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Postberg J, Schubert MT, Nin V, Wagner L, Piefke M. A perspective on epigenomic aging processes in the human brain and their plasticity in patients with mental disorders - a systematic review. Neurogenetics 2024:10.1007/s10048-024-00771-x. [PMID: 38967831 DOI: 10.1007/s10048-024-00771-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: 03/15/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
The debate surrounding nature versus nurture remains a central question in neuroscience, psychology, and in psychiatry, holding implications for both aging processes and the etiology of mental illness. Epigenetics can serve as a bridge between genetic predisposition and environmental influences, thus offering a potential avenue for addressing these questions. Epigenetic clocks, in particular, offer a theoretical framework for measuring biological age based on DNA methylation signatures, enabling the identification of disparities between biological and chronological age. This structured review seeks to consolidate current knowledge regarding the relationship between mental disorders and epigenetic age within the brain. Through a comprehensive literature search encompassing databases such as EBSCO, PubMed, and ClinicalTrials.gov, relevant studies were identified and analyzed. Studies that met inclusion criteria were scrutinized, focusing on those with large sample sizes, analyses of both brain tissue and blood samples, investigation of frontal cortex markers, and a specific emphasis on schizophrenia and depressive disorders. Our review revealed a paucity of significant findings, yet notable insights emerged from studies meeting specific criteria. Studies characterized by extensive sample sizes, analysis of brain tissue and blood samples, assessment of frontal cortex markers, and a focus on schizophrenia and depressive disorders yielded particularly noteworthy results. Despite the limited number of significant findings, these studies shed light on the complex interplay between epigenetic aging and mental illness. While the current body of literature on epigenetic aging in mental disorders presents limited significant findings, it underscores the importance of further research in this area. Future studies should prioritize large sample sizes, comprehensive analyses of brain tissue and blood samples, exploration of specific brain regions such as the frontal cortex, and a focus on key mental disorders. Such endeavors will contribute to a deeper understanding of the relationship between epigenetic aging and mental illness, potentially informing novel diagnostic and therapeutic approaches.
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Affiliation(s)
- Jan Postberg
- Clinical Molecular Genetics and Epigenetics, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany.
- Centre for Biomedical Education & Research (ZBAF), Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany.
| | - Michèle Tina Schubert
- Neurobiology and Genetics of Behavior, Department of Psychology and Psychotherapy, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
| | - Vincent Nin
- Neurobiology and Genetics of Behavior, Department of Psychology and Psychotherapy, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
| | - Lukas Wagner
- Neurobiology and Genetics of Behavior, Department of Psychology and Psychotherapy, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
| | - Martina Piefke
- Centre for Biomedical Education & Research (ZBAF), Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
- Neurobiology and Genetics of Behavior, Department of Psychology and Psychotherapy, Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448, Witten, Germany
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2
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Ori APS, Olde Loohuis LM, Guintivano J, Hannon E, Dempster E, St Clair D, Bass NJ, McQuillin A, Mill J, Sullivan PF, Kahn RS, Horvath S, Ophoff RA. Meta-analysis of epigenetic aging in schizophrenia reveals multifaceted relationships with age, sex, illness duration, and polygenic risk. Clin Epigenetics 2024; 16:53. [PMID: 38589929 PMCID: PMC11003125 DOI: 10.1186/s13148-024-01660-8] [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: 11/30/2023] [Accepted: 03/16/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND The study of biological age acceleration may help identify at-risk individuals and reduce the rising global burden of age-related diseases. Using DNA methylation (DNAm) clocks, we investigated biological aging in schizophrenia (SCZ), a mental illness that is associated with an increased prevalence of age-related disabilities and morbidities. In a whole blood DNAm sample of 1090 SCZ cases and 1206 controls across four European cohorts, we performed a meta-analysis of differential aging using three DNAm clocks (i.e., Hannum, Horvath, and Levine). To dissect how DNAm aging contributes to SCZ, we integrated information on duration of illness and SCZ polygenic risk, as well as stratified our analyses by chronological age and biological sex. RESULTS We found that blood-based DNAm aging is significantly altered in SCZ independent from duration of the illness since onset. We observed sex-specific and nonlinear age effects that differed between clocks and point to possible distinct age windows of altered aging in SCZ. Most notably, intrinsic cellular age (Horvath clock) is decelerated in SCZ cases in young adulthood, while phenotypic age (Levine clock) is accelerated in later adulthood compared to controls. Accelerated phenotypic aging was most pronounced in women with SCZ carrying a high polygenic burden with an age acceleration of + 3.82 years (CI 2.02-5.61, P = 1.1E-03). Phenotypic aging and SCZ polygenic risk contributed additively to the illness and together explained up to 14.38% of the variance in disease status. CONCLUSIONS Our study contributes to the growing body of evidence of altered DNAm aging in SCZ and points to intrinsic age deceleration in younger adulthood and phenotypic age acceleration in later adulthood in SCZ. Since increased phenotypic age is associated with increased risk of all-cause mortality, our findings indicate that specific and identifiable patient groups are at increased mortality risk as measured by the Levine clock. Our study did not find that DNAm aging could be explained by the duration of illness of patients, but we did observe age- and sex-specific effects that warrant further investigation. Finally, our results show that combining genetic and epigenetic predictors can improve predictions of disease outcomes and may help with disease management in schizophrenia.
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Affiliation(s)
- Anil P S Ori
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Gonda Center, Room 4357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-176, USA.
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
| | - Loes M Olde Loohuis
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Gonda Center, Room 4357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-176, USA
| | - Jerry Guintivano
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma Dempster
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - David St Clair
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | - Nick J Bass
- Division of Psychiatry, University College London, London, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Rene S Kahn
- Icahn School of Medicine at Mount Sinai, Department of Psychiatry, New York, NY, USA
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Gonda Center, Room 4357B, 695 Charles E. Young Drive South, Los Angeles, CA, 90095-176, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands.
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3
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Garcia-Ruiz B, Jiménez E, Aranda S, Verdolini N, Gutiérrez-Zotes A, Sáez C, Losantos E, Alonso-Lana S, Fatjó-Vilas M, Sarró S, Torres L, Panicalli F, Bonnin CDM, Pomarol-Clotet E, Vieta E, Vilella E. Associations of altered leukocyte DDR1 promoter methylation and childhood trauma with bipolar disorder and suicidal behavior in euthymic patients. Mol Psychiatry 2024:10.1038/s41380-024-02522-8. [PMID: 38503928 DOI: 10.1038/s41380-024-02522-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Altered DNA methylation (DNAm) patterns of discoidin domain receptor 1 (DDR1) have been found in the blood and brain of patients with schizophrenia (SCZ) and the brain of patients with bipolar disorder (BD). Childhood trauma (CT) is associated with changes in DNAm that in turn are related to suicidal behavior (SB) in patients with several psychiatric disorders. Here, using MassARRAY® technology, we studied 128 patients diagnosed with BD in remission and 141 healthy controls (HCs) to compare leukocyte DDR1 promoter DNAm patterns between patients and HCs and between patients with and without SB. Additionally, we investigated whether CT was associated with DDR1 DNAm and mediated SB. We found hypermethylation at DDR1 cg19215110 and cg23953820 sites and hypomethylation at cg14279856 and cg03270204 sites in patients with BD compared to HCs. Logistic regression models showed that hypermethylation of DDR1 cg23953820 but not cg19215110 and CT were risk factors for BD, while cg14279856 and cg03270204 hypomethylation were protective factors. In patients, CT was a risk factor for SB, but DDR1 DNAm, although associated with CT, did not mediate the association of CT with SB. This is the first study demonstrating altered leukocyte DDR1 promoter DNAm in euthymic patients with BD. We conclude that altered DDR1 DNAm may be related to immune and inflammatory mechanisms and could be a potential blood biomarker for the diagnosis and stratification of psychiatric patients.
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Affiliation(s)
- Beatriz Garcia-Ruiz
- Hospital Universitari Institut Pere Mata, Reus, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV)-CERCA, Tarragona, Spain
- Universitat Rovira i Virgili (URV), Reus, Spain
| | - Esther Jiménez
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- Bipolar and Depressive Disorders Unit, Hospital Clínic de Barcelona, Barcelona, Spain
- Departament de Medicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Institute of Neurosciences (UBNeuro), Universitat de Barcelona, Barcelon, Spain
| | - Selena Aranda
- Hospital Universitari Institut Pere Mata, Reus, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV)-CERCA, Tarragona, Spain
- Universitat Rovira i Virgili (URV), Reus, Spain
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
| | - Norma Verdolini
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- Bipolar and Depressive Disorders Unit, Hospital Clínic de Barcelona, Barcelona, Spain
- Departament de Medicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Institute of Neurosciences (UBNeuro), Universitat de Barcelona, Barcelon, Spain
- FIDMAG Research Foundation, Germanes Hospitalàries, Barcelona, Spain
| | - Alfonso Gutiérrez-Zotes
- Hospital Universitari Institut Pere Mata, Reus, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV)-CERCA, Tarragona, Spain
- Universitat Rovira i Virgili (URV), Reus, Spain
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Sáez
- Hospital Universitari Institut Pere Mata, Reus, Spain
- Institut d'Investigació Sanitària Pere Virgili (IISPV)-CERCA, Tarragona, Spain
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
| | | | - Silvia Alonso-Lana
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- FIDMAG Research Foundation, Germanes Hospitalàries, Barcelona, Spain
- Research Center and Memory Clinic Fundació ACE, Barcelona, Spain
- Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mar Fatjó-Vilas
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- FIDMAG Research Foundation, Germanes Hospitalàries, Barcelona, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Salvador Sarró
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- FIDMAG Research Foundation, Germanes Hospitalàries, Barcelona, Spain
| | - Llanos Torres
- Hospital Mare de Déu de la Mercè, Unitat Polivalent, Germanes Hospitalàries, Barcelona, Spain
| | - Francesco Panicalli
- Benito Menni Complex Assistencial en Salut Mental, Germanes Hospitalàries, Sant Boi de Llobregat, Barcelona, Spain
| | - Caterina Del Mar Bonnin
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- Bipolar and Depressive Disorders Unit, Hospital Clínic de Barcelona, Barcelona, Spain
- Departament de Medicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Institute of Neurosciences (UBNeuro), Universitat de Barcelona, Barcelon, Spain
| | - Edith Pomarol-Clotet
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- FIDMAG Research Foundation, Germanes Hospitalàries, Barcelona, Spain
| | - Eduard Vieta
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain
- Bipolar and Depressive Disorders Unit, Hospital Clínic de Barcelona, Barcelona, Spain
- Departament de Medicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Institute of Neurosciences (UBNeuro), Universitat de Barcelona, Barcelon, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata, Reus, Spain.
- Institut d'Investigació Sanitària Pere Virgili (IISPV)-CERCA, Tarragona, Spain.
- Universitat Rovira i Virgili (URV), Reus, Spain.
- Centro de investigación biomédica en red en salud mental (CIBERSAM)-Instituto de Salud Carlos III, Madrid, Spain.
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4
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Hannon E, Dempster EL, Davies JP, Chioza B, Blake GET, Burrage J, Policicchio S, Franklin A, Walker EM, Bamford RA, Schalkwyk LC, Mill J. Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles. BMC Biol 2024; 22:17. [PMID: 38273288 PMCID: PMC10809680 DOI: 10.1186/s12915-024-01827-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] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Due to interindividual variation in the cellular composition of the human cortex, it is essential that covariates that capture these differences are included in epigenome-wide association studies using bulk tissue. As experimentally derived cell counts are often unavailable, computational solutions have been adopted to estimate the proportion of different cell types using DNA methylation data. Here, we validate and profile the use of an expanded reference DNA methylation dataset incorporating two neuronal and three glial cell subtypes for quantifying the cellular composition of the human cortex. RESULTS We tested eight reference panels containing different combinations of neuronal- and glial cell types and characterised their performance in deconvoluting cell proportions from computationally reconstructed or empirically derived human cortex DNA methylation data. Our analyses demonstrate that while these novel brain deconvolution models produce accurate estimates of cellular proportions from profiles generated on postnatal human cortex samples, they are not appropriate for the use in prenatal cortex or cerebellum tissue samples. Applying our models to an extensive collection of empirical datasets, we show that glial cells are twice as abundant as neuronal cells in the human cortex and identify significant associations between increased Alzheimer's disease neuropathology and the proportion of specific cell types including a decrease in NeuNNeg/SOX10Neg nuclei and an increase of NeuNNeg/SOX10Pos nuclei. CONCLUSIONS Our novel deconvolution models produce accurate estimates for cell proportions in the human cortex. These models are available as a resource to the community enabling the control of cellular heterogeneity in epigenetic studies of brain disorders performed on bulk cortex tissue.
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Affiliation(s)
- Eilis Hannon
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK.
| | - Emma L Dempster
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Jonathan P Davies
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Barry Chioza
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Georgina E T Blake
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Joe Burrage
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Stefania Policicchio
- Italian Institute of Technology, Center for Human Technologies (CHT), Genova, Italy
| | - Alice Franklin
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Emma M Walker
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Rosemary A Bamford
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Leonard C Schalkwyk
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex, CO4 3SQ, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter, Devon, EX2 5DW, UK
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5
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Liu L, Qi X, Cheng S, Meng P, Yang X, Pan C, Zhang N, Chen Y, Li C, Zhang H, Zhang Z, Zhang J, Cheng B, Wen Y, Jia Y, Liu H, Zhang F. Epigenetic analysis suggests aberrant cerebellum brain aging in old-aged adults with autism spectrum disorder and schizophrenia. Mol Psychiatry 2023; 28:4867-4876. [PMID: 37612365 DOI: 10.1038/s41380-023-02233-6] [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: 11/13/2022] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
The aberrant aging hypothesis of schizophrenia (SCZ) and autism spectrum disorder (ASD) has been proposed, and the DNA methylation (DNAm) clock, which is a cumulative evaluation of DNAm levels at age-related CpGs, could serve as a biological aging indicator. This study evaluated epigenetic brain aging of ASD and SCZ using Horvath's epigenetic clock, based on two public genome-wide DNA methylation datasets of post-mortem brain samples (NASD = 222; NSCZ = 142). Total subjects were further divided into subgroups by gender and age. The epigenetic age acceleration (AgeAccel) for each sample was calculated as the residual value resulting from the regression model and compared between groups. Results showed DNAm age has a strong correlation with chronological age in both datasets across multiple brain regions (P < 0.05). When divided into equally sized age groups, the AgeAccel of the cerebellum (CB) region from people over 45 years of age was greater compared to the control sample (AgeAccel of ASD vs control: 5.069 vs -6.249; P < 0.001). And a decelerated epigenetic aging process was observed in the CB region of individuals with SCZ aged 50-70 years (AgeAccel of SCZ vs control: -3.171 vs 2.418; P < 0.05). However, our results showed no significant difference in AgeAccel between ASD and control groups, and between SCZ and control groups in the total and gender-specific groups (P > 0.05). This study's results revealed some evidence for aberrant epigenetic CB brain aging in old-aged patients with ASD and SCZ, indicating a different pattern of CB aging in older adults with these two diseases. However, further studies of larger ASD and SCZ cohorts are necessary to make definitive conclusions on this observation.
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Affiliation(s)
- Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P. R. China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Na Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yujing Chen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Chune Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Huijie Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Zhen Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Jingxi Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Huan Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education of China, Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China.
- Department of Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P. R. China.
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6
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Zhang Z, Wiencke JK, Kelsey KT, Koestler DC, Molinaro AM, Pike SC, Karra P, Christensen BC, Salas LA. Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation. Front Neurosci 2023; 17:1198243. [PMID: 37404460 PMCID: PMC10315586 DOI: 10.3389/fnins.2023.1198243] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/30/2023] [Indexed: 07/06/2023] Open
Abstract
Introduction The human brain comprises heterogeneous cell types whose composition can be altered with physiological and pathological conditions. New approaches to discern the diversity and distribution of brain cells associated with neurological conditions would significantly advance the study of brain-related pathophysiology and neuroscience. Unlike single-nuclei approaches, DNA methylation-based deconvolution does not require special sample handling or processing, is cost-effective, and easily scales to large study designs. Existing DNA methylation-based methods for brain cell deconvolution are limited in the number of cell types deconvolved. Methods Using DNA methylation profiles of the top cell-type-specific differentially methylated CpGs, we employed a hierarchical modeling approach to deconvolve GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells. Results We demonstrate the utility of our method by applying it to data on normal tissues from various brain regions and in aging and diseased tissues, including Alzheimer's disease, autism, Huntington's disease, epilepsy, and schizophrenia. Discussion We expect that the ability to determine the cellular composition in the brain using only DNA from bulk samples will accelerate understanding brain cell type composition and cell-type-specific epigenetic states in normal and diseased brain tissues.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
| | - John K. Wiencke
- Department of Neurological Surgery, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, United States
| | - Karl T. Kelsey
- Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University School of Public Health, Providence, RI, United States
| | - Devin C. Koestler
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS, United States
| | - Annette M. Molinaro
- Department of Neurological Surgery, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, United States
| | - Steven C. Pike
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
- Department of Neurology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
| | - Prasoona Karra
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
| | - Lucas A. Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States
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7
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Psychosis in Alzheimer disease - mechanisms, genetics and therapeutic opportunities. Nat Rev Neurol 2022; 18:131-144. [PMID: 34983978 PMCID: PMC9074132 DOI: 10.1038/s41582-021-00597-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2021] [Indexed: 12/14/2022]
Abstract
Psychosis is a common and distressing symptom in people with Alzheimer disease, and few safe and effective treatments are available. However, new approaches to symptom assessment and treatment are beginning to drive the field forward. New nosological perspectives have been provided by incorporating the emergence of psychotic symptoms in older adults - even in advance of dementia - into epidemiological and neurobiological frameworks as well as into diagnostic and research criteria such as the International Psychogeriatric Association criteria for psychosis in neurocognitive disorders, the Alzheimer's Association International Society to Advance Alzheimer's Research and Treatment (ISTAART) research criteria for psychosis in neurodegenerative disease, and the ISTAART criteria for mild behavioural impairment. Here, we highlight the latest findings in genomics, neuroimaging and neurobiology that are informing approaches to drug discovery and repurposing. Current pharmacological and non-pharmacological treatment options are discussed, with a focus on safety and precision medicine. We also explore trial data for pimavanserin, a novel agent that shows promise for the treatment of psychosis in people with dementia, and discuss existing agents that might be useful but need further exploration such as escitalopram, lithium, cholinesterase inhibitors and vitamin D. Although the assessment and management of psychosis in people with dementia remain challenging, new opportunities are providing direction and hope to the field.
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8
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Wagh VV, Vyas P, Agrawal S, Pachpor TA, Paralikar V, Khare SP. Peripheral Blood-Based Gene Expression Studies in Schizophrenia: A Systematic Review. Front Genet 2021; 12:736483. [PMID: 34721526 PMCID: PMC8548640 DOI: 10.3389/fgene.2021.736483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022] Open
Abstract
Schizophrenia is a disorder that is characterized by delusions, hallucinations, disorganized speech or behavior, and socio-occupational impairment. The duration of observation and variability in symptoms can make the accurate diagnosis difficult. Identification of biomarkers for schizophrenia (SCZ) can help in early diagnosis, ascertaining the diagnosis, and development of effective treatment strategies. Here we review peripheral blood-based gene expression studies for identification of gene expression biomarkers for SCZ. A literature search was carried out in PubMed and Web of Science databases for blood-based gene expression studies in SCZ. A list of differentially expressed genes (DEGs) was compiled and analyzed for overlap with genetic markers, differences based on drug status of the participants, functional enrichment, and for effect of antipsychotics. This literature survey identified 61 gene expression studies. Seventeen out of these studies were based on expression microarrays. A comparative analysis of the DEGs (n = 227) from microarray studies revealed differences between drug-naive and drug-treated SCZ participants. We found that of the 227 DEGs, 11 genes (ACOT7, AGO2, DISC1, LDB1, RUNX3, SIGIRR, SLC18A1, NRG1, CHRNB2, PRKAB2, and ZNF74) also showed genetic and epigenetic changes associated with SCZ. Functional enrichment analysis of the DEGs revealed dysregulation of proline and 4-hydroxyproline metabolism. Also, arginine and proline metabolism was the most functionally enriched pathway for SCZ in our analysis. Follow-up studies identified effect of antipsychotic treatment on peripheral blood gene expression. Of the 27 genes compiled from the follow-up studies AKT1, DISC1, HP, and EIF2D had no effect on their expression status as a result of antipsychotic treatment. Despite the differences in the nature of the study, ethnicity of the population, and the gene expression analysis method used, we identified several coherent observations. An overlap, though limited, of genetic, epigenetic and gene expression changes supports interplay of genetic and environmental factors in SCZ. The studies validate the use of blood as a surrogate tissue for biomarker analysis. We conclude that well-designed cohort studies across diverse populations, use of high-throughput sequencing technology, and use of artificial intelligence (AI) based computational analysis will significantly improve our understanding and diagnostic capabilities for this complex disorder.
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Affiliation(s)
- Vipul Vilas Wagh
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Parin Vyas
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Suchita Agrawal
- The Psychiatry Unit, KEM Hospital and KEM Hospital Research Centre, Pune, India
| | | | - Vasudeo Paralikar
- The Psychiatry Unit, KEM Hospital and KEM Hospital Research Centre, Pune, India
| | - Satyajeet P Khare
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
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9
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Alfimova MV, Kondratyev NV, Golov AK, Kaleda VG, Abramova LI, Golimbet VE. Relationship between DNA Methylation within the YJEFN3 Gene and Cognitive Deficit in Schizophrenia Spectrum Disorders. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421080019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Wu X, Huai C, Shen L, Li M, Yang C, Zhang J, Chen L, Zhu W, Fan L, Zhou W, Xing Q, He L, Wan C, Qin S. Genome-wide study of copy number variation implicates multiple novel loci for schizophrenia risk in Han Chinese family trios. iScience 2021; 24:102894. [PMID: 34401673 PMCID: PMC8358640 DOI: 10.1016/j.isci.2021.102894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/17/2021] [Accepted: 07/19/2021] [Indexed: 01/22/2023] Open
Abstract
Schizophrenia (SCZ) is a severe neuropsychiatric disorder that affects 1% of the global population. Copy number variations (CNVs) have been shown to play a critical role in its pathophysiology; however, only case-control studies on SCZ susceptibility CNVs have been conducted in Han Chinese. Here, we performed an array comparative genomic hybridization-based genome-wide CNV analysis in 100 Chinese family trios with SCZ. Burden test suggested that the SCZ probands carried more duplications than their healthy parents and unrelated healthy controls. Besides, five CNV loci were firstly reported to be associated with SCZ here, including both unbalanced transmitted CNVs and enriched de novo CNVs. Moreover, two genes (CTDSPL and MGAM) in these CNVs showed significant SCZ relevance in the expression level. Our findings support the crucial role of CNVs in the etiology of SCZ and provide new insights into the underlying mechanism of SCZ pathogenesis.
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Affiliation(s)
- Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Mo Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Chao Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Juan Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Luan Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wenli Zhu
- The Fourth People's Hospital of Wuhu, Wuhu, Anhui, 241000, China
| | - Lingzi Fan
- Zhumadian Psychiatric Hospital, Zhumadian, Henan, 463000, China
| | - Wei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qinghe Xing
- Children's Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Corresponding author
| | - Chunling Wan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Corresponding author
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
- Corresponding author
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11
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Berdenis van Berlekom A, Notman N, Sneeboer MAM, Snijders GJLJ, Houtepen LC, Nispeling DM, He Y, Dracheva S, Hol EM, Kahn RS, de Witte LD, Boks MP. DNA methylation differences in cortical grey and white matter in schizophrenia. Epigenomics 2021; 13:1157-1169. [PMID: 34323598 PMCID: PMC8386513 DOI: 10.2217/epi-2021-0077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/09/2021] [Indexed: 01/27/2023] Open
Abstract
Aim: Identify grey- and white-matter-specific DNA-methylation differences between schizophrenia (SCZ) patients and controls in postmortem brain cortical tissue. Materials & methods: Grey and white matter were separated from postmortem brain tissue of the superior temporal and medial frontal gyrus from SCZ (n = 10) and control (n = 11) cases. Genome-wide DNA-methylation analysis was performed using the Infinium EPIC Methylation Array (Illumina, CA, USA). Results: Four differentially methylated regions associated with SCZ status and tissue type (grey vs white matter) were identified within or near KLF9, SFXN1, SPRED2 and ALS2CL genes. Gene-expression analysis showed differential expression of KLF9 and SFXN1 in SCZ. Conclusion: Our data show distinct differences in DNA methylation between grey and white matter that are unique to SCZ, providing new leads to unravel the pathogenesis of SCZ.
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Affiliation(s)
- Amber Berdenis van Berlekom
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nina Notman
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marjolein AM Sneeboer
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Gijsje JLJ Snijders
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lotte C Houtepen
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Danny M Nispeling
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Yujie He
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research, Education, & Clinical Center (VISN 2 South), James J Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Elly M Hol
- Department of Translational Neuroscience, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - René S Kahn
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research, Education, & Clinical Center (VISN 2 South), James J Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Lot D de Witte
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marco P Boks
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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12
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Petralia MC, Ciurleo R, Bramanti A, Bramanti P, Saraceno A, Mangano K, Quattropani MC, Nicoletti F, Fagone P. Transcriptomic Data Analysis Reveals a Down-Expression of Galectin-8 in Schizophrenia Hippocampus. Brain Sci 2021; 11:brainsci11080973. [PMID: 34439592 PMCID: PMC8392448 DOI: 10.3390/brainsci11080973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 12/31/2022] Open
Abstract
Schizophrenia (SCZ) is a severe psychiatric disorder with several clinical manifestations that include cognitive dysfunction, decline in motivation, and psychosis. Current standards of care treatment with antipsychotic agents are often ineffective in controlling the disease, as only one-third of SCZ patients respond to medications. The mechanisms underlying the pathogenesis of SCZ remain elusive. It is believed that inflammatory processes may play a role as contributing factors to the etiology of SCZ. Galectins are a family of β-galactoside-binding lectins that contribute to the regulation of immune and inflammatory responses, and previous reports have shown their role in the maintenance of central nervous system (CNS) homeostasis and neuroinflammation. In the current study, we evaluated the expression levels of the galectin gene family in post-mortem samples of the hippocampus, associative striatum, and dorsolateral prefrontal cortex from SCZ patients. We found a significant downregulation of LGALS8 (Galectin-8) in the hippocampus of SCZ patients as compared to otherwise healthy donors. Interestingly, the reduction of LGALS8 was disease-specific, as no modulation was observed in the hippocampus from bipolar nor major depressive disorder (MDD) patients. Prediction analysis identified TBL1XR1, BRF2, and TAF7 as potential transcription factors controlling LGALS8 expression. In addition, MIR3681HG and MIR4296 were negatively correlated with LGALS8 expression, suggesting a role for epigenetics in the regulation of LGALS8 levels. On the other hand, no differences in the methylation levels of LGALS8 were observed between SCZ and matched control hippocampus. Finally, ontology analysis of the genes negatively correlated with LGALS8 expression identified an enrichment of the NGF-stimulated transcription pathway and of the oligodendrocyte differentiation pathway. Our study identified LGALS8 as a disease-specific gene, characterizing SCZ patients, that may in the future be exploited as a potential therapeutic target.
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Affiliation(s)
- Maria Cristina Petralia
- Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy; (M.C.P.); (M.C.Q.)
| | - Rosella Ciurleo
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (R.C.); (P.B.)
| | - Alessia Bramanti
- Department of Medicine, University of Salerno, 84084 Salerno, Italy;
| | - Placido Bramanti
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (R.C.); (P.B.)
| | - Andrea Saraceno
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (A.S.); (K.M.); (F.N.)
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (A.S.); (K.M.); (F.N.)
| | - Maria Catena Quattropani
- Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy; (M.C.P.); (M.C.Q.)
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (A.S.); (K.M.); (F.N.)
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (A.S.); (K.M.); (F.N.)
- Correspondence:
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13
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Hidden Role of Gut Microbiome Dysbiosis in Schizophrenia: Antipsychotics or Psychobiotics as Therapeutics? Int J Mol Sci 2021; 22:ijms22147671. [PMID: 34299291 PMCID: PMC8307070 DOI: 10.3390/ijms22147671] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 02/06/2023] Open
Abstract
Schizophrenia is a chronic, heterogeneous neurodevelopmental disorder that has complex symptoms and uncertain etiology. Mounting evidence indicates the involvement of genetics and epigenetic disturbances, alteration in gut microbiome, immune system abnormalities, and environmental influence in the disease, but a single root cause and mechanism involved has yet to be conclusively determined. Consequently, the identification of diagnostic markers and the development of psychotic drugs for the treatment of schizophrenia faces a high failure rate. This article surveys the etiology of schizophrenia with a particular focus on gut microbiota regulation and the microbial signaling system that correlates with the brain through the vagus nerve, enteric nervous system, immune system, and production of postbiotics. Gut microbially produced molecules may lay the groundwork for further investigations into the role of gut microbiota dysbiosis and the pathophysiology of schizophrenia. Current treatment of schizophrenia is limited to psychotherapy and antipsychotic drugs that have significant side effects. Therefore, alternative therapeutic options merit exploration. The use of psychobiotics alone or in combination with antipsychotics may promote the development of novel therapeutic strategies. In view of the individual gut microbiome structure and personalized response to antipsychotic drugs, a tailored and targeted manipulation of gut microbial diversity naturally by novel prebiotics (non-digestible fiber) may be a successful alternative therapeutic for the treatment of schizophrenia patients.
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14
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Munawar N, Ahsan K, Muhammad K, Ahmad A, Anwar MA, Shah I, Al Ameri AK, Al Mughairbi F. Hidden Role of Gut Microbiome Dysbiosis in Schizophrenia: Antipsychotics or Psychobiotics as Therapeutics? Int J Mol Sci 2021. [DOI: https://doi.org/10.3390/ijms22147671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Schizophrenia is a chronic, heterogeneous neurodevelopmental disorder that has complex symptoms and uncertain etiology. Mounting evidence indicates the involvement of genetics and epigenetic disturbances, alteration in gut microbiome, immune system abnormalities, and environmental influence in the disease, but a single root cause and mechanism involved has yet to be conclusively determined. Consequently, the identification of diagnostic markers and the development of psychotic drugs for the treatment of schizophrenia faces a high failure rate. This article surveys the etiology of schizophrenia with a particular focus on gut microbiota regulation and the microbial signaling system that correlates with the brain through the vagus nerve, enteric nervous system, immune system, and production of postbiotics. Gut microbially produced molecules may lay the groundwork for further investigations into the role of gut microbiota dysbiosis and the pathophysiology of schizophrenia. Current treatment of schizophrenia is limited to psychotherapy and antipsychotic drugs that have significant side effects. Therefore, alternative therapeutic options merit exploration. The use of psychobiotics alone or in combination with antipsychotics may promote the development of novel therapeutic strategies. In view of the individual gut microbiome structure and personalized response to antipsychotic drugs, a tailored and targeted manipulation of gut microbial diversity naturally by novel prebiotics (non-digestible fiber) may be a successful alternative therapeutic for the treatment of schizophrenia patients.
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15
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Patkar S, Heselmeyer-Haddad K, Auslander N, Hirsch D, Camps J, Bronder D, Brown M, Chen WD, Lokanga R, Wangsa D, Wangsa D, Hu Y, Lischka A, Braun R, Emons G, Ghadimi BM, Gaedcke J, Grade M, Montagna C, Lazebnik Y, Difilippantonio MJ, Habermann JK, Auer G, Ruppin E, Ried T. Hard wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer type-specific aneuploidies. Genome Med 2021; 13:93. [PMID: 34034815 PMCID: PMC8147418 DOI: 10.1186/s13073-021-00905-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
Background Many carcinomas have recurrent chromosomal aneuploidies specific to the tissue of tumor origin. The reason for this specificity is not completely understood. Methods In this study, we looked at the frequency of chromosomal arm gains and losses in different cancer types from the The Cancer Genome Atlas (TCGA) and compared them to the mean gene expression of each chromosome arm in corresponding normal tissues of origin from the Genotype-Tissue Expression (GTEx) database, in addition to the distribution of tissue-specific oncogenes and tumor suppressors on different chromosome arms. Results This analysis revealed a complex picture of factors driving tumor karyotype evolution in which some recurrent chromosomal copy number reflect the chromosome arm-wide gene expression levels of the their normal tissue of tumor origin. Conclusions We conclude that the cancer type-specific distribution of chromosomal arm gains and losses is potentially “hardwiring” gene expression levels characteristic of the normal tissue of tumor origin, in addition to broadly modulating the expression of tissue-specific tumor driver genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00905-y.
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Affiliation(s)
- Sushant Patkar
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Department of Computer Science, University of Maryland, College Park, USA
| | - Kerstin Heselmeyer-Haddad
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Noam Auslander
- Department of Computer Science, University of Maryland, College Park, USA.,National Center for Biotechnology Information, NIH, Bethesda, MD, 20892, USA
| | - Daniela Hirsch
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer, (IDIBAPS), Hospital Clínic of Barcelona, CIBEREHD, 08036, Barcelona, Spain
| | - Daniel Bronder
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Markus Brown
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Wei-Dong Chen
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Rachel Lokanga
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Darawalee Wangsa
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Danny Wangsa
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yue Hu
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Annette Lischka
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Rüdiger Braun
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Georg Emons
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - B Michael Ghadimi
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Jochen Gaedcke
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Cristina Montagna
- Department of Genetics and Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Michael J Difilippantonio
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Gert Auer
- Department of Oncology and Pathology, CancerCenter Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Thomas Ried
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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Guevara EE, Hopkins WD, Hof PR, Ely JJ, Bradley BJ, Sherwood CC. Comparative analysis reveals distinctive epigenetic features of the human cerebellum. PLoS Genet 2021; 17:e1009506. [PMID: 33956822 PMCID: PMC8101944 DOI: 10.1371/journal.pgen.1009506] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying the molecular underpinnings of the neural specializations that underlie human cognitive and behavioral traits has long been of considerable interest. Much research on human-specific changes in gene expression and epigenetic marks has focused on the prefrontal cortex, a brain structure distinguished by its role in executive functions. The cerebellum shows expansion in great apes and is gaining increasing attention for its role in motor skills and cognitive processing, including language. However, relatively few molecular studies of the cerebellum in a comparative evolutionary context have been conducted. Here, we identify human-specific methylation in the lateral cerebellum relative to the dorsolateral prefrontal cortex, in a comparative study with chimpanzees (Pan troglodytes) and rhesus macaques (Macaca mulatta). Specifically, we profiled genome-wide methylation levels in the three species for each of the two brain structures and identified human-specific differentially methylated genomic regions unique to each structure. We further identified which differentially methylated regions (DMRs) overlap likely regulatory elements and determined whether associated genes show corresponding species differences in gene expression. We found greater human-specific methylation in the cerebellum than the dorsolateral prefrontal cortex, with differentially methylated regions overlapping genes involved in several conditions or processes relevant to human neurobiology, including synaptic plasticity, lipid metabolism, neuroinflammation and neurodegeneration, and neurodevelopment, including developmental disorders. Moreover, our results show some overlap with those of previous studies focused on the neocortex, indicating that such results may be common to multiple brain structures. These findings further our understanding of the cerebellum in human brain evolution. Humans are distinguished from other species by several aspects of cognition. While much comparative evolutionary neuroscience has focused on the neocortex, increasing recognition of the cerebellum’s role in cognition and motor processing has inspired considerable new research. Comparative molecular studies, however, generally continue to focus on the neocortex. We sought to characterize potential genetic regulatory traits distinguishing the human cerebellum by undertaking genome-wide epigenetic profiling of the lateral cerebellum, and compared this to the prefrontal cortex of humans, chimpanzees, and rhesus macaque monkeys. We found that humans showed greater differential CpG methylation–an epigenetic modification of DNA that can reflect past or present gene expression–in the cerebellum than the prefrontal cortex, highlighting the importance of this structure in human brain evolution. Humans also specifically show methylation differences at genes involved in neurodevelopment, neuroinflammation, synaptic plasticity, and lipid metabolism. These differences are relevant for understanding processes specific to humans, such as extensive plasticity, as well as pronounced and prevalent neurodegenerative conditions associated with aging.
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Affiliation(s)
- Elaine E. Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
- * E-mail:
| | - William D. Hopkins
- Keeling Center for Comparative Medicine and Research, University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- New York Consortium in Evolutionary Primatology, New York, New York, United States of America
| | - John J. Ely
- MAEBIOS, Alamogordo, New Mexico, United States of America
| | - Brenda J. Bradley
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
| | - Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, United States of America
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17
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Zhang L, Young JI, Gomez L, Silva TC, Schmidt MA, Cai J, Chen X, Martin ER, Wang L. Sex-specific DNA methylation differences in Alzheimer's disease pathology. Acta Neuropathol Commun 2021; 9:77. [PMID: 33902726 PMCID: PMC8074512 DOI: 10.1186/s40478-021-01177-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/10/2021] [Indexed: 12/14/2022] Open
Abstract
Sex is an important factor that contributes to the clinical and biological heterogeneities in Alzheimer's disease (AD), but the regulatory mechanisms underlying sex disparity in AD are still not well understood. DNA methylation is an important epigenetic modification that regulates gene transcription and is known to be involved in AD. We performed the first large-scale sex-specific meta-analysis of DNA methylation differences in AD neuropathology, by re-analyzing four recent epigenome-wide association studies totaling more than 1000 postmortem prefrontal cortex brain samples using a uniform analytical pipeline. For each cohort, we employed two complementary analytical strategies, a sex-stratified analysis that examined methylation-Braak stage associations in male and female samples separately, and a sex-by-Braak stage interaction analysis that compared the magnitude of these associations between different sexes. Our analysis uncovered 14 novel CpGs, mapped to genes such as TMEM39A and TNXB that are associated with the AD Braak stage in a sex-specific manner. TMEM39A is known to be involved in inflammation, dysregulated type I interferon responses, and other immune processes. TNXB encodes tenascin proteins, which are extracellular matrix glycoproteins demonstrated to modulate synaptic plasticity in the brain. Moreover, for many previously implicated genes in AD neuropathology, such as MBP and AZU1, our analysis provided the new insights that they were predominately driven by effects in only one sex. These sex-specific DNA methylation differences were enriched in divergent biological processes such as integrin activation in females and complement activation in males. Our study implicated multiple new loci and biological processes that affected AD neuropathology in a sex-specific manner.
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Affiliation(s)
- Lanyu Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Juan I Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Tiago C Silva
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Michael A Schmidt
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Jesse Cai
- Brentwood High School, 5304 Murray Ln, Brentwood, TN, 37027, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Eden R Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
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18
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Nabais MF, Laws SM, Lin T, Vallerga CL, Armstrong NJ, Blair IP, Kwok JB, Mather KA, Mellick GD, Sachdev PS, Wallace L, Henders AK, Zwamborn RAJ, Hop PJ, Lunnon K, Pishva E, Roubroeks JAY, Soininen H, Tsolaki M, Mecocci P, Lovestone S, Kłoszewska I, Vellas B, Furlong S, Garton FC, Henderson RD, Mathers S, McCombe PA, Needham M, Ngo ST, Nicholson G, Pamphlett R, Rowe DB, Steyn FJ, Williams KL, Anderson TJ, Bentley SR, Dalrymple-Alford J, Fowder J, Gratten J, Halliday G, Hickie IB, Kennedy M, Lewis SJG, Montgomery GW, Pearson J, Pitcher TL, Silburn P, Zhang F, Visscher PM, Yang J, Stevenson AJ, Hillary RF, Marioni RE, Harris SE, Deary IJ, Jones AR, Shatunov A, Iacoangeli A, van Rheenen W, van den Berg LH, Shaw PJ, Shaw CE, Morrison KE, Al-Chalabi A, Veldink JH, Hannon E, Mill J, Wray NR, McRae AF. Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders. Genome Biol 2021; 22:90. [PMID: 33771206 PMCID: PMC8004462 DOI: 10.1186/s13059-021-02275-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND People with neurodegenerative disorders show diverse clinical syndromes, genetic heterogeneity, and distinct brain pathological changes, but studies report overlap between these features. DNA methylation (DNAm) provides a way to explore this overlap and heterogeneity as it is determined by the combined effects of genetic variation and the environment. In this study, we aim to identify shared blood DNAm differences between controls and people with Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. RESULTS We use a mixed-linear model method (MOMENT) that accounts for the effect of (un)known confounders, to test for the association of each DNAm site with each disorder. While only three probes are found to be genome-wide significant in each MOMENT association analysis of amyotrophic lateral sclerosis and Parkinson's disease (and none with Alzheimer's disease), a fixed-effects meta-analysis of the three disorders results in 12 genome-wide significant differentially methylated positions. Predicted immune cell-type proportions are disrupted across all neurodegenerative disorders. Protein inflammatory markers are correlated with profile sum-scores derived from disease-associated immune cell-type proportions in a healthy aging cohort. In contrast, they are not correlated with MOMENT DNAm-derived profile sum-scores, calculated using effect sizes of the 12 differentially methylated positions as weights. CONCLUSIONS We identify shared differentially methylated positions in whole blood between neurodegenerative disorders that point to shared pathogenic mechanisms. These shared differentially methylated positions may reflect causes or consequences of disease, but they are unlikely to reflect cell-type proportion differences.
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Grants
- U24 AG021886 NIA NIH HHS
- U01 AG016976 NIA NIH HHS
- Department of Health
- U01 AG024904 NIA NIH HHS
- 108890/Z/15/Z Wellcome Trust
- 503480 Medical Research Council
- TURNER/OCT15/972-797 Motor Neurone Disease Association
- U01 AG032984 NIA NIH HHS
- R01 HL105756 NHLBI NIH HHS
- 082604/2/07/Z Wellcome Trust
- R01 AG033193 NIA NIH HHS
- National Health and Medical Research Council
- Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge
- Medical Research Council (UK)
- Economic and Social Research Council
- National Institute for Health Research (NIHR)
- the European Community’s Health Seventh Framework Programme
- Horizon 2020 Programme
- MND Association and the Wellcome Trust.
- European Research Council (ERC)
- EU Joint Programme – Neurodegenerative Disease Research ()
- EU Joint Programme - Neurodegenerative Disease Research (JPND)
- Australian Research Council
- Mater Foundation
- ForeFront - NHMRC
- Australian National Health and Medical Research Council
- University of Otago Research Grant, together with financial support from the Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd
- National Health and Medical Research Council and the Dementia Collaborative Research Centres program (DCRC2), as well as funding from the Science and Industry Endowment Fund (SIEF) and the Cooperative Research Centre (CRC) for Mental Health – funded throug
- EU Joint Programme - Neurodegenerative Disease Research (JPND), co-funded through the Australian National Health and Medical Research (NHMRC) Council, Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge,
- EU Joint Programme - Neurodegenerative Disease Research (JPND), United Kingdom Medical Research Council, Economic and Social Research Council, Motor Neuro Disease Association (GB), National Institute for Health Research (NIHR) Biomedical Research Centre at
- EU Joint Programme - Neurodegenerative Disease Research (JPND), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program, PPP Allowance made available by Health~Holland, Top Sector Life Sciences & Health, Unit
- National Health and Medical Research Council, Australian Research Council, Mater Foundation,
- Australian National Health and Medical Research Council (
- University of Otago Research Grant, Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd., National Health and Medical Research Counc
- EFPIA companies and SMEs as part of InnoMed (Innovative Medicines in Europe), an Integrated Project funded by the European Union of the Sixth Framework program
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Affiliation(s)
- Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Simon M Laws
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Costanza L Vallerga
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Internal Medicine, Erasmus MC, University Medical Center, 3015GD, Rotterdam, The Netherlands
| | | | - Ian P Blair
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, School of Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - John B Kwok
- Brain and Mind Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuroscience Research Australia Institute, Randwick, NSW, 2031, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuropsychiatric Institute, The Prince of Wales Hospital, UNSW, Randwick, NSW, 2031, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ramona A J Zwamborn
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Paul J Hop
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Katie Lunnon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Ehsan Pishva
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Janou A Y Roubroeks
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Hilkka Soininen
- Institute of Clinical Medicine, Neurology, University of Eastern Finland, Kuopio, Finland
| | - Magda Tsolaki
- 1st Department of Neurology, Memory and Dementia Unit, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Patrizia Mecocci
- Department of Medicine, Institute of Gerontology and Geriatrics, University of Perugia, Perugia, Italy
| | - Simon Lovestone
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK
| | | | - Bruno Vellas
- INSERM U 558, University of Toulouse, Toulouse, France
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Fleur C Garton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Robert D Henderson
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, VIC, 3195, Australia
| | - Pamela A McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, WA, 6150, Australia
- Notre Dame University, Fremantle, WA, 6160, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, 6150, Australia
| | - Shyuan T Ngo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Garth Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW, 2139, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2050, Australia
| | - Dominic B Rowe
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Tim J Anderson
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Steven R Bentley
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - John Dalrymple-Alford
- New Zealand Brain Research Institute, Christchurch, New Zealand
- School of Psychology, Speech and Hearing, University of Canterbury, Christchurch, New Zealand
| | - Javed Fowder
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Jacob Gratten
- Mater Research, Translational Research Institute, Brisbane, Australia
- Mater Research Institute, The University of Queensland, Brisbane, Australia
| | - Glenda Halliday
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Ian B Hickie
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Martin Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simon J G Lewis
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - John Pearson
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Toni L Pitcher
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Peter Silburn
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Wouter van Rheenen
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | | | - Cristopher E Shaw
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | | | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
- King's College Hospital, London, SE5 9RS, UK
| | - Jan H Veldink
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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19
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Emanetci E, Çakır T. Network-Based Analysis of Cognitive Impairment and Memory Deficits from Transcriptome Data. J Mol Neurosci 2021; 71:2415-2428. [PMID: 33713319 DOI: 10.1007/s12031-021-01807-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022]
Abstract
Aging is an inevitable process that negatively affects all living organisms and their vital functions. The brain is one of the most important organs in living beings and is primarily impacted by aging. The molecular mechanisms of learning, memory and cognition are altered over time, and the impairment in these mechanisms can lead to neurodegenerative diseases. Transcriptomics can be used to study these impairments to acquire more detailed information on the affected molecular mechanisms. Here we analyzed learning- and memory-related transcriptome data by mapping it on the organism-specific protein-protein interactome network. Subnetwork discovery algorithms were applied to discover highly dysregulated subnetworks, which were complemented with co-expression-based interactions. The functional analysis shows that the identified subnetworks are enriched with genes having roles in synaptic plasticity, gliogenesis, neurogenesis and cognition, which are reported to be related to memory and learning. With a detailed analysis, we show that the results from different subnetwork discovery algorithms or from different transcriptomic datasets can be successfully reconciled, leading to a memory-learning network that sheds light on the molecular mechanisms behind aging and memory-related impairments.
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Affiliation(s)
- Elif Emanetci
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey.
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20
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Bhattacharya A, Li Y, Love MI. MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies. PLoS Genet 2021; 17:e1009398. [PMID: 33684137 PMCID: PMC7971899 DOI: 10.1371/journal.pgen.1009398] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 03/18/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023] Open
Abstract
Traditional predictive models for transcriptome-wide association studies (TWAS) consider only single nucleotide polymorphisms (SNPs) local to genes of interest and perform parameter shrinkage with a regularization process. These approaches ignore the effect of distal-SNPs or other molecular effects underlying the SNP-gene association. Here, we outline multi-omics strategies for transcriptome imputation from germline genetics to allow more powerful testing of gene-trait associations by prioritizing distal-SNPs to the gene of interest. In one extension, we identify mediating biomarkers (CpG sites, microRNAs, and transcription factors) highly associated with gene expression and train predictive models for these mediators using their local SNPs. Imputed values for mediators are then incorporated into the final predictive model of gene expression, along with local SNPs. In the second extension, we assess distal-eQTLs (SNPs associated with genes not in a local window around it) for their mediation effect through mediating biomarkers local to these distal-eSNPs. Distal-eSNPs with large indirect mediation effects are then included in the transcriptomic prediction model with the local SNPs around the gene of interest. Using simulations and real data from ROS/MAP brain tissue and TCGA breast tumors, we show considerable gains of percent variance explained (1-2% additive increase) of gene expression and TWAS power to detect gene-trait associations. This integrative approach to transcriptome-wide imputation and association studies aids in identifying the complex interactions underlying genetic regulation within a tissue and important risk genes for various traits and disorders.
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Affiliation(s)
- Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, University of California-Los Angeles, Los Angeles, California, United States of America
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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21
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Hannon E, Dempster EL, Mansell G, Burrage J, Bass N, Bohlken MM, Corvin A, Curtis CJ, Dempster D, Di Forti M, Dinan TG, Donohoe G, Gaughran F, Gill M, Gillespie A, Gunasinghe C, Hulshoff HE, Hultman CM, Johansson V, Kahn RS, Kaprio J, Kenis G, Kowalec K, MacCabe J, McDonald C, McQuillin A, Morris DW, Murphy KC, Mustard CJ, Nenadic I, O'Donovan MC, Quattrone D, Richards AL, Rutten BPF, St Clair D, Therman S, Toulopoulou T, Van Os J, Waddington JL, Sullivan P, Vassos E, Breen G, Collier DA, Murray RM, Schalkwyk LS, Mill J. DNA methylation meta-analysis reveals cellular alterations in psychosis and markers of treatment-resistant schizophrenia. eLife 2021; 10:e58430. [PMID: 33646943 PMCID: PMC8009672 DOI: 10.7554/elife.58430] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 02/23/2021] [Indexed: 12/30/2022] Open
Abstract
We performed a systematic analysis of blood DNA methylation profiles from 4483 participants from seven independent cohorts identifying differentially methylated positions (DMPs) associated with psychosis, schizophrenia, and treatment-resistant schizophrenia. Psychosis cases were characterized by significant differences in measures of blood cell proportions and elevated smoking exposure derived from the DNA methylation data, with the largest differences seen in treatment-resistant schizophrenia patients. We implemented a stringent pipeline to meta-analyze epigenome-wide association study (EWAS) results across datasets, identifying 95 DMPs associated with psychosis and 1048 DMPs associated with schizophrenia, with evidence of colocalization to regions nominated by genetic association studies of disease. Many schizophrenia-associated DNA methylation differences were only present in patients with treatment-resistant schizophrenia, potentially reflecting exposure to the atypical antipsychotic clozapine. Our results highlight how DNA methylation data can be leveraged to identify physiological (e.g., differential cell counts) and environmental (e.g., smoking) factors associated with psychosis and molecular biomarkers of treatment-resistant schizophrenia.
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Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter, Barrack RoadExeterUnited Kingdom
| | - Emma L Dempster
- University of Exeter Medical School, University of Exeter, Barrack RoadExeterUnited Kingdom
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter, Barrack RoadExeterUnited Kingdom
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Barrack RoadExeterUnited Kingdom
| | - Nick Bass
- Division of Psychiatry, University College LondonLondonUnited Kingdom
| | - Marc M Bohlken
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, HeidelberglaanUtrechtNetherlands
| | - Aiden Corvin
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Trinity Translational Medicine Institute, Trinity College Dublin, St. James HospitalDublinIreland
| | - Charles J Curtis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
- NIHR BioResource Centre Maudsley, South London and Maudsley NHS Foundation Trust (SLaM), King’s College LondonLondonUnited Kingdom
| | - David Dempster
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
| | - Marta Di Forti
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
- South London and Maudsley NHS Mental Health Foundation TrustLondonUnited Kingdom
- National Institute for Health Research (NIHR), Mental Health Biomedical Research Centre, South London and Maudsley NHS Foundation Trust and King's College LondonLondonUnited Kingdom
| | | | - Gary Donohoe
- Centre for Neuroimaging and Cognitive Genomics (NICOG), School of Psychology and Discipline of Biochemistry, National University of Ireland GalwayGalwayIreland
| | - Fiona Gaughran
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
- National Psychosis Service, South London and Maudsley NHS Foundation TrustLondonUnited Kingdom
| | - Michael Gill
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Trinity Translational Medicine Institute, Trinity College DublinDublinIreland
| | - Amy Gillespie
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
- Department of Psychiatry, Medical Sciences Division, University of OxfordOxfordUnited Kingdom
| | - Cerisse Gunasinghe
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
| | - Hilleke E Hulshoff
- Department of Psychiatry, University Medical Center UtrechtUtrechtNetherlands
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
| | - Viktoria Johansson
- Department of Medical Epidemiology and Biostatistics Sweden, Karolinska InstitutetStockholmSweden
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm Health Care ServicesStockholmSweden
| | - René S Kahn
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center UtrechtUtrechtNetherlands
- Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Jaakko Kaprio
- Institute for Molecular Medicine FIMM, University of HelsinkiHelsinkiFinland
- Department of Public Health, University of HelsinkiHelsinkiFinland
| | - Gunter Kenis
- Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastrichtNetherlands
| | - Kaarina Kowalec
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
- College of Pharmacy, University of ManitobaWinnipegCanada
| | - James MacCabe
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
| | - Colm McDonald
- Centre for Neuroimaging and Cognitive Genomics (NICOG), School of Medicine, National University of Ireland GalwayGalwayIreland
| | - Andrew McQuillin
- Division of Psychiatry, University College LondonLondonUnited Kingdom
- Division of Psychiatry, University College LondonLondonUnited Kingdom
| | - Derek W Morris
- Centre for Neuroimaging and Cognitive Genomics (NICOG), School of Psychology and Discipline of Biochemistry, National University of Ireland GalwayGalwayIreland
| | - Kieran C Murphy
- Department of Psychiatry, Royal College of Surgeons in IrelandDublinIreland
| | - Colette J Mustard
- Division of Biomedical Sciences, Institute of Health Research and Innovation, University of the Highlands and IslandsInvernessUnited Kingdom
| | - Igor Nenadic
- Department of Psychiatry and Psychotherapy, Jena University HospitalJenaGermany
- Department of Psychiatry and Psychotherapy, Philipps University Marburg/ Marburg University Hospital UKGMMarburgGermany
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Diego Quattrone
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
- South London and Maudsley NHS Mental Health Foundation TrustLondonUnited Kingdom
| | - Alexander L Richards
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Bart PF Rutten
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastrichtNetherlands
| | - David St Clair
- The Institute of Medical Sciences, Univeristy of AberdeenAberdeenUnited Kingdom
| | - Sebastian Therman
- Department of Public Health Solutions, Mental Health Unit, National Institute for Health and WelfareHelsinkiFinland
| | - Timothea Toulopoulou
- Department of Psychology and National Magnetic Resonance Research Center (UMRAM), Aysel Sabuncu Brain Research Centre (ASBAM), Bilkent UniversityAnkaraTurkey
| | - Jim Van Os
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center UtrechtUtrechtNetherlands
| | - John L Waddington
- Molecular and Cellular Therapeutics, Royal College of Surgeons in IrelandDublinIreland
| | - Wellcome Trust Case Control Consortium (WTCCC)
- University of Exeter Medical School, University of Exeter, Barrack RoadExeterUnited Kingdom
- Division of Psychiatry, University College LondonLondonUnited Kingdom
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, HeidelberglaanUtrechtNetherlands
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Trinity Translational Medicine Institute, Trinity College Dublin, St. James HospitalDublinIreland
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
- NIHR BioResource Centre Maudsley, South London and Maudsley NHS Foundation Trust (SLaM), King’s College LondonLondonUnited Kingdom
- South London and Maudsley NHS Mental Health Foundation TrustLondonUnited Kingdom
- National Institute for Health Research (NIHR), Mental Health Biomedical Research Centre, South London and Maudsley NHS Foundation Trust and King's College LondonLondonUnited Kingdom
- APC Microbiome Ireland, University College CorkCorkIreland
- Centre for Neuroimaging and Cognitive Genomics (NICOG), School of Psychology and Discipline of Biochemistry, National University of Ireland GalwayGalwayIreland
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
- National Psychosis Service, South London and Maudsley NHS Foundation TrustLondonUnited Kingdom
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Trinity Translational Medicine Institute, Trinity College DublinDublinIreland
- Department of Psychiatry, Medical Sciences Division, University of OxfordOxfordUnited Kingdom
- Department of Psychiatry, University Medical Center UtrechtUtrechtNetherlands
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
- Department of Medical Epidemiology and Biostatistics Sweden, Karolinska InstitutetStockholmSweden
- Department of Clinical Neuroscience, Center for Psychiatry Research, Karolinska Institutet and Stockholm Health Care ServicesStockholmSweden
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center UtrechtUtrechtNetherlands
- Department of Psychiatry, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Institute for Molecular Medicine FIMM, University of HelsinkiHelsinkiFinland
- Department of Public Health, University of HelsinkiHelsinkiFinland
- Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastrichtNetherlands
- College of Pharmacy, University of ManitobaWinnipegCanada
- Centre for Neuroimaging and Cognitive Genomics (NICOG), School of Medicine, National University of Ireland GalwayGalwayIreland
- Division of Psychiatry, University College LondonLondonUnited Kingdom
- Department of Psychiatry, Royal College of Surgeons in IrelandDublinIreland
- Division of Biomedical Sciences, Institute of Health Research and Innovation, University of the Highlands and IslandsInvernessUnited Kingdom
- Department of Psychiatry and Psychotherapy, Jena University HospitalJenaGermany
- Department of Psychiatry and Psychotherapy, Philipps University Marburg/ Marburg University Hospital UKGMMarburgGermany
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastrichtNetherlands
- The Institute of Medical Sciences, Univeristy of AberdeenAberdeenUnited Kingdom
- Department of Public Health Solutions, Mental Health Unit, National Institute for Health and WelfareHelsinkiFinland
- Department of Psychology and National Magnetic Resonance Research Center (UMRAM), Aysel Sabuncu Brain Research Centre (ASBAM), Bilkent UniversityAnkaraTurkey
- Molecular and Cellular Therapeutics, Royal College of Surgeons in IrelandDublinIreland
- Departments of Genetics and Psychiatry, University of North Carolina at Chapel HillChapel HillUnited States
- Neuroscience Genetics, Eli Lilly and CompanySurreyUnited Kingdom
- Department of Psychosis Studies, Institute of Psychiatry, King’s College LondonLondonUnited Kingdom
- School of Life Sciences, University of EssexColchesterUnited Kingdom
| | | | - Patrick Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
- Departments of Genetics and Psychiatry, University of North Carolina at Chapel HillChapel HillUnited States
| | - Evangelos Vassos
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
| | - Gerome Breen
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College LondonLondonUnited Kingdom
- NIHR BioResource Centre Maudsley, South London and Maudsley NHS Foundation Trust (SLaM), King’s College LondonLondonUnited Kingdom
| | | | - Robin M Murray
- Department of Psychosis Studies, Institute of Psychiatry, King’s College LondonLondonUnited Kingdom
| | | | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Barrack RoadExeterUnited Kingdom
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22
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Price AJ, Jaffe AE, Weinberger DR. Cortical cellular diversity and development in schizophrenia. Mol Psychiatry 2021; 26:203-217. [PMID: 32404946 PMCID: PMC7666011 DOI: 10.1038/s41380-020-0775-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/23/2020] [Accepted: 04/30/2020] [Indexed: 12/31/2022]
Abstract
While a definitive understanding of schizophrenia etiology is far from current reality, an increasing body of evidence implicates perturbations in early development that alter the trajectory of brain maturation in this disorder, leading to abnormal function in early childhood and adulthood. This atypical development likely arises from an interaction of many brain cell types that follow distinct developmental paths. Because both cellular identity and development are governed by the transcriptome and epigenome, two levels of gene regulation that have the potential to reflect both genetic and environmental influences, mapping "omic" changes over development in diverse cells is a fruitful avenue for schizophrenia research. In this review, we provide a survey of human brain cellular composition and development, levels of genomic regulation that determine cellular identity and developmental trajectories, and what is known about how genomic regulation is dysregulated in specific cell types in schizophrenia. We also outline technical challenges and solutions to conducting cell type-specific functional genomic studies in human postmortem brain.
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Affiliation(s)
- Amanda J. Price
- Lieber Institute for Brain Development, Baltimore, MD,McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
| | - Andrew E. Jaffe
- Lieber Institute for Brain Development, Baltimore, MD,McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Baltimore, MD,McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
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23
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Zhang L, Silva TC, Young JI, Gomez L, Schmidt MA, Hamilton-Nelson KL, Kunkle BW, Chen X, Martin ER, Wang L. Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer's disease. Nat Commun 2020; 11:6114. [PMID: 33257653 PMCID: PMC7704686 DOI: 10.1038/s41467-020-19791-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
DNA methylation differences in Alzheimer's disease (AD) have been reported. Here, we conducted a meta-analysis of more than 1000 prefrontal cortex brain samples to prioritize the most consistent methylation differences in multiple cohorts. Using a uniform analysis pipeline, we identified 3751 CpGs and 119 differentially methylated regions (DMRs) significantly associated with Braak stage. Our analysis identified differentially methylated genes such as MAMSTR, AGAP2, and AZU1. The most significant DMR identified is located on the MAMSTR gene, which encodes a cofactor that stimulates MEF2C. Notably, MEF2C cooperates with another transcription factor, PU.1, a central hub in the AD gene network. Our enrichment analysis highlighted the potential roles of the immune system and polycomb repressive complex 2 in pathological AD. These results may help facilitate future mechanistic and biomarker discovery studies in AD.
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Affiliation(s)
- Lanyu Zhang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Tiago C Silva
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Juan I Young
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Michael A Schmidt
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Brian W Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Eden R Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
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24
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Rovira P, Sánchez-Mora C, Pagerols M, Richarte V, Corrales M, Fadeuilhe C, Vilar-Ribó L, Arribas L, Shireby G, Hannon E, Mill J, Casas M, Ramos-Quiroga JA, Soler Artigas M, Ribasés M. Epigenome-wide association study of attention-deficit/hyperactivity disorder in adults. Transl Psychiatry 2020; 10:199. [PMID: 32561708 PMCID: PMC7305172 DOI: 10.1038/s41398-020-0860-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 05/05/2020] [Accepted: 05/15/2020] [Indexed: 12/16/2022] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a highly heritable neurodevelopmental disorder that often persists into adulthood. There is growing evidence that epigenetic dysregulation participates in ADHD. Given that only a limited number of epigenome-wide association studies (EWASs) of ADHD have been conducted so far and they have mainly focused on pediatric and population-based samples, we performed an EWAS in a clinical sample of adults with ADHD. We report one CpG site and four regions differentially methylated between patients and controls, which are located in or near genes previously involved in autoimmune diseases, cancer or neuroticism. Our sensitivity analyses indicate that smoking status is not responsible for these results and that polygenic risk burden for ADHD does not greatly impact the signatures identified. Additionally, we show an overlap of our EWAS findings with genetic signatures previously described for ADHD and with epigenetic signatures for smoking behavior and maternal smoking. These findings support a role of DNA methylation in ADHD and emphasize the need for additional efforts in larger samples to clarify the role of epigenetic mechanisms on ADHD across the lifespan.
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Affiliation(s)
- Paula Rovira
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Cristina Sánchez-Mora
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, University of Barcelona, Catalonia, Spain
| | - Mireia Pagerols
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Vanesa Richarte
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montserrat Corrales
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Christian Fadeuilhe
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Lorena Arribas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Gemma Shireby
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Miquel Casas
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Antoni Ramos-Quiroga
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain
- Department of Psychiatry and Legal Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain.
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, University of Barcelona, Catalonia, Spain.
| | - Marta Ribasés
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain.
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, University of Barcelona, Catalonia, Spain.
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25
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Forero DA, González-Giraldo Y. Integrative In Silico Analysis of Genome-Wide DNA Methylation Profiles in Schizophrenia. J Mol Neurosci 2020; 70:1887-1893. [PMID: 32451840 DOI: 10.1007/s12031-020-01585-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022]
Abstract
Schizophrenia (SZ) is a complex and severe psychiatric disorder, which has a global lifetime prevalence of 0.4% and a heritability of around 0.81. A number of epigenome-wide association studies (EWAS) have been carried out for SZ, with discordant results. The main aim of this study was to carry out an integrative in silico analysis of available genome-wide DNA methylation profiles in schizophrenia. In this work, an integration of multiple lines of evidence (top candidate genes from several EWAS and genome-wide expression and association data) was carried out, in order to identify top differentially methylated (DM) genes for SZ. In addition, functional enrichment and protein-protein interaction analyses were carried out. Several top differentially methylated genes, such as APC, CACNB2, and PRKN, were found, and an enrichment of binding sites for brain-expressed transcription factors, such as FOXO1, MYB, and ZIC3, was also observed. Moreover, a protein-protein interaction network showed a central role for DISC1 and ZNF688 genes, and experimentally validated targets of MIR-137, such as and KCNB2, NRXN1, and SYN2, were identified among DM genes. This is the first integrative in silico analysis of available genome-wide DNA methylation profiles in schizophrenia. This work identified novel candidate genes and pathways for SZ and provides the basis to explore their role in the pathogenesis of SZ in future studies.
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Affiliation(s)
- Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia.
| | - Yeimy González-Giraldo
- Center for Psychosocial Studies for Latin America and the Caribbean, School of Psychosocial Therapies, Universidad Antonio Nariño, Bogotá, Colombia
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26
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Profiling haplotype specific CpG and CpH methylation within a schizophrenia GWAS locus on chromosome 14 in schizophrenia and healthy subjects. Sci Rep 2020; 10:4704. [PMID: 32170143 PMCID: PMC7069985 DOI: 10.1038/s41598-020-61671-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 03/02/2020] [Indexed: 11/17/2022] Open
Abstract
Interrogating DNA methylation within schizophrenia risk loci holds promise to identify mechanisms by which genes influence the disease. Based on the hypothesis that allele specific methylation (ASM) of a single CpG, or perhaps CpH, might mediate or mark the effects of genetic variants on disease risk and phenotypes, we explored haplotype specific methylation levels of individual cytosines within a genomic region harbouring the BAG5, APOPT1 and KLC1 genes in peripheral blood of schizophrenia patients and healthy controls. Three DNA fragments located in promoter, intronic and intergenic areas were studied by single-molecule real-time bisulfite sequencing enabling the analysis of long reads of DNA with base-pair resolution and the determination of haplotypes directly from sequencing data. Among 1,012 cytosines studied, we did not find any site where methylation correlated with the disease or cognitive deficits after correction for multiple testing. At the same time, we determined the methylation profile associated with the schizophrenia risk haplotype within the KLC1 fourth intron and confirmed ASM for cytosines located in the vicinity of rs67899457. These genetically associated DNA methylation variations may be related to the pathophysiological mechanism differentiating the risk and non-risk haplotypes and merit further investigation.
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27
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Policicchio S, Washer S, Viana J, Iatrou A, Burrage J, Hannon E, Turecki G, Kaminsky Z, Mill J, Dempster EL, Murphy TM. Genome-wide DNA methylation meta-analysis in the brains of suicide completers. Transl Psychiatry 2020; 10:69. [PMID: 32075955 PMCID: PMC7031296 DOI: 10.1038/s41398-020-0752-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/09/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
Suicide is the second leading cause of death globally among young people representing a significant global health burden. Although the molecular correlates of suicide remains poorly understood, it has been hypothesised that epigenomic processes may play a role. The objective of this study was to identify suicide-associated DNA methylation changes in the human brain by utilising previously published and unpublished methylomic datasets. We analysed prefrontal cortex (PFC, n = 211) and cerebellum (CER, n = 114) DNA methylation profiles from suicide completers and non-psychiatric, sudden-death controls, meta-analysing data from independent cohorts for each brain region separately. We report evidence for altered DNA methylation at several genetic loci in suicide cases compared to controls in both brain regions with suicide-associated differentially methylated positions enriched among functional pathways relevant to psychiatric phenotypes and suicidality, including nervous system development (PFC) and regulation of long-term synaptic depression (CER). In addition, we examined the functional consequences of variable DNA methylation within a PFC suicide-associated differentially methylated region (PSORS1C3 DMR) using a dual luciferase assay and examined expression of nearby genes. DNA methylation within this region was associated with decreased expression of firefly luciferase but was not associated with expression of nearby genes, PSORS1C3 and POU5F1. Our data suggest that suicide is associated with DNA methylation, offering novel insights into the molecular pathology associated with suicidality.
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Affiliation(s)
- Stefania Policicchio
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Sam Washer
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joana Viana
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Artemis Iatrou
- grid.240684.c0000 0001 0705 3621Rush Alzheimer’s Neurodisease Center, Rush University Medical Center, 600 South Paulina Street, Chicago, IL 60612 USA
| | - Joe Burrage
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Gustavo Turecki
- grid.14709.3b0000 0004 1936 8649Douglas Institute, Department of Psychiatry, McGill University, Verdun, QC H4H 1R3 Canada
| | - Zachary Kaminsky
- grid.21107.350000 0001 2171 9311Department of Psychiatry, School of Medicine, Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Jonathan Mill
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L. Dempster
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Therese M. Murphy
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK ,grid.497880.aSchool of Biological and Health Sciences, Technological University Dublin, City Campus, Dublin, 2 Ireland
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A Novel Schizophrenia Diagnostic Model Based on Statistically Significant Changes in Gene Methylation in Specific Brain Regions. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8047146. [PMID: 32104705 PMCID: PMC7037884 DOI: 10.1155/2020/8047146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/28/2019] [Accepted: 11/15/2019] [Indexed: 12/23/2022]
Abstract
Objective The present study identified methylation patterns of schizophrenia- (SCZ-) related genes in different brain regions and used them to construct a novel DNA methylation-based SCZ diagnostic model. Methods Four DNA methylation datasets representing different brain regions were downloaded from the Gene Expression Omnibus. The common differentially methylated genes (CDMGs) in all datasets were identified to perform functional enrichment analysis. The differential methylation sites of 10 CDMGs involved in the largest numbers of neurological or psychiatric-related biological processes were used to construct a DNA methylation-based diagnostic model for SCZ in the respective datasets. Results A total of 849 CDMGs were identified in the four datasets, but the methylation sites as well as degree of methylation differed across the brain regions. Functional enrichment analysis showed CDMGs were significantly involved in biological processes associated with neuronal axon development, intercellular adhesion, and cell morphology changes and, specifically, in PI3K-Akt, AMPK, and MAPK signaling pathways. Four DNA methylation-based classifiers for diagnosing SCZ were constructed in the four datasets, respectively. The sample recognition efficiency of the classifiers showed an area under the receiver operating characteristic curve of 1.00 in three datasets and >0.9 in one dataset. Conclusion DNA methylation patterns in SCZ vary across different brain regions, which may be a useful epigenetic characteristic for diagnosing SCZ. Our novel model based on SCZ-gene methylation shows promising diagnostic power.
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El Khoury LY, Gorrie-Stone T, Smart M, Hughes A, Bao Y, Andrayas A, Burrage J, Hannon E, Kumari M, Mill J, Schalkwyk LC. Systematic underestimation of the epigenetic clock and age acceleration in older subjects. Genome Biol 2019; 20:283. [PMID: 31847916 PMCID: PMC6915902 DOI: 10.1186/s13059-019-1810-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/03/2019] [Indexed: 11/18/2022] Open
Abstract
Background The Horvath epigenetic clock is widely used. It predicts age quite well from 353 CpG sites in the DNA methylation profile in unknown samples and has been used to calculate “age acceleration” in various tissues and environments. Results The model systematically underestimates age in tissues from older people. This is seen in all examined tissues but most strongly in the cerebellum and is consistently observed in multiple datasets. Age acceleration is thus age-dependent, and this can lead to spurious associations. The current literature includes examples of association tests with age acceleration calculated in a wide variety of ways. Conclusions The concept of an epigenetic clock is compelling, but caution should be taken in interpreting associations with age acceleration. Association tests of age acceleration should include age as a covariate.
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Affiliation(s)
- Louis Y El Khoury
- School of Life Sciences, University of Essex, Colchester, UK.,Present Address: Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | - Melissa Smart
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - Amanda Hughes
- MRC Integrative Epidemiology Unit - University of Bristol, Bristol, UK
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | - Joe Burrage
- Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- Medical School, University of Exeter, Exeter, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
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Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. Transl Psychiatry 2019; 9:256. [PMID: 31624234 PMCID: PMC6797775 DOI: 10.1038/s41398-019-0596-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
Both heritability and environment contribute to risk for schizophrenia. However, the molecular mechanisms of interactions between genetic and non-genetic factors remain unclear. Epigenetic regulation of neuronal genome may be a presumable mechanism in pathogenesis of schizophrenia. Here, we performed analysis of open chromatin landscape of gene promoters in prefrontal cortical (PFC) neurons from schizophrenic patients. We cataloged cell-type-based epigenetic signals of transcriptional start sites (TSS) marked by histone H3-K4 trimethylation (H3K4me3) across the genome in PFC from multiple schizophrenia subjects and age-matched control individuals. One of the top-ranked chromatin alterations was found in the major histocompatibility (MHC) locus on chromosome 6 highlighting the overlap between genetic and epigenetic risk factors in schizophrenia. The chromosome conformation capture (3C) analysis in human brain cells revealed the architecture of multipoint chromatin interactions between the schizophrenia-associated genetic and epigenetic polymorphic sites and distantly located HLA-DRB5 and BTNL2 genes. In addition, schizophrenia-specific chromatin modifications in neurons were particularly prominent for non-coding RNA genes, including an uncharacterized LINC01115 gene and recently identified BNRNA_052780. Notably, protein-coding genes with altered epigenetic state in schizophrenia are enriched for oxidative stress and cell motility pathways. Our results imply the rare individual epigenetic alterations in brain neurons are involved in the pathogenesis of schizophrenia.
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31
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Wong CCY, Smith RG, Hannon E, Ramaswami G, Parikshak NN, Assary E, Troakes C, Poschmann J, Schalkwyk LC, Sun W, Prabhakar S, Geschwind DH, Mill J. Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue. Hum Mol Genet 2019; 28:2201-2211. [PMID: 31220268 PMCID: PMC6602383 DOI: 10.1093/hmg/ddz052] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 12/13/2022] Open
Abstract
Autism spectrum disorder (ASD) encompasses a collection of complex neuropsychiatric disorders characterized by deficits in social functioning, communication and repetitive behaviour. Building on recent studies supporting a role for developmentally moderated regulatory genomic variation in the molecular aetiology of ASD, we quantified genome-wide patterns of DNA methylation in 223 post-mortem tissues samples isolated from three brain regions [prefrontal cortex, temporal cortex and cerebellum (CB)] dissected from 43 ASD patients and 38 non-psychiatric control donors. We identified widespread differences in DNA methylation associated with idiopathic ASD (iASD), with consistent signals in both cortical regions that were distinct to those observed in the CB. Individuals carrying a duplication on chromosome 15q (dup15q), representing a genetically defined subtype of ASD, were characterized by striking differences in DNA methylationacross a discrete domain spanning an imprinted gene cluster within the duplicated region. In addition to the dramatic cis-effects on DNA methylation observed in dup15q carriers, we identified convergent methylomic signatures associated with both iASD and dup15q, reflecting the findings from previous studies of gene expression and H3K27ac. Cortical co-methylation network analysis identified a number of co-methylated modules significantly associated with ASD that are enriched for genomic regions annotated to genes involved in the immune system, synaptic signalling and neuronal regulation. Our study represents the first systematic analysis of DNA methylation associated with ASD across multiple brain regions, providing novel evidence for convergent molecular signatures associated with both idiopathic and syndromic autism.
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Affiliation(s)
- Chloe C Y Wong
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, De Crespigny Park, London, UK
| | - Rebecca G Smith
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Gokul Ramaswami
- Center for Autism Research and Treatment, and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Neelroop N Parikshak
- Center for Autism Research and Treatment, and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Elham Assary
- Department of Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Claire Troakes
- King’s College London, Institute of Psychiatry, Psychology and Neuroscience, De Crespigny Park, London, UK
| | - Jeremie Poschmann
- Centre de Recherche en Transplantation et Immunologie, Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Inserm, Université de Nantes, Nantes, France
| | | | - Wenjie Sun
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, and Program in Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
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32
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Methylation age acceleration does not predict mortality in schizophrenia. Transl Psychiatry 2019; 9:157. [PMID: 31164630 PMCID: PMC6548770 DOI: 10.1038/s41398-019-0489-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 12/31/2022] Open
Abstract
Schizophrenia (SCZ) is associated with high mortality. DNA methylation levels vary over the life course, and pre-selected combinations of methylation array probes can be used to estimate "methylation age" (mAge). mAge correlates highly with chronological age but when it differs, termed mAge acceleration, it has been previously associated with all-cause mortality. We tested the association between mAge acceleration and mortality in SCZ and controls. We selected 190 SCZ cases and 190 controls from the Sweden Schizophrenia Study. Cases were identified from the Swedish Hospital Discharge Register with ≥5 specialist treatment contacts and ≥5 antipsychotic prescriptions. Controls had no psychotic disorder or antipsychotics. Subjects were selected if they had died or survived during follow-up (2:1 oversampling). Extracted DNA was assayed on the Illumina MethylationEPIC array. mAge was regressed on age at sampling to obtain mAge acceleration. Using Cox proportional hazards regression, the association between mAge acceleration and mortality was tested. After quality control, the following were available: n = 126 SCZ died, 63 SCZ alive, 127 controls died, 62 controls alive. In the primary analyses, we did not find a significant association between mAge acceleration and SCZ mortality (adjusted p > 0.005). Sensitivity analyses excluding SCZ cases with pre-existing cancer demonstrated a significant association between the Hannum mAge acceleration and mortality (hazard ratio = 1.13, 95% confidence interval = 1.04-1.22, p = 0.005). Per our pre-specified criteria, we did not confirm our primary hypothesis that mAge acceleration would predict subsequent mortality in people with SCZ, but we cannot rule out smaller effects or effects in patient subsets.
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Egervari G, Kozlenkov A, Dracheva S, Hurd YL. Molecular windows into the human brain for psychiatric disorders. Mol Psychiatry 2019; 24:653-673. [PMID: 29955163 PMCID: PMC6310674 DOI: 10.1038/s41380-018-0125-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 12/20/2022]
Abstract
Delineating the pathophysiology of psychiatric disorders has been extremely challenging but technological advances in recent decades have facilitated a deeper interrogation of molecular processes in the human brain. Initial candidate gene expression studies of the postmortem brain have evolved into genome wide profiling of the transcriptome and the epigenome, a critical regulator of gene expression. Here, we review the potential and challenges of direct molecular characterization of the postmortem human brain, and provide a brief overview of recent transcriptional and epigenetic studies with respect to neuropsychiatric disorders. Such information can now be leveraged and integrated with the growing number of genome-wide association databases to provide a functional context of trait-associated genetic variants linked to psychiatric illnesses and related phenotypes. While it is clear that the field is still developing and challenges remain to be surmounted, these recent advances nevertheless hold tremendous promise for delineating the neurobiological underpinnings of mental diseases and accelerating the development of novel medication strategies.
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Affiliation(s)
- Gabor Egervari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Yasmin L Hurd
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA.
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34
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Zeng Y, Amador C, Xia C, Marioni R, Sproul D, Walker RM, Morris SW, Bretherick A, Canela-Xandri O, Boutin TS, Clark DW, Campbell A, Rawlik K, Hayward C, Nagy R, Tenesa A, Porteous DJ, Wilson JF, Deary IJ, Evans KL, McIntosh AM, Navarro P, Haley CS. Parent of origin genetic effects on methylation in humans are common and influence complex trait variation. Nat Commun 2019; 10:1383. [PMID: 30918249 PMCID: PMC6437195 DOI: 10.1038/s41467-019-09301-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 02/28/2019] [Indexed: 01/11/2023] Open
Abstract
Parent-of-origin effects (POE) exist when there is differential expression of alleles inherited from the two parents. A genome-wide scan for POE on DNA methylation at 639,238 CpGs in 5,101 individuals identifies 733 independent methylation CpGs potentially influenced by POE at a false discovery rate ≤ 0.05 of which 331 had not previously been identified. Cis and trans methylation quantitative trait loci (mQTL) regulate methylation variation through POE at 54% (399/733) of the identified POE-influenced CpGs. The combined results provide strong evidence for previously unidentified POE-influenced CpGs at 171 independent loci. Methylation variation at 14 of the POE-influenced CpGs is associated with multiple metabolic traits. A phenome-wide association analysis using the POE mQTL SNPs identifies a previously unidentified imprinted locus associated with waist circumference. These results provide a high resolution population-level map for POE on DNA methylation sites, their local and distant regulators and potential consequences for complex traits.
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Affiliation(s)
- Yanni Zeng
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Carmen Amador
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Charley Xia
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Riccardo Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Duncan Sproul
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Rosie M Walker
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew Bretherick
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Oriol Canela-Xandri
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Thibaud S Boutin
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Konrad Rawlik
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Caroline Hayward
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Reka Nagy
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - James F Wilson
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kathryn L Evans
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Division of Psychiatry, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Pau Navarro
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Chris S Haley
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK.
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Walton E, Relton CL, Caramaschi D. Using Openly Accessible Resources to Strengthen Causal Inference in Epigenetic Epidemiology of Neurodevelopment and Mental Health. Genes (Basel) 2019; 10:E193. [PMID: 30832291 PMCID: PMC6470715 DOI: 10.3390/genes10030193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
The recent focus on the role of epigenetic mechanisms in mental health has led to several studies examining the association of epigenetic processes with psychiatric conditions and neurodevelopmental traits. Some studies suggest that epigenetic changes might be causal in the development of the psychiatric condition under investigation. However, other scenarios are possible, e.g., statistical confounding or reverse causation, making it particularly challenging to derive conclusions on causality. In the present review, we examine the evidence from human population studies for a possible role of epigenetic mechanisms in neurodevelopment and mental health and discuss methodological approaches on how to strengthen causal inference, including the need for replication, (quasi-)experimental approaches and Mendelian randomization. We signpost openly accessible resources (e.g., "MR-Base" "EWAS catalog" as well as tissue-specific methylation and gene expression databases) to aid the application of these approaches.
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Affiliation(s)
- Esther Walton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
- Department of Psychology, University of Bath, BA2 7AY Bath, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
| | - Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
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36
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Okazaki S, Otsuka I, Numata S, Horai T, Mouri K, Boku S, Ohmori T, Sora I, Hishimoto A. Epigenetic clock analysis of blood samples from Japanese schizophrenia patients. NPJ SCHIZOPHRENIA 2019; 5:4. [PMID: 30814520 PMCID: PMC6393510 DOI: 10.1038/s41537-019-0072-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/07/2019] [Indexed: 01/01/2023]
Abstract
The accelerated aging hypothesis of schizophrenia (SCZ) has been proposed. DNA methylation profiles were developed for determining “epigenetic age.” Here, we assessed intrinsic and extrinsic epigenetic age acceleration (IEAA and EEAA, respectively) in SCZ. We examined two independent cohorts of Japanese ancestry. The first cohort consisted of 80 patients with SCZ under long-term or repeated hospitalization and 40 controls, with the economical DNA pooling technique. The second cohort consisted of 24 medication-free patients with SCZ and 23 controls. Blood of SCZ subjects exhibited decreased EEAA in the first cohort (p = 0.0162), but not in the second cohort. IEAA did not differ in either cohort. We performed replication analyses using publicly available datasets from European ancestry (three blood and one brain datasets). One blood dataset showed increased EEAA in SCZ (p = 0.0228). Overall, our results provide evidence for decreased EEAA in SCZ associated with hospitalization in the Japanese population.
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Affiliation(s)
- Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Tadasu Horai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kentaro Mouri
- Department of Internal Medicine, Division of Biosignal Pathophysiology, Kobe University Graduate School of Medicine, Kobe, Japan.,Medical Center for Student's Health Service, Kobe University, Kobe, Japan
| | - Shuken Boku
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tetsuro Ohmori
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Ichiro Sora
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.
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Föcking M, Doyle B, Munawar N, Dillon ET, Cotter D, Cagney G. Epigenetic Factors in Schizophrenia: Mechanisms and Experimental Approaches. MOLECULAR NEUROPSYCHIATRY 2019; 5:6-12. [PMID: 31019914 DOI: 10.1159/000495063] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Schizophrenia is a chronic mental disorder that is still poorly understood despite decades of study. Many factors have been found to contribute to the pathogenesis, including neurodevelopmental disturbance, genetic risk, and environmental insult, but no single root cause has emerged. While evidence from twin studies suggests a strong heritable component, few individual loci have been identified in genomewide screens, suggesting a role for epigenetic effects. Rather, large numbers of weakly acting loci may cumulatively increase disease risk, including several mapping to epigenetic pathways. In this review, we discuss mechanisms of epigenetic regulation and evidence for an epigenetic contribution to disease phenotype. We further describe the range of experimental tools currently available to study epigenetic effects associated with the disease.
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Affiliation(s)
- Melanie Föcking
- Department of Psychiatry, Royal College of Surgeons in Ireland (RCSI), Beaumont Hospital, Dublin, Ireland
| | - Benjamin Doyle
- Department of Psychiatry, Royal College of Surgeons in Ireland (RCSI), Beaumont Hospital, Dublin, Ireland
| | - Nayla Munawar
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - David Cotter
- Department of Psychiatry, Royal College of Surgeons in Ireland (RCSI), Beaumont Hospital, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
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Föcking M, Doyle B, Munawar N, Dillon E, Cotter D, Cagney G. Epigenetic Factors in Schizophrenia: Mechanisms and Experimental Approaches. MOLECULAR NEUROPSYCHIATRY 2019. [DOI: https://doi.org/10.1159/000495063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Roberts S, Suderman M, Zammit S, Watkins SH, Hannon E, Mill J, Relton C, Arseneault L, Wong CCY, Fisher HL. Longitudinal investigation of DNA methylation changes preceding adolescent psychotic experiences. Transl Psychiatry 2019; 9:69. [PMID: 30718501 PMCID: PMC6361958 DOI: 10.1038/s41398-019-0407-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 12/26/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Childhood psychotic experiences (PEs), such as seeing or hearing things that others do not, or extreme paranoia, are relatively common with around 1 in 20 children reporting them at age 12. Childhood PEs are often distressing and can be predictive of schizophrenia, other psychiatric disorders, and suicide attempts in adulthood, particularly if they persist during adolescence. Previous research has demonstrated that methylomic signatures in blood could be potential biomarkers of psychotic phenomena. This study explores the association between DNA methylation (DNAm) and the emergence, persistence, and remission of PEs in childhood and adolescence. DNAm profiles were obtained from the ALSPAC cohort at birth, age 7, and age 15/17 (n = 901). PEs were assessed through interviews with participants at ages 12 and 18. We identified PE-associated probes (p < 5 × 10-5) and regions (corrected p < 0.05) at ages 12 and 18. Several of the differentially methylated probes were also associated with the continuity of PEs across adolescence. One probe (cg16459265), detected consistently at multiple timepoints in the study sample, was replicated in an independent sample of twins (n = 1658). Six regions, including those spanning the HLA-DBP2 and GDF7 genes, were consistently differentially methylated at ages 7 and 15-17. Findings from this large, population-based study suggest that DNAm at multiple stages of development may be associated with PEs in late childhood and adolescence, though further replication is required. Research uncovering biomarkers associated with pre-clinical PEs is important as it has the potential to facilitate early identification of individuals at increased risk who could benefit from preventive interventions.
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Affiliation(s)
- Susanna Roberts
- King’s College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
| | - Matthew Suderman
- 0000 0004 1936 7603grid.5337.2University of Bristol, MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Stanley Zammit
- University of Bristol, School of Medicine, Centre for Academic Mental Health, Bristol, UK ,Cardiff University School of Medicine, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff, UK
| | - Sarah H. Watkins
- University of Bristol, School of Medicine, Centre for Academic Mental Health, Bristol, UK
| | - Eilis Hannon
- 0000 0004 1936 8024grid.8391.3University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- 0000 0004 1936 8024grid.8391.3University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Caroline Relton
- 0000 0004 1936 7603grid.5337.2University of Bristol, MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Louise Arseneault
- King’s College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
| | - Chloe C. Y. Wong
- King’s College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
| | - Helen L. Fisher
- King’s College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, London, UK
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Rizzardi LF, Hickey PF, Rodriguez DiBlasi V, Tryggvadóttir R, Callahan CM, Idrizi A, Hansen KD, Feinberg AP. Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. Nat Neurosci 2019; 22:307-316. [PMID: 30643296 PMCID: PMC6348048 DOI: 10.1038/s41593-018-0297-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/13/2018] [Indexed: 12/21/2022]
Abstract
Epigenetic modifications confer stable transcriptional patterns in the brain and both normal and abnormal brain function involve specialized brain regions. We examined DNA methylation by whole genome bisulfite sequencing in neuronal and non-neuronal populations from four brain regions (anterior cingulate gyrus, hippocampus, prefrontal cortex, and nucleus accumbens) as well as chromatin accessibility in the latter two. We find pronounced differences in CpG and non-CpG differentially methylated regions (CG- and CH-DMRs) only in neuronal cells across regions. While neuronal CH-DMRs were highly associated with differential gene expression, CG-DMRs were consistent with chromatin accessibility and enriched for regulatory regions. These CG-DMRs comprise ~12 Mb of the genome that is highly enriched for genomic regions associated with heritability of neuropsychiatric traits including addictive behavior, schizophrenia, and neuroticism, suggesting a mechanistic link between pathology and differential neuron-specific epigenetic regulation in distinct brain regions.
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Affiliation(s)
- Lindsay F Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter F Hickey
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Varenka Rodriguez DiBlasi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rakel Tryggvadóttir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Colin M Callahan
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kasper D Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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41
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Liang W, Huang Y, Tan X, Wu J, Duan J, Zhang H, Yin B, Li Y, Zheng P, Wei H, Xie P. Alterations Of Glycerophospholipid And Fatty Acyl Metabolism In Multiple Brain Regions Of Schizophrenia Microbiota Recipient Mice. Neuropsychiatr Dis Treat 2019; 15:3219-3229. [PMID: 31819450 PMCID: PMC6876209 DOI: 10.2147/ndt.s225982] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/11/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Schizophrenia is a debilitating psychiatric disorder characterized by molecular and anatomical abnormalities of multiple brain regions. Our recent study showed that dysbiosis of the gut microbiota contributes to the onset of schizophrenia-relevant behaviors, but the underlying mechanisms remain largely unknown. PURPOSE This study aimed to investigate how gut microbiota shapes metabolic signatures in multiple brain regions of schizophrenia microbiota recipient mice. METHODS Gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) were used to compare the metabolic signatures in the cortex, cerebellum and striatum of schizophrenia microbiota and healthy microbiota recipient mice. Enrichment analysis was further conducted to uncover the crucial metabolic pathways related to schizophrenia-relevant behaviors. RESULTS We found that the metabolic phenotypes of these three regions were substantially different in schizophrenia microbiota recipient mice from those in healthy microbiota recipient mice. In total, we identified 499 differential metabolites that could discriminate the two groups in the three brain regions. These differential metabolites were mainly involved in glycerophospholipid and fatty acyl metabolism. Moreover, we found four of fatty acyl metabolites that were consistently altered in the three brain regions. CONCLUSION Taken together, our study suggests that alterations of glycerophospholipid and fatty acyl metabolism are implicated in the onset of schizophrenia-relevant behaviors, which may provide a new understanding of the etiology of schizophrenia.
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Affiliation(s)
- Weiwei Liang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Department of Neurology, Yongchuan Hospital, Chongqing Medical University, Chongqing 402460, People's Republic of China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Yu Huang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Xunmin Tan
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Jing Wu
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China.,The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Jiajia Duan
- Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China.,The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Hanping Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Bangmin Yin
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Yifan Li
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Peng Zheng
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Hong Wei
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, People's Republic of China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China.,Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing 400016, People's Republic of China
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42
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Boks MP, Houtepen LC, Xu Z, He Y, Ursini G, Maihofer AX, Rajarajan P, Yu Q, Xu H, Wu Y, Wang S, Shi JP, Hulshoff Pol HE, Strengman E, Rutten BPF, Jaffe AE, Kleinman JE, Baker DG, Hol EM, Akbarian S, Nievergelt CM, De Witte LD, Vinkers CH, Weinberger DR, Yu J, Kahn RS. Genetic vulnerability to DUSP22 promoter hypermethylation is involved in the relation between in utero famine exposure and schizophrenia. NPJ SCHIZOPHRENIA 2018; 4:16. [PMID: 30131491 PMCID: PMC6104043 DOI: 10.1038/s41537-018-0058-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 01/27/2023]
Abstract
Epigenetic changes may account for the doubled risk to develop schizophrenia in individuals exposed to famine in utero. We therefore investigated DNA methylation in a unique sample of patients and healthy individuals conceived during the great famine in China. Subsequently, we examined two case-control samples without famine exposure in whole blood and brain tissue. To shed light on the causality of the relation between famine exposure and DNA methylation, we exposed human fibroblasts to nutritional deprivation. In the famine-exposed schizophrenia patients, we found significant hypermethylation of the dual specificity phosphatase 22 (DUSP22) gene promoter (Chr6:291687-293285) (N = 153, p = 0.01). In this sample, DUSP22 methylation was also significantly higher in patients independent of famine exposure (p = 0.025), suggesting that hypermethylation of DUSP22 is also more generally involved in schizophrenia risk. Similarly, DUSP22 methylation was also higher in two separate case-control samples not exposed to famine using DNA from whole blood (N = 64, p = 0.03) and postmortem brains (N = 214, p = 0.007). DUSP22 methylation showed strong genetic regulation across chromosomes by a region on chromosome 16 which was consistent with new 3D genome interaction data. The presence of a direct link between famine and DUSP22 transcription was supported by data from cultured human fibroblasts that showed increased methylation (p = 0.048) and expression (p = 0.019) in response to nutritional deprivation (N = 10). These results highlight an epigenetic locus that is genetically regulated across chromosomes and that is involved in the response to early-life exposure to famine and that is relevant for a major psychiatric disorder.
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Affiliation(s)
- M P Boks
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - L C Houtepen
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Z Xu
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Y He
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - G Ursini
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, USA
| | - A X Maihofer
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, USA.,VA Center of Excellence for Stress and Mental Health, San Diego, CA, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - P Rajarajan
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Q Yu
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - H Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - Y Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - S Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - J P Shi
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - H E Hulshoff Pol
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - E Strengman
- Molecular Pathology, Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - B P F Rutten
- School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - A E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, USA
| | - J E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, USA
| | - D G Baker
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, USA.,VA Center of Excellence for Stress and Mental Health, San Diego, CA, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - E M Hol
- Brain Center Rudolf Magnus, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - S Akbarian
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - C M Nievergelt
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, USA.,VA Center of Excellence for Stress and Mental Health, San Diego, CA, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - L D De Witte
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C H Vinkers
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - D R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, USA
| | - J Yu
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - R S Kahn
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands.,Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
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Dmitrijeva M, Ossowski S, Serrano L, Schaefer MH. Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates. Nucleic Acids Res 2018; 46:7022-7039. [PMID: 29893918 PMCID: PMC6101545 DOI: 10.1093/nar/gky498] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an epigenetic mechanism known to affect gene expression and aberrant DNA methylation patterns have been described in cancer. However, only a small fraction of differential methylation events target genes with a defined role in cancer, raising the question of how aberrant DNA methylation contributes to carcinogenesis. As recently a link has been suggested between methylation patterns arising in ageing and those arising in cancer, we asked which aberrations are unique to cancer and which are the product of normal ageing processes. We therefore compared the methylation patterns between ageing and cancer in multiple tissues. We observed that hypermethylation preferentially occurs in regulatory elements, while hypomethylation is associated with structural features of the chromatin. Specifically, we observed consistent hypomethylation of late-replicating, lamina-associated domains. The extent of hypomethylation was stronger in cancer, but in both ageing and cancer it was proportional to the replication timing of the region and the cell division rate of the tissue. Moreover, cancer patients who displayed more hypomethylation in late-replicating, lamina-associated domains had higher expression of cell division genes. These findings suggest that different cell division rates contribute to tissue- and cancer type-specific DNA methylation profiles.
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Affiliation(s)
- Marija Dmitrijeva
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Martin H Schaefer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
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Crawford B, Craig Z, Mansell G, White I, Smith A, Spaull S, Imm J, Hannon E, Wood A, Yaghootkar H, Ji Y, Mullins N, Lewis CM, Mill J, Murphy TM. DNA methylation and inflammation marker profiles associated with a history of depression. Hum Mol Genet 2018; 27:2840-2850. [PMID: 29790996 PMCID: PMC6680088 DOI: 10.1093/hmg/ddy199] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/30/2018] [Accepted: 05/16/2018] [Indexed: 11/13/2022] Open
Abstract
Depression is a common and disabling disorder, representing a major social and economic health issue. Moreover, depression is associated with the progression of diseases with an inflammatory etiology including many inflammatory-related disorders. At the molecular level, the mechanisms by which depression might promote the onset of these diseases and associated immune-dysfunction are not well understood. In this study we assessed genome-wide patterns of DNA methylation in whole blood-derived DNA obtained from individuals with a self-reported history of depression (n = 100) and individuals without a history of depression (n = 100) using the Illumina 450K microarray. Our analysis identified six significant (Šidák corrected P < 0.05) depression-associated differentially methylated regions (DMRs); the top-ranked DMR was located in exon 1 of the LTB4R2 gene (Šidák corrected P = 1.27 × 10-14). Polygenic risk scores (PRS) for depression were generated and known biological markers of inflammation, telomere length (TL) and IL-6, were measured in DNA and serum samples, respectively. Next, we employed a systems-level approach to identify networks of co-methylated loci associated with a history of depression, in addition to depression PRS, TL and IL-6 levels. Our analysis identified one depression-associated co-methylation module (P = 0.04). Interestingly, the depression-associated module was highly enriched for pathways related to immune function and was also associated with TL and IL-6 cytokine levels. In summary, our genome-wide DNA methylation analysis of individuals with and without a self-reported history of depression identified several candidate DMRs of potential relevance to the pathogenesis of depression and its associated immune-dysfunction phenotype.
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Affiliation(s)
- Bethany Crawford
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Zoe Craig
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Isobel White
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Adam Smith
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Steve Spaull
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, Exeter, UK
| | - Jennifer Imm
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Andrew Wood
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Hanieh Yaghootkar
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Yingjie Ji
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | | | - Niamh Mullins
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- Division of Genetics and Molecular Medicine, King’s College London, London SE1 9RT, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
| | - Therese M Murphy
- University of Exeter Medical School, University of Exeter, EX2 5DW Exeter, UK
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45
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McKinney BC, Lin H, Ding Y, Lewis DA, Sweet RA. DNA methylation age is not accelerated in brain or blood of subjects with schizophrenia. Schizophr Res 2018; 196:39-44. [PMID: 28988914 PMCID: PMC5886835 DOI: 10.1016/j.schres.2017.09.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/18/2017] [Accepted: 09/21/2017] [Indexed: 01/01/2023]
Abstract
Individuals with schizophrenia (SZ) exhibit multiple premature age-related phenotypes and die ~20years prematurely. The accelerated aging hypothesis of SZ has been advanced to explain these observations, it posits that SZ-associated factors accelerate the progressive biological changes associated with normal aging. Testing the hypothesis has been limited by the absence of robust, meaningful, and multi-tissue measures of biological age. Recently, a method was described in which DNA methylation (DNAm) levels at 353 genomic sites are used to produce "DNAm age", an estimate of biological age with advantages over existing measures. We used this method and 3 publicly-available DNAm datasets, 1 from brain and 2 from blood, to test the hypothesis. The brain dataset was composed of data from the dorsolateral prefrontal cortex of 232 non-psychiatric control (NPC) and 195 SZ subjects. Blood dataset #1 was composed of data from whole blood of 304 NPC and 332 SZ subjects, and blood dataset #2 was composed of data from whole blood of 405 NPC and 260 SZ subjects. DNAm age and chronological age correlated strongly (r=0.92-0.95, p<0.0001) in both NPC and SZ subjects in all 3 datasets. DNAm age acceleration did not differ between NPC and SZ subjects in the brain dataset (t=0.52, p=0.60), blood dataset #1 (t=1.51, p=0.13), or blood dataset #2 (t=0.93, p=0.35). Consistent with our previous findings from a smaller study of postmortem brains, our findings suggest there is no acceleration of brain or blood aging in SZ and, thus, do not support the accelerated aging hypothesis of SZ.
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Affiliation(s)
| | - Huang Lin
- University of Pittsburgh, Department of Biostatistics, Pittsburgh, PA
| | - Ying Ding
- University of Pittsburgh, Department of Biostatistics, Pittsburgh, PA
| | - David A. Lewis
- University of Pittsburgh, Department of Psychiatry, Pittsburgh, PA
| | - Robert A. Sweet
- University of Pittsburgh, Department of Psychiatry, Pittsburgh, PA,University of Pittsburgh, Department of Neurology, Pittsburgh, PA,VISN4 Mental Illness Research, Education, and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA
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Bogdan R, Baranger DAA, Agrawal A. Polygenic Risk Scores in Clinical Psychology: Bridging Genomic Risk to Individual Differences. Annu Rev Clin Psychol 2018; 14:119-157. [PMID: 29579395 PMCID: PMC7772939 DOI: 10.1146/annurev-clinpsy-050817-084847] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genomewide association studies (GWASs) across psychiatric phenotypes have shown that common genetic variants generally confer risk with small effect sizes (odds ratio < 1.1) that additively contribute to polygenic risk. Summary statistics derived from large discovery GWASs can be used to generate polygenic risk scores (PRS) in independent, target data sets to examine correlates of polygenic disorder liability (e.g., does genetic liability to schizophrenia predict cognition?). The intuitive appeal and generalizability of PRS have led to their widespread use and new insights into mechanisms of polygenic liability. However, when currently applied across traits they account for small amounts of variance (<3%), are relatively uninformative for clinical treatment, and, in isolation, provide no insight into molecular mechanisms. Larger GWASs are needed to increase the precision of PRS, and novel approaches integrating various data sources (e.g., multitrait analysis of GWASs) may improve the utility of current PRS.
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Affiliation(s)
- Ryan Bogdan
- BRAINLab, Department of Psychological and Brain Sciences, and Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri 63110, USA;
| | - David A A Baranger
- BRAINLab, Department of Psychological and Brain Sciences, and Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri 63110, USA;
| | - Arpana Agrawal
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, Missouri 63110, USA
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Hannon E, Schendel D, Ladd-Acosta C, Grove J, Hansen CS, Andrews SV, Hougaard DM, Bresnahan M, Mors O, Hollegaard MV, Bækvad-Hansen M, Hornig M, Mortensen PB, Børglum AD, Werge T, Pedersen MG, Nordentoft M, Buxbaum J, Daniele Fallin M, Bybjerg-Grauholm J, Reichenberg A, Mill J. Elevated polygenic burden for autism is associated with differential DNA methylation at birth. Genome Med 2018; 10:19. [PMID: 29587883 PMCID: PMC5872584 DOI: 10.1186/s13073-018-0527-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/20/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD involves both inherited and environmental risk factors, with epigenetic processes hypothesized as one mechanism by which both genetic and non-genetic variation influence gene regulation and pathogenesis. The aim of this study was to identify DNA methylation biomarkers of ASD detectable at birth. METHODS We quantified neonatal methylomic variation in 1263 infants-of whom ~ 50% went on to subsequently develop ASD-using DNA isolated from archived blood spots taken shortly after birth. We used matched genotype data from the same individuals to examine the molecular consequences of ASD-associated genetic risk variants, identifying methylomic variation associated with elevated polygenic burden for ASD. In addition, we performed DNA methylation quantitative trait loci (mQTL) mapping to prioritize target genes from ASD GWAS findings. RESULTS We identified robust epigenetic signatures of gestational age and prenatal tobacco exposure, confirming the utility of DNA methylation data generated from neonatal blood spots. Although we did not identify specific loci showing robust differences in neonatal DNA methylation associated with later ASD, there was a significant association between increased polygenic burden for autism and methylomic variation at specific loci. Each unit of elevated ASD polygenic risk score was associated with a mean increase in DNA methylation of - 0.14% at two CpG sites located proximal to a robust GWAS signal for ASD on chromosome 8. CONCLUSIONS This study is the largest analysis of DNA methylation in ASD undertaken and the first to integrate genetic and epigenetic variation at birth. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with disease, and of using mQTL to refine the functional and regulatory variation associated with ASD risk variants.
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Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter, RILD Building, Level 4, Barrack Rd, Exeter, EX2 5DW UK
| | - Diana Schendel
- Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Christine Søholm Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Shan V. Andrews
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - David Michael Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michaeline Bresnahan
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, USA
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Mads Vilhelm Hollegaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Mady Hornig
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University; Aarhus University Hospital, Risskov, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Anders D. Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Giørtz Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Buxbaum
- Department of Psychiatry, Mount Sinai School of Medicine, New York City, USA
| | - M. Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, USA
- Department of Psychiatry, Columbia University, New York, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Abraham Reichenberg
- Department of Psychiatry, Mount Sinai School of Medicine, New York City, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, RILD Building, Level 4, Barrack Rd, Exeter, EX2 5DW UK
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48
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Ovenden ES, McGregor NW, Emsley RA, Warnich L. DNA methylation and antipsychotic treatment mechanisms in schizophrenia: Progress and future directions. Prog Neuropsychopharmacol Biol Psychiatry 2018; 81:38-49. [PMID: 29017764 DOI: 10.1016/j.pnpbp.2017.10.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022]
Abstract
Antipsychotic response in schizophrenia is a complex, multifactorial trait influenced by pharmacogenetic factors. With genetic studies thus far providing little biological insight or clinical utility, the field of pharmacoepigenomics has emerged to tackle the so-called "missing heritability" of drug response in disease. Research on psychiatric disorders has only recently started to assess the link between epigenetic alterations and treatment outcomes. DNA methylation, the best characterised epigenetic mechanism to date, is discussed here in the context of schizophrenia and antipsychotic treatment outcomes. The majority of published studies have assessed the influence of antipsychotics on methylation levels in specific neurotransmitter-associated candidate genes or at the genome-wide level. While these studies illustrate the epigenetic modifications associated with antipsychotics, very few have assessed clinical outcomes and the potential of differential DNA methylation profiles as predictors of antipsychotic response. Results from other psychiatric disorder studies, such as depression and bipolar disorder, provide insight into what may be achieved by schizophrenia pharmacoepigenomics. Other aspects that should be addressed in future research include methodological challenges, such as tissue specificity, and the influence of genetic variation on differential methylation patterns.
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Affiliation(s)
- Ellen S Ovenden
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Nathaniel W McGregor
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Robin A Emsley
- Department of Psychiatry, Stellenbosch University, Tygerberg 7505, South Africa
| | - Louise Warnich
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa.
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49
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Peedicayil J, Grayson DR. An epigenetic basis for an omnigenic model of psychiatric disorders. J Theor Biol 2018; 443:52-55. [PMID: 29378208 DOI: 10.1016/j.jtbi.2018.01.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 11/19/2022]
Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology, Christian Medical College, Vellore, India.
| | - Dennis R Grayson
- Department of Psychiatry, Center for Alcohol Research in Epigenetics, The Psychiatric Institute, College of Medicine, University of Illinois, Chicago 60612, USA.
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50
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Iurato S, Carrillo-Roa T, Arloth J, Czamara D, Diener-Hölzl L, Lange J, Müller-Myhsok B, Binder EB, Erhardt A. "DNA Methylation signatures in panic disorder". Transl Psychiatry 2017; 7:1287. [PMID: 29249830 PMCID: PMC5802688 DOI: 10.1038/s41398-017-0026-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 01/15/2023] Open
Abstract
Panic disorder (PD) affects about four million Europeans, with women affected twice as likely as men, causing substantial suffering and high economic costs. The etiopathogenesis of PD remains largely unknown, but both genetic and environmental factors contribute to risk. An epigenome-wide association study (EWAS) was conducted to compare medication-free PD patients (n = 89) with healthy controls (n = 76) stratified by gender. Replication was sought in an independent sample (131 cases, 169 controls) and functional analyses were conducted in a third sample (N = 71). DNA methylation was assessed in whole blood using the Infinium HumanMethylation450 BeadChip. One genome-wide association surviving FDR of 5% (cg07308824, P = 1.094 × 10-7, P-adj = 0.046) was identified in female PD patients (N = 49) compared to controls (N = 48). The same locus, located in an enhancer region of the HECA gene, was also hypermethylated in female PD patients in the replication sample (P = 0.035) and the significance of the association improved in the meta-analysis (P-adj = 0.004). Methylation at this CpG site was associated with HECA mRNA expression in another independent female sample (N = 71) both at baseline (P = 0.046) and after induction by dexamethasone (P = 0.029). Of 15 candidates, 5 previously reported as associated with PD or anxiety traits also showed differences in DNA methylation after gene-wise correction and included SGK1, FHIT, ADCYAP1, HTR1A, HTR2A. Our study examines epigenome-wide differences in peripheral blood for PD patients. Our results point to possible sex-specific methylation changes in the HECA gene for PD but overall highlight that this disorder is not associated with extensive changes in DNA methylation in peripheral blood.
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Affiliation(s)
- Stella Iurato
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.
| | - Tania Carrillo-Roa
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Janine Arloth
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Laura Diener-Hölzl
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Jennifer Lange
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Bertram Müller-Myhsok
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth B. Binder
- 0000 0000 9497 5095grid.419548.5Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany ,0000 0001 0941 6502grid.189967.8Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA USA
| | - Angelika Erhardt
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.
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