in time and space. By leveraging neural network regression modeling of DNA methylation data in pigs, we show that specific methylations in the adult blood can reliably predict methylation changes that occurred in the fetal brain. Genes associated with these methylations represented known markers of specific cell types of blood including bone marrow hematopoietic progenitor cells, and ependymal and oligodendrocyte cells of brain. This suggested that methylation changes that occurred in the developing brain were maintained as an epigenetic memory in the blood through the adult life.
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Affiliation(s)
- Monica Strawn
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Timothy J Safranski
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, United States; Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, United States.
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31
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Carrizosa-Molina T, Casillas-Díaz N, Pérez-Nadador I, Vales-Villamarín C, López-Martínez MÁ, Riveiro-Álvarez R, Wilhelm L, Cervera-Juanes R, Garcés C, Lomniczi A, Soriano-Guillén L. Methylation analysis by targeted bisulfite sequencing in large for gestational age (LGA) newborns: the LARGAN cohort. Clin Epigenetics 2023; 15:191. [PMID: 38093359 PMCID: PMC10717641 DOI: 10.1186/s13148-023-01612-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND In 1990, David Barker proposed that prenatal nutrition is directly linked to adult cardiovascular disease. Since then, the relationship between adult cardiovascular risk, metabolic syndrome and birth weight has been widely documented. Here, we used the TruSeq Methyl Capture EPIC platform to compare the methylation patterns in cord blood from large for gestational age (LGA) vs adequate for gestational age (AGA) newborns from the LARGAN cohort. RESULTS We found 1672 differentially methylated CpGs (DMCs) with a nominal p < 0.05 and 48 differentially methylated regions (DMRs) with a corrected p < 0.05 between the LGA and AGA groups. A systems biology approach identified several biological processes significantly enriched with genes in association with DMCs with FDR < 0.05, including regulation of transcription, regulation of epinephrine secretion, norepinephrine biosynthesis, receptor transactivation, forebrain regionalization and several terms related to kidney and cardiovascular development. Gene ontology analysis of the genes in association with the 48 DMRs identified several significantly enriched biological processes related to kidney development, including mesonephric duct development and nephron tubule development. Furthermore, our dataset identified several DNA methylation markers enriched in gene networks involved in biological pathways and rare diseases of the cardiovascular system, kidneys, and metabolism. CONCLUSIONS Our study identified several DMCs/DMRs in association with fetal overgrowth. The use of cord blood as a material for the identification of DNA methylation biomarkers gives us the possibility to perform follow-up studies on the same patients as they grow. These studies will not only help us understand how the methylome responds to continuum postnatal growth but also link early alterations of the DNA methylome with later clinical markers of growth and metabolic fitness.
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Affiliation(s)
- Tamara Carrizosa-Molina
- Department of Pediatrics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Natalia Casillas-Díaz
- Department of Pediatrics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | | | | | - Miguel Ángel López-Martínez
- Department of Genetics and Genomics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rosa Riveiro-Álvarez
- Department of Genetics and Genomics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Larry Wilhelm
- Department of Physiology and Pharmacology, Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Rita Cervera-Juanes
- Department of Physiology and Pharmacology, Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Carmen Garcés
- Lipid Research Laboratory, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Alejandro Lomniczi
- Department of Physiology and Biophysics, Dalhousie University School of Medicine, 5850 College Street, Halifax, NS, B3H 4R2, Canada.
| | - Leandro Soriano-Guillén
- Department of Pediatrics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
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Yang T, Xiao Y, Cheng Y, Huang J, Wei Q, Li C, Shang H. Epigenetic clocks in neurodegenerative diseases: a systematic review. J Neurol Neurosurg Psychiatry 2023; 94:1064-1070. [PMID: 36963821 DOI: 10.1136/jnnp-2022-330931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/03/2023] [Indexed: 03/26/2023]
Abstract
BACKGROUND Biological ageing is one of the principal risk factors for neurodegenerative diseases. It is becoming increasingly clear that acceleration of DNA methylation age, as measured by the epigenetic clock, is closely associated with many age-related diseases. METHODS We searched the PubMed and Web of Science databases to identify eligible studies reporting epigenetic clocks in several neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD). RESULTS Twenty-three studies (12 for AD, 4 for PD, 5 for ALS, and 2 for HD) were included. We systematically summarised the clinical utility of 11 epigenetic clocks (based on blood and brain tissues) in assessing the risk factors, age of onset, diagnosis, progression, prognosis and pathology of AD, PD, ALS and HD. We also critically described our current understandings to these evidences, and further discussed key challenges, potential mechanisms and future perspectives of epigenetic ageing in neurodegenerative diseases. CONCLUSIONS Epigenetic clocks hold great potential in neurodegenerative diseases. Further research is encouraged to evaluate the clinical utility and promote the application. PROSPERO REGISTRATION NUMBER CRD42022365233.
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Affiliation(s)
- Tianmi Yang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Yi Xiao
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Yangfan Cheng
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Jingxuan Huang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Chunyu Li
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Huifang Shang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
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Sarnowski C, Huan T, Ma Y, Joehanes R, Beiser A, DeCarli CS, Heard-Costa NL, Levy D, Lin H, Liu CT, Liu C, Meigs JB, Satizabal CL, Florez JC, Hivert MF, Dupuis J, De Jager PL, Bennett DA, Seshadri S, Morrison AC. Multi-tissue epigenetic analysis identifies distinct associations underlying insulin resistance and Alzheimer's disease at CPT1A locus. Clin Epigenetics 2023; 15:173. [PMID: 37891690 PMCID: PMC10612362 DOI: 10.1186/s13148-023-01589-4] [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: 07/17/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Insulin resistance (IR) is a major risk factor for Alzheimer's disease (AD) dementia. The mechanisms by which IR predisposes to AD are not well-understood. Epigenetic studies may help identify molecular signatures of IR associated with AD, thus improving our understanding of the biological and regulatory mechanisms linking IR and AD. METHODS We conducted an epigenome-wide association study of IR, quantified using the homeostatic model assessment of IR (HOMA-IR) and adjusted for body mass index, in 3,167 participants from the Framingham Heart Study (FHS) without type 2 diabetes at the time of blood draw used for methylation measurement. We identified DNA methylation markers associated with IR at the genome-wide level accounting for multiple testing (P < 1.1 × 10-7) and evaluated their association with neurological traits in participants from the FHS (N = 3040) and the Religious Orders Study/Memory and Aging Project (ROSMAP, N = 707). DNA methylation profiles were measured in blood (FHS) or dorsolateral prefrontal cortex (ROSMAP) using the Illumina HumanMethylation450 BeadChip. Linear regressions (ROSMAP) or mixed-effects models accounting for familial relatedness (FHS) adjusted for age, sex, cohort, self-reported race, batch, and cell type proportions were used to assess associations between DNA methylation and neurological traits accounting for multiple testing. RESULTS We confirmed the strong association of blood DNA methylation with IR at three loci (cg17901584-DHCR24, cg17058475-CPT1A, cg00574958-CPT1A, and cg06500161-ABCG1). In FHS, higher levels of blood DNA methylation at cg00574958 and cg17058475 were both associated with lower IR (P = 2.4 × 10-11 and P = 9.0 × 10-8), larger total brain volumes (P = 0.03 and P = 9.7 × 10-4), and smaller log lateral ventricular volumes (P = 0.07 and P = 0.03). In ROSMAP, higher levels of brain DNA methylation at the same two CPT1A markers were associated with greater risk of cognitive impairment (P = 0.005 and P = 0.02) and higher AD-related indices (CERAD score: P = 5 × 10-4 and 0.001; Braak stage: P = 0.004 and P = 0.01). CONCLUSIONS Our results suggest potentially distinct epigenetic regulatory mechanisms between peripheral blood and dorsolateral prefrontal cortex tissues underlying IR and AD at CPT1A locus.
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Affiliation(s)
- Chloé Sarnowski
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Tianxiao Huan
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
| | - Yiyi Ma
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung and Blood Institutes of Health, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Alexa Beiser
- The Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | | | - Nancy L Heard-Costa
- The Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Daniel Levy
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Honghuang Lin
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia L Satizabal
- The Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Harvard University, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Josée Dupuis
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University, Montreal, Canada
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Sudha Seshadri
- The Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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Morales-Marín ME, Castro Martínez XH, Centeno Cruz F, Barajas-Olmos F, Náfate López O, Gómez Cotero AG, Orozco L, Nicolini Sánchez H. Differential DNA Methylation from Autistic Children Enriches Evidence for Genes Associated with ASD and New Candidate Genes. Brain Sci 2023; 13:1420. [PMID: 37891789 PMCID: PMC10605446 DOI: 10.3390/brainsci13101420] [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: 08/15/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
The etiology of Autism Spectrum Disorders (ASD) is a result of the interaction between genes and the environment. The study of epigenetic factors that affect gene expression, such as DNA methylation, has become an important area of research in ASD. In recent years, there has been an increasing body of evidence pointing to epigenetic mechanisms that influence brain development, as in the case of ASD, when gene methylation dysregulation is present. Our analysis revealed 853 differentially methylated CpG in ASD patients, affecting 509 genes across the genome. Enrichment analysis showed five related diseases, including autistic disorder and mental disorders, which are particularly significant. In this work, we identified 64 genes that were previously reported in the SFARI gene database, classified according to their impact index. Additionally, we identified new genes that have not been previously reported as candidates with differences in the methylation patterns of Mexican children with ASD.
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Affiliation(s)
- Mirna Edith Morales-Marín
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (X.H.C.M.); (H.N.S.)
| | - Xochitl Helga Castro Martínez
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (X.H.C.M.); (H.N.S.)
| | - Federico Centeno Cruz
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (F.C.C.); (F.B.-O.); (L.O.)
| | - Francisco Barajas-Olmos
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (F.C.C.); (F.B.-O.); (L.O.)
| | - Omar Náfate López
- Hospital de Especialidades Pediátricas, Tuxtla Gutiérrez 29045, Mexico;
| | - Amalia Guadalupe Gómez Cotero
- Centro de Investigación en Ciencias de la Salud, Unidad Santo Tomás, Instituto Politécnico Nacional, Mexico City 07738, Mexico;
| | - Lorena Orozco
- Laboratorio de Inmunogenómica y Enfermedades Metabólicas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (F.C.C.); (F.B.-O.); (L.O.)
| | - Humberto Nicolini Sánchez
- Laboratorio de Genómica de Enfermedades Psiquiátricas y Neurodegenerativas, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (X.H.C.M.); (H.N.S.)
- Grupo Médico Carracci, Mexico City 03740, Mexico
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Zhang S, Shi K, Lyu N, Zhang Y, Liang G, Zhang W, Wang X, Wen H, Wen L, Ma H, Wang J, Yu X, Guan L. Genome-wide DNA methylation analysis in families with multiple individuals diagnosed with schizophrenia and intellectual disability. World J Biol Psychiatry 2023; 24:741-753. [PMID: 37017099 DOI: 10.1080/15622975.2023.2198595] [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: 12/27/2022] [Revised: 03/21/2023] [Accepted: 03/30/2023] [Indexed: 04/06/2023]
Abstract
OBJECTIVES Schizophrenia (SZ) and intellectual disability (ID) are both included in the continuum of neurodevelopmental disorders (NDDs). DNA methylation is known to be important in the occurrence of NDDs. The family study is conducive to eliminate the effects of relative epigenetic backgrounds, and to screen for differentially methylated positions (DMPs) and regions (DMRs) that are truly associated with NDDs. METHODS Four monozygotic twin families were recruited, and both twin individuals suffered from NDDs (either SZ, ID, or SZ plus ID). Genome-wide methylation analysis was performed in all samples and each family. DMPs and DMRs between NDD patients and unaffected individuals were identified. Functional and pathway enrichment analyses were performed on the annotated genes. RESULTS Two significant DMPs annotated to CYP2E1 were found in all samples. In Family One, 1476 DMPs mapped to 880 genes, and 162 DMRs overlapping with 153 unique genes were recognised. Our results suggested that the altered methylation levels of FYN, STAT3, RAC1, and NR4A2 were associated with the development of SZ and ID. Neurodevelopment and the immune system may participate in the occurrence of SZ and ID. CONCLUSIONS Our findings suggested that DNA methylation participated in the development of NDDs by affecting neurodevelopment and the immune system.
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Affiliation(s)
- Shengmin Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Kaiyu Shi
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Nan Lyu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- Beijing Anding Hospital, Beijing Key Laboratory of Mental Disorders, The National Clinical Research Centre for Mental Disorders, The Advanced Innovation Centre for Human Brain Protection, Capital Medical University, Beijing, China
| | - Yunshu Zhang
- The Sixth People's Hospital of Hebei Province, Hebei Mental Health Centre, Baoding, Hebei, China
| | | | - Wufang Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Xijin Wang
- The First Psychiatric Hospital of Harbin, Harbin, Heilongjiang, China
| | - Hong Wen
- The Third Hospital of Mianyang, Mianyang, Sichuan, China
| | - Liping Wen
- Zigong Mental Health Centre, Zigong, Sichuan, China
| | - Hong Ma
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Jijun Wang
- Shanghai Mental Health Centre, Shanghai Jiaotong University School of Medicine, Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Xin Yu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Lili Guan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Centre for Mental Disorders (Peking University Sixth Hospital), Beijing, China
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Zeng X, Tan Z, Wang W, Li W, Li S, Zhang D, Tan Q. Long-term Impact of Prenatal Famine on Differential DNA Methylation of Genes in the Serotonin Receptor Signalling Pathway in Adults. Neuroscience 2023; 529:107-115. [PMID: 37598834 DOI: 10.1016/j.neuroscience.2023.08.008] [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: 06/13/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
The correlation of early life adversity with adulthood psychopathology has already been revealed by epidemiological studies. To find the biological mechanisms underlying the cross-talk between prenatal adversity and mental health, molecular genetic studies have been performed using animal models of prenatal undernutrition and stress, reporting altered expression of serotonin receptors which modulate the release of many neurotransmitters that regulate a broad range of physiological functions including psychopathology. Unfortunately, no such study has been possible on humans due to ethical reasons. Using the Chinese Famine of 1959-1961 as a natural experiment, we investigated DNA methylation patterns in genes of the serotonin receptor signaling pathway in the whole blood of adults born during the famine. A significant pattern of reduced DNA methylation was observed in sex combined samples (p value, 0.022). In a sex-stratified analysis, the pattern was only significant in females (p-value, 0.019) but not in males. We further tested the DNA methylation patterns specifically in HTR1A, HTR2A and the X-linked HTR2C and found reduced DNA methylation in females for HTR2A (p-value 0.033) and HTR2C (p-value 0.014) but not in males. Overall, this study reveals altered epigenetic regulation of the serotonin receptor signaling pathway in association with prenatal adversity in humans providing novel epigenetic evidence in support of neurodevelopmental origin of psychiatric disorders.
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Affiliation(s)
- Xin Zeng
- The Second People's Hospital of Lishui, Zhejiang, China.
| | - Zhen Tan
- The Second People's Hospital of Lishui, Zhejiang, China.
| | - Weijing Wang
- Qingdao University School of Public Health, Qingdao, China.
| | - Weilong Li
- Unit of Demography, Faculty of Social Science, University of Helsinki, Helsinki, Finland.
| | - Shuxia Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Dongfeng Zhang
- Qingdao University School of Public Health, Qingdao, China.
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.
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McKenna BG, Knight AK, Smith AK, Corwin EJ, Carter SE, Palmer RHC, Dunlop AL, Brennan PA. Infant epigenetic aging moderates the link between Black maternal childhood trauma and offspring symptoms of psychopathology. Dev Psychopathol 2023:1-13. [PMID: 37771149 DOI: 10.1017/s0954579423001232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Although offspring of women exposed to childhood trauma exhibit elevated rates of psychopathology, many children demonstrate resilience to these intergenerational impacts. Among the variety of factors that likely contribute to resilience, epigenetic processes have been suggested to play an important role. The current study used a prospective design to test the novel hypothesis that offspring epigenetic aging - a measure of methylation differences that are associated with infant health outcomes - moderates the relationship between maternal exposure to childhood adversity and offspring symptomatology. Maternal childhood adversity was self-reported during pregnancy via the ACEs survey and the CTQ, which assessed total childhood trauma as well as maltreatment subtypes (i.e., emotional, physical, and sexual abuse). Offspring blood samples were collected at or shortly after birth and assayed on a DNA methylation microarray, and offspring symptomatology was assessed with the CBCL/1.5-5 when offspring were 2-4 years old. Results indicated that maternal childhood trauma, particularly sexual abuse, was predictive of offspring symptoms (ps = 0.003-0.03). However, the associations between maternal sexual abuse and offspring symptomatology were significantly attenuated in offspring with accelerated epigenetic aging. These findings further our understanding of how epigenetic processes may contribute to and attenuate the intergenerational link between stress and psychopathology.
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Affiliation(s)
| | - Anna K Knight
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | | | - Sierra E Carter
- Department of Psychology, Georgia State University, Atlanta, GA, USA
| | | | - Anne L Dunlop
- School of Nursing, Emory University, Atlanta, GA, USA
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Sumalde AAM, Yang IV, Yarza TKL, Tobias-Grasso CAM, Tantoco MLC, Davidson E, Chan AL, Azamian MS, Cruz TLG, Lalani SR, Reyes-Quintos MRT, Cutiongco-de la Paz EM, Santos-Cortez RLP, Chiong CM. Lack of Methylation Changes in GJB2 and RB1 Non-coding Regions of Cochlear Implant Patients with Sensorineural Hearing Loss. ACTA MEDICA PHILIPPINA 2023; 57:116-120. [PMID: 37990697 PMCID: PMC10662870 DOI: 10.47895/amp.v57i9.5200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Objective Recent advances in epigenetic studies continue to reveal novel mechanisms of gene regulation and control, however little is known on the role of epigenetics in sensorineural hearing loss (SNHL) in humans. We aimed to investigate the methylation patterns of two regions, one in RB1 and another in GJB2 in Filipino patients with SNHL compared to hearing control individuals. Methods We investigated an RB1 promoter region that was previously identified as differentially methylated in children with SNHL and lead exposure. Additionally, we investigated a sequence in an enhancer-like region within GJB2 that contains four CpGs in close proximity. Bisulfite conversion was performed on salivary DNA samples from 15 children with SNHL and 45 unrelated ethnically-matched individuals. We then performed methylation-specific real-time PCR analysis (qMSP) using TaqMan® probes to determine percentage methylation of the two regions. Results Using qMSP, both our cases and controls had zero methylation at the targeted GJB2 and RB1 regions. Conclusion Our study showed no changes in methylation at the selected CpG regions in RB1 and GJB2 in the two comparison groups with or without SNHL. This may be due to a lack of environmental exposures to these target regions. Other epigenetic marks may be present around these regions as well as those of other HL-associated genes.
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Affiliation(s)
- Angelo Augusto M. Sumalde
- College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Otolaryngology – Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), Aurora, Colorado, USA
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
| | - Ivana V. Yang
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), Aurora, Colorado, USA
| | - Talitha Karisse L. Yarza
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | | | - Ma. Leah C. Tantoco
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Elizabeth Davidson
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), Aurora, Colorado, USA
| | - Abner L. Chan
- College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Teresa Luisa G. Cruz
- College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Maria Rina T. Reyes-Quintos
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
| | - Eva Maria Cutiongco-de la Paz
- National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Philippine Genome Center, UP Diliman Campus, Quezon City, Philippines
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology – Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus (CU-AMC), Aurora, Colorado, USA
| | - Charlotte M. Chiong
- College of Medicine, University of the Philippines Manila, Manila, Philippines
- Department of Otolaryngology-Head and Neck Surgery, Philippine General Hospital, University of the Philippines Manila, Manila, Philippines
- Philippine National Ear Institute, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
- Newborn Hearing Screening Reference Center, National Institutes of Health, University of the Philippines Manila, Manila, Philippines
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Van Asselt AJ, Beck JJ, Finnicum CT, Johnson BN, Kallsen N, Hottenga JJ, de Geus EJC, Boomsma DI, Ehli EA, van Dongen J. Genome-Wide DNA Methylation Profiles in Whole-Blood and Buccal Samples-Cross-Sectional, Longitudinal, and across Platforms. Int J Mol Sci 2023; 24:14640. [PMID: 37834090 PMCID: PMC10572275 DOI: 10.3390/ijms241914640] [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: 08/21/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/15/2023] Open
Abstract
The field of DNA methylation research is rapidly evolving, focusing on disease and phenotype changes over time using methylation measurements from diverse tissue sources and multiple array platforms. Consequently, identifying the extent of longitudinal, inter-tissue, and inter-platform variation in DNA methylation is crucial for future advancement. DNA methylation was measured in 375 individuals, with 197 of those having 2 blood sample measurements ~10 years apart. Whole-blood samples were measured on Illumina Infinium 450K and EPIC methylation arrays, and buccal samples from a subset of 58 participants were measured on EPIC array. The data were analyzed with the aims to examine the correlation between methylation levels in longitudinal blood samples in 197 individuals, examine the correlation between methylation levels in the blood and buccal samples in 58 individuals, and examine the correlation between blood methylation profiles assessed on the EPIC and 450K arrays in 83 individuals. We identified 136,833, 7674, and 96,891 CpGs significantly and strongly correlated (>0.50) longitudinally, across blood and buccal samples as well as array platforms, respectively. A total of 3674 of these CpGs were shared across all three sets. Analysis of these shared CpGs identified previously found associations with aging, ancestry, and 7016 mQTLs as well.
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Affiliation(s)
- Austin J. Van Asselt
- Avera McKennan Hospital, University Health Center, Sioux Falls, SD 57105, USA; (A.J.V.A.)
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Jeffrey J. Beck
- Avera McKennan Hospital, University Health Center, Sioux Falls, SD 57105, USA; (A.J.V.A.)
| | - Casey T. Finnicum
- Avera McKennan Hospital, University Health Center, Sioux Falls, SD 57105, USA; (A.J.V.A.)
| | - Brandon N. Johnson
- Avera McKennan Hospital, University Health Center, Sioux Falls, SD 57105, USA; (A.J.V.A.)
| | - Noah Kallsen
- Avera McKennan Hospital, University Health Center, Sioux Falls, SD 57105, USA; (A.J.V.A.)
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Eco J. C. de Geus
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | | | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Erik A. Ehli
- Avera McKennan Hospital, University Health Center, Sioux Falls, SD 57105, USA; (A.J.V.A.)
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
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Herrgott GA, Snyder JM, She R, Malta TM, Sabedot TS, Lee IY, Pawloski J, Podolsky-Gondim GG, Asmaro KP, Zhang J, Cannella CE, Nelson K, Thomas B, deCarvalho AC, Hasselbach LA, Tundo KM, Newaz R, Transou A, Morosini N, Francisco V, Poisson LM, Chitale D, Mukherjee A, Mosella MS, Robin AM, Walbert T, Rosenblum M, Mikkelsen T, Kalkanis S, Tirapelli DPC, Weisenberger DJ, Carlotti CG, Rock J, Castro AV, Noushmehr H. Detection of diagnostic and prognostic methylation-based signatures in liquid biopsy specimens from patients with meningiomas. Nat Commun 2023; 14:5669. [PMID: 37704607 PMCID: PMC10499807 DOI: 10.1038/s41467-023-41434-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Recurrence of meningiomas is unpredictable by current invasive methods based on surgically removed specimens. Identification of patients likely to recur using noninvasive approaches could inform treatment strategy, whether intervention or monitoring. In this study, we analyze the DNA methylation levels in blood (serum and plasma) and tissue samples from 155 meningioma patients, compared to other central nervous system tumor and non-tumor entities. We discover DNA methylation markers unique to meningiomas and use artificial intelligence to create accurate and universal models for identifying and predicting meningioma recurrence, using either blood or tissue samples. Here we show that liquid biopsy is a potential noninvasive and reliable tool for diagnosing and predicting outcomes in meningioma patients. This approach can improve personalized management strategies for these patients.
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Affiliation(s)
- Grayson A Herrgott
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - James M Snyder
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ruicong She
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Thais S Sabedot
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ian Y Lee
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Jacob Pawloski
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Guilherme G Podolsky-Gondim
- Department of Neurosurgery, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Karam P Asmaro
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Jiaqi Zhang
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | - Cara E Cannella
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | - Kevin Nelson
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Bartow Thomas
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ana C deCarvalho
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Laura A Hasselbach
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Kelly M Tundo
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Rehnuma Newaz
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Andrea Transou
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Natalia Morosini
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Victor Francisco
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Laila M Poisson
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
- Department of Public Health, Biostatistics, Henry Ford Health, Detroit, MI, USA
| | | | - Abir Mukherjee
- Department of Pathology, Henry Ford Health, Detroit, MI, USA
| | - Maritza S Mosella
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Adam M Robin
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Tobias Walbert
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Mark Rosenblum
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Tom Mikkelsen
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Steven Kalkanis
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Daniela P C Tirapelli
- Department of Neurosurgery, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Carlos G Carlotti
- Department of Neurosurgery, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Jack Rock
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA
| | - Ana Valeria Castro
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA.
- Department of Physiology, Michigan State University, E. Lansing, MI, USA.
| | - Houtan Noushmehr
- Department of Neurosurgery, Omics Laboratory, Hermelin Brain Tumor Center, Henry Ford Health, Detroit, MI, USA.
- Department of Physiology, Michigan State University, E. Lansing, MI, USA.
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Dubnov S, Yayon N, Yakov O, Bennett DA, Seshadri S, Mufson E, Tzur Y, Bennet ER, Greenberg D, Kuro-O M, Paldor I, Abraham CR, Soreq H. Knockout of the longevity gene Klotho perturbs aging- and Alzheimer's disease-linked brain microRNAs and tRNA fragments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.557032. [PMID: 37745362 PMCID: PMC10515819 DOI: 10.1101/2023.09.10.557032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Overexpression of the longevity gene Klotho prolongs, while its knockout shortens lifespan and impairs cognition via altered fibroblast growth factor signaling that perturbs myelination and synapse formation; however, comprehensive analysis of Klotho's knockout consequences on mammalian brain transcriptomics is lacking. Here, we report the altered levels under Klotho knockout of 1059 long RNAs, 27 microRNAs (miRs) and 6 tRNA fragments (tRFs), reflecting effects upon aging and cognition. Perturbed transcripts included key neuronal and glial pathway regulators that are notably changed in murine models of aging and Alzheimer's Disease (AD) and in corresponding human post-mortem brain tissue. To seek cell type distributions of the affected short RNAs, we isolated and FACS-sorted neurons and microglia from live human brain tissue, yielding detailed cell type-specific short RNA-seq datasets. Together, our findings revealed multiple Klotho deficiency-perturbed aging- and neurodegeneration-related long and short RNA transcripts in both neurons and glia from murine and human brain.
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Theron D, Hopkins LN, Sutherland HG, Griffiths LR, Fernandez F. Can Genetic Markers Predict the Sporadic Form of Alzheimer's Disease? An Updated Review on Genetic Peripheral Markers. Int J Mol Sci 2023; 24:13480. [PMID: 37686283 PMCID: PMC10488021 DOI: 10.3390/ijms241713480] [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: 08/04/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia that affects millions of individuals worldwide. Although the research over the last decades has provided new insight into AD pathophysiology, there is currently no cure for the disease. AD is often only diagnosed once the symptoms have become prominent, particularly in the late-onset (sporadic) form of AD. Consequently, it is essential to further new avenues for early diagnosis. With recent advances in genomic analysis and a lower cost of use, the exploration of genetic markers alongside RNA molecules can offer a key avenue for early diagnosis. We have here provided a brief overview of potential genetic markers differentially expressed in peripheral tissues in AD cases compared to controls, as well as considering the changes to the dynamics of RNA molecules. By integrating both genotype and RNA changes reported in AD, biomarker profiling can be key for developing reliable AD diagnostic tools.
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Affiliation(s)
- Danelda Theron
- School of Behavioural and Health Sciences, Faculty of Heath Sciences, Australian Catholic University, Banyo, QLD 4014, Australia;
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
| | - Lloyd N. Hopkins
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
| | - Heidi G. Sutherland
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
| | - Lyn R. Griffiths
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
| | - Francesca Fernandez
- School of Behavioural and Health Sciences, Faculty of Heath Sciences, Australian Catholic University, Banyo, QLD 4014, Australia;
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia; (L.N.H.); (H.G.S.); (L.R.G.)
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Yuan M, Yang B, Rothschild G, Mann JJ, Sanford LD, Tang X, Huang C, Wang C, Zhang W. Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential. Signal Transduct Target Ther 2023; 8:309. [PMID: 37644009 PMCID: PMC10465587 DOI: 10.1038/s41392-023-01519-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/14/2023] [Accepted: 05/31/2023] [Indexed: 08/31/2023] Open
Abstract
Major depressive disorder (MDD) is a chronic, generally episodic and debilitating disease that affects an estimated 300 million people worldwide, but its pathogenesis is poorly understood. The heritability estimate of MDD is 30-40%, suggesting that genetics alone do not account for most of the risk of major depression. Another factor known to associate with MDD involves environmental stressors such as childhood adversity and recent life stress. Recent studies have emerged to show that the biological impact of environmental factors in MDD and other stress-related disorders is mediated by a variety of epigenetic modifications. These epigenetic modification alterations contribute to abnormal neuroendocrine responses, neuroplasticity impairment, neurotransmission and neuroglia dysfunction, which are involved in the pathophysiology of MDD. Furthermore, epigenetic marks have been associated with the diagnosis and treatment of MDD. The evaluation of epigenetic modifications holds promise for further understanding of the heterogeneous etiology and complex phenotypes of MDD, and may identify new therapeutic targets. Here, we review preclinical and clinical epigenetic findings, including DNA methylation, histone modification, noncoding RNA, RNA modification, and chromatin remodeling factor in MDD. In addition, we elaborate on the contribution of these epigenetic mechanisms to the pathological trait variability in depression and discuss how such mechanisms can be exploited for therapeutic purposes.
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Affiliation(s)
- Minlan Yuan
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Biao Yang
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY, 10032, USA
- Department of Radiology, Columbia University, New York, NY, 10032, USA
| | - Larry D Sanford
- Sleep Research Laboratory, Center for Integrative Neuroscience and Inflammatory Diseases, Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Xiangdong Tang
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, Translational Neuroscience Center, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Canhua Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chuang Wang
- Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Wei Zhang
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Medical Big Data Center, Sichuan University, Chengdu, 610041, China.
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Larsen M, He F, Kawasawa YI, Berg A, Vgontzas AN, Liao D, Bixler EO, Fernandez-Mendoza J. Objective and subjective measures of sleep initiation are differentially associated with DNA methylation in adolescents. Clin Epigenetics 2023; 15:136. [PMID: 37634000 PMCID: PMC10464279 DOI: 10.1186/s13148-023-01553-2] [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: 01/19/2023] [Accepted: 08/14/2023] [Indexed: 08/28/2023] Open
Abstract
INTRODUCTION The onset of puberty is associated with a shift in the circadian timing of sleep, leading to delayed sleep initiation [i.e., later sleep onset time (SOT)] due to later bedtimes and/or longer sleep onset latency (SOL). Several genome-wide association studies (GWAS) have identified genes that may be involved in the etiology of sleep phenotypes. However, circadian rhythms are also epigenetically regulated; therefore, epigenetic biomarkers may provide insight into the physiology of the pubertal sleep onset shift and the pathophysiology of prolonged or delayed sleep initiation. RESULTS The gene-wide analysis indicated differential methylation within or around 1818 unique genes across the sleep initiation measurements using self-report, actigraphy (ACT), and polysomnography (PSG), while GWAS-informed analysis yielded 67 genes. Gene hits were identified for bedtime (PSG), SOL (subjective, ACT and PSG) and SOT (subjective and PSG). DNA methylation within 12 genes was associated with both subjective and PSG-measured SOL, 31 with both ACT- and PSG-measured SOL, 19 with both subjective and ACT-measured SOL, and one gene (SMG1P2) had methylation sites associated with subjective, ACT- and PSG-measured SOL. CONCLUSIONS Objective and subjective sleep initiation in adolescents is associated with altered DNA methylation in genes previously identified in adult GWAS of sleep and circadian phenotypes. Additionally, our data provide evidence for a potential epigenetic link between habitual (subjective and ACT) SOL and in-lab SOT and DNA methylation in and around genes involved in circadian regulation (i.e., RASD1, RAI1), cardiometabolic disorders (i.e., FADS1, WNK1, SLC5A6), and neuropsychiatric disorders (i.e., PRR7, SDK1, FAM172A). If validated, these sites may provide valuable targets for early detection and prevention of disorders involving prolonged or delayed SOT, such as insomnia, delayed sleep phase, and their comorbidity.
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Affiliation(s)
- Michael Larsen
- Sleep Research and Treatment Center, Department of Psychiatry & Behavioral Health, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Fan He
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Yuka Imamura Kawasawa
- Departments of Biochemistry and Molecular Biology and Pharmacology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Arthur Berg
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Alexandros N Vgontzas
- Sleep Research and Treatment Center, Department of Psychiatry & Behavioral Health, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Duanping Liao
- Department of Public Health Sciences, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Edward O Bixler
- Sleep Research and Treatment Center, Department of Psychiatry & Behavioral Health, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Julio Fernandez-Mendoza
- Sleep Research and Treatment Center, Department of Psychiatry & Behavioral Health, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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Tsalenchuk M, Gentleman SM, Marzi SJ. Linking environmental risk factors with epigenetic mechanisms in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:123. [PMID: 37626097 PMCID: PMC10457362 DOI: 10.1038/s41531-023-00568-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Sporadic Parkinson's disease (PD) is a progressive neurodegenerative disease, with a complex risk structure thought to be influenced by interactions between genetic variants and environmental exposures, although the full aetiology is unknown. Environmental factors, including pesticides, have been reported to increase the risk of developing the disease. Growing evidence suggests epigenetic changes are key mechanisms by which these environmental factors act upon gene regulation, in disease-relevant cell types. We present a systematic review critically appraising and summarising the current body of evidence of the relationship between epigenetic mechanisms and environmental risk factors in PD to inform future research in this area. Epigenetic studies of relevant environmental risk factors in animal and cell models have yielded promising results, however, research in humans is just emerging. While published studies in humans are currently relatively limited, the importance of the field for the elucidation of molecular mechanisms of pathogenesis opens clear and promising avenues for the future of PD research. Carefully designed epidemiological studies carried out in PD patients hold great potential to uncover disease-relevant gene regulatory mechanisms. Therefore, to advance this burgeoning field, we recommend broadening the scope of investigations to include more environmental exposures, increasing sample sizes, focusing on disease-relevant cell types, and recruiting more diverse cohorts.
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Affiliation(s)
- Maria Tsalenchuk
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK.
- Department of Brain Sciences, Imperial College London, London, UK.
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Van Assche E, Hohoff C, Zang J, Knight MJ, Baune BT. Longitudinal early epigenomic signatures inform molecular paths of therapy response and remission in depressed patients. Front Mol Neurosci 2023; 16:1223216. [PMID: 37664245 PMCID: PMC10472456 DOI: 10.3389/fnmol.2023.1223216] [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: 05/15/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction The etiology of major depressive disorder (MDD) involves the interaction between genes and environment, including treatment. Early molecular signatures for treatment response and remission are relevant in a context of personalized medicine and stratification and reduce the time-to-decision. Therefore, we focused the analyses on patients that responded or remitted following a cognitive intervention of 8 weeks. Methods We used data from a randomized controlled trial (RCT) with MDD patients (N = 112) receiving a cognitive intervention. At baseline and 8 weeks, blood for DNA methylation (Illumina Infinium MethylationEPIC 850k BeadChip) was collected, as well as MADRS. First, responders (N = 24; MADRS-reduction of at least 50%) were compared with non-responders (N = 60). Then, we performed longitudinal within-individual analyses, for response (N = 21) and for remission (N = 18; MADRS smaller or equal to 9 and higher than 9 at baseline), respectively, as well as patients with no change in MADRS over time. At 8 weeks the sample comprised 84 individuals; 73 patients had DNA methylation for both time-points. The RnBeads package (R) was used for data cleaning, quality control, and differential DNA-methylation (limma). The within-individual paired longitudinal analysis was performed using Welch's t-test. Subsequently gene-ontology (GO) pathway analyses were performed. Results No CpG was genome-wide significant CpG (p < 5 × 10-8). The most significant CpG in the differential methylation analysis comparing response versus non-response was in the IQSEC1 gene (cg01601845; p = 1.53 × 10-6), linked to neurotransmission. The most significant GO-terms were linked to telomeres. The longitudinal response analysis returned 67 GO pathways with a p < 0.05. Two of the three most significant pathways were linked to sodium transport. The analysis for remission returned 46 GO terms with a p-value smaller than 0.05 with pathways linked to phosphatase regulation and synaptic functioning. The analysis with stable patients returned mainly GO-terms linked to basic cellular processes. Discussion Our result suggest that DNA methylation can be suitable to capture early signs of treatment response and remission following a cognitive intervention in depression. Despite not being genome-wide significant, the CpG locations and GO-terms returned by our analysis comparing patients with and without cognitive impairment, are in line with prior knowledge on pathways and genes relevant for depression treatment and cognition. Our analysis provides new hypotheses for the understanding of how treatment for depression can act through DNA methylation and induce response and remission.
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Affiliation(s)
| | - Christa Hohoff
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Johannes Zang
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Matthew J. Knight
- Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Bernhard T. Baune
- Department of Psychiatry, University of Münster, Münster, Germany
- Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
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Camerota M, Lester BM, Everson TM. Epigenetic studies of child neurodevelopment: what can we learn from a developmental science perspective? Epigenomics 2023; 15:799-804. [PMID: 37702026 PMCID: PMC10520751 DOI: 10.2217/epi-2023-0218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/08/2023] [Indexed: 09/14/2023] Open
Affiliation(s)
- Marie Camerota
- Departments of Pediatrics & Psychiatry and Human Behavior, Center for the Study of Children at Risk, Brown Alpert Medical School & Women & Infants Hospital, Providence, RI 02905, USA
| | - Barry M Lester
- Departments of Pediatrics & Psychiatry and Human Behavior, Center for the Study of Children at Risk, Brown Alpert Medical School & Women & Infants Hospital, Providence, RI 02905, USA
| | - Todd M Everson
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
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Gao J, Pang X, Zhang L, Li S, Qin Z, Xie X, Liu J. Transcriptome analysis reveals the neuroprotective effect of Dlg4 against fastigial nucleus stimulation-induced ischemia/reperfusion injury in rats. BMC Neurosci 2023; 24:40. [PMID: 37525090 PMCID: PMC10391810 DOI: 10.1186/s12868-023-00811-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Previous studies have demonstrated that electrical stimulation of the cerebellar fastigial nucleus (FNS) can considerably decrease infarction volume and improve neurofunction restoration following cerebral ischemia. Nevertheless, the molecular mechanism of the neuroprotective effect of FNS is still vague. METHODS In this study, we developed a rat model of ischemia/reperfusion that included 1 h FNS followed by reperfusion for 3, 6, 12, 24, and 72 h. The expression profile of molecular alterations in brain tissues was obtained by transcriptome sequencing at five different time points. The function and pathway of miRNA expression pattern and core genes were annotated by Allen Brain Atlas, STRING database and Cytoscape software, so as to explore the mechanism of FNS-mediated neuroprotection. RESULTS The results indicated that FNS is associated with the neurotransmitter cycle pathway. FNS may regulate the release of monoamine neurotransmitters in synaptic vesicles by targeting the corresponding miRNAs through core Dlg4 gene, stimulate the Alternative polyadenylation (APA) incident's anti -apoptosis effect on the brain, and stimulate the interaction activation of neurons in cerebellum, cortex/thalamus and other brain regions, regulate neurovascular coupling, and reduce cerebral damage. CONCLUSION FNS may activate neuronal and neurovascular coupling by regulating the release of neurotransmitters in synaptic vesicles through the methylation of core Dlg4 gene and the corresponding transcription factors and protein kinases, inducing the anti-apoptotic mechanism of APA events. The findings from our investigation offer a new perspective on the way brain tissue responds to FNS-driven neuroprotection.
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Affiliation(s)
- Jinggui Gao
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Xiaomin Pang
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Lei Zhang
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Shenghua Li
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Zhenxiu Qin
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Xiaoyun Xie
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Jingli Liu
- Department of Neurology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China.
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Mirza S, de Carvalho Lima CN, Del Favero-Campbell A, Rubinstein A, Topolski N, Cabrera-Mendoza B, Kovács EH, Blumberg HP, Richards JG, Williams AJ, Wemmie JA, Magnotta VA, Fiedorowicz JG, Gaine ME, Walss-Bass C, Quevedo J, Soares JC, Fries GR. Blood epigenome-wide association studies of suicide attempt in adults with bipolar disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.20.23292968. [PMID: 37546994 PMCID: PMC10402220 DOI: 10.1101/2023.07.20.23292968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Suicide attempt (SA) risk is elevated in individuals with bipolar disorder (BD), and DNA methylation patterns may serve as possible biomarkers of SA. We conducted epigenome-wide association studies (EWAS) of blood DNA methylation associated with BD and SA. DNA methylation was measured at > 700,000 positions in a discovery cohort of n = 84 adults with BD with a history of SA (BD/SA), n = 79 adults with BD without history of SA (BD/non-SA), and n = 76 non-psychiatric controls (CON). EWAS revealed six differentially methylated positions (DMPs) and seven differentially methylated regions (DMRs) between BD/SA and BD/non-SA, with multiple immune-related genes implicated. There were no epigenome-wide significant differences when BD/SA and BD/non-SA were each compared to CON, and patterns suggested that epigenetics differentiating BD/SA from BD/non-SA do not differentiate BD/non-SA from CON. Weighted gene co-methylation network analysis and trait enrichment analysis of the BD/SA vs. BD/non-SA contrast further corroborated immune system involvement, while gene ontology analysis implicated calcium signalling. In an independent replication cohort of n = 48 BD/SA and n = 47 BD/non-SA, fold-changes at the discovery cohort's significant sites showed moderate correlation across cohorts and agreement on direction. In both cohorts, classification accuracy for SA history among individuals with BD was highest when methylation at the significant CpG sites as well as information from clinical interviews were combined, with an AUC of 88.8% (CI = 83.8-93.8%) and 82.1% (CI = 73.6-90.5%) for the combined epigenetic-clinical predictor in the discovery and replication cohorts, respectively. Our results provide novel insight to the role of immune system functioning in SA and BD and also suggest that integrating information from multiple levels of analysis holds promise to improve risk assessment for SA in adults with BD.
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Affiliation(s)
- Salahudeen Mirza
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Institute of Child Development, University of Minnesota, 55455 Minneapolis, Minnesota, USA
| | - Camila N. de Carvalho Lima
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
| | - Alexandra Del Favero-Campbell
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
| | - Alexandre Rubinstein
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
| | - Natasha Topolski
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
| | | | - Emese H.C. Kovács
- Department of Neuroscience and Pharmacology, The University of Iowa, 51 Newton Rd, 52242 Iowa City, Iowa, USA
| | - Hilary P. Blumberg
- Department of Psychiatry, Yale School of Medicine, 06510 New Haven, Connecticut, USA
| | - Jenny Gringer Richards
- Department of Radiology, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
| | - Aislinn J. Williams
- Department of Psychiatry, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
- Iowa Neuroscience Institute, The University of Iowa. 169 Newton Rd, 52242 Iowa City, Iowa USA
| | - John A. Wemmie
- Department of Psychiatry, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
- Iowa Neuroscience Institute, The University of Iowa. 169 Newton Rd, 52242 Iowa City, Iowa USA
- Department of Veterans Affairs Medical Center, Iowa City, Iowa, USA
| | - Vincent A. Magnotta
- Department of Radiology, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
- Department of Psychiatry, The University of Iowa. 200 Hawkins Dr, 52242 Iowa City, Iowa, USA
| | - Jess G. Fiedorowicz
- University of Ottawa Brain and Mind Research Institute, Ottawa Hospital Research Institute. 501 Smyth, K1H 8L6, Ottawa, Ontario, Canada
| | - Marie E. Gaine
- Iowa Neuroscience Institute, The University of Iowa. 169 Newton Rd, 52242 Iowa City, Iowa USA
- Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, 180 South Grand Ave, 52242, Iowa City, Iowa, USA
| | - Consuelo Walss-Bass
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, Texas, USA
| | - Jair C. Soares
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, Texas, USA
| | - Gabriel R. Fries
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston, (UTHealth), 77054 Houston, Texas, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 77054 Houston, Texas, USA
- Center of Excellence in Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, 1941 East Rd, 77054, Houston, Texas, USA
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Jensen D, Chen J, Turner JA, Stephen JM, Wang YP, Wilson TW, Calhoun VD, Liu J. Epigenetic associations with adolescent grey matter maturation and cognitive development. Front Genet 2023; 14:1222619. [PMID: 37529779 PMCID: PMC10390095 DOI: 10.3389/fgene.2023.1222619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Introduction: Adolescence, a critical phase of human neurodevelopment, is marked by a tremendous reorganization of the brain and accompanied by improved cognitive performance. This development is driven in part by gene expression, which in turn is partly regulated by DNA methylation (DNAm). Methods: We collected brain imaging, cognitive assessments, and DNAm in a longitudinal cohort of approximately 200 typically developing participants, aged 9-14. This data, from three time points roughly 1 year apart, was used to explore the relationships between seven cytosine-phosphate-guanine (CpG) sites in genes highly expressed in brain tissues (GRIN2D, GABRB3, KCNC1, SLC12A9, CHD5, STXBP5, and NFASC), seven networks of grey matter (GM) volume change, and scores from seven cognitive tests. Results: The demethylation of the CpGs as well as the rates of change in DNAm were significantly related to improvements in total, crystalized, and fluid cognition scores, executive function, episodic memory, and processing speed, as well as several networks of GM volume increases and decreases that highlight typical patterns of brain maturation. Discussion: Our study provides a first look at the DNAm of genes involved in myelination, excitatory and inhibitory receptors, and connectivity, how they are related to the large-scale changes occurring in the brain structure as well as cognition during adolescence.
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Affiliation(s)
- Dawn Jensen
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Jiayu Chen
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
| | - Jessica A. Turner
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Wexnar Medical Center, Department of Psychiatry and Behavioral Health, Ohio State University, Columbus, OH, United States
| | | | - Yu-Ping Wang
- Department of Biomedical Engineering, Tulane University, New Orleans, LA, United States
| | - Tony W. Wilson
- Institute for Human Neuroscience, Boys Town National Research Hospital, Omaha, NE, United States
| | - Vince D. Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
- The Mind Research Network, Albuquerque, NM, United States
- Psychology Department and Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Jingyu Liu
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
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