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Caspi A, Shireby G, Mill J, Moffitt TE, Sugden K, Hannon E. Accelerated Pace of Aging in Schizophrenia: Five Case-Control Studies. Biol Psychiatry 2024; 95:1038-1047. [PMID: 37924924 PMCID: PMC11063120 DOI: 10.1016/j.biopsych.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/29/2023] [Accepted: 10/21/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Schizophrenia is associated with increased risk of developing multiple aging-related diseases, including metabolic, respiratory, and cardiovascular diseases, and Alzheimer's and related dementias, leading to the hypothesis that schizophrenia is accompanied by accelerated biological aging. This has been difficult to test because there is no widely accepted measure of biological aging. Epigenetic clocks are promising algorithms that are used to calculate biological age on the basis of information from combined cytosine-phosphate-guanine sites (CpGs) across the genome, but they have yielded inconsistent and often negative results about the association between schizophrenia and accelerated aging. Here, we tested the schizophrenia-aging hypothesis using a DNA methylation measure that is uniquely designed to predict an individual's rate of aging. METHODS We brought together 5 case-control datasets to calculate DunedinPACE (Pace of Aging Calculated from the Epigenome), a new measure trained on longitudinal data to detect differences between people in their pace of aging over time. Data were available from 1812 psychosis cases (schizophrenia or first-episode psychosis) and 1753 controls. Mean chronological age was 38.9 (SD = 13.6) years. RESULTS We observed consistent associations across datasets between schizophrenia and accelerated aging as measured by DunedinPACE. These associations were not attributable to tobacco smoking or clozapine medication. CONCLUSIONS Schizophrenia is accompanied by accelerated biological aging by midlife. This may explain the wide-ranging risk among people with schizophrenia for developing multiple different age-related physical diseases, including metabolic, respiratory, and cardiovascular diseases, and dementia. Measures of biological aging could prove valuable for assessing patients' risk for physical and cognitive decline and for evaluating intervention effectiveness.
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Affiliation(s)
- Avshalom Caspi
- Department of Psychology & Neuroscience, Duke University, Durham, North Carolina; Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, Psychology, & Neuroscience, King's College London, London, United Kingdom; PROMENTA, Department of Psychology, University of Oslo, Oslo, Norway.
| | - Gemma Shireby
- Centre of Longitudinal Studies, University College London, Exeter, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Terrie E Moffitt
- Department of Psychology & Neuroscience, Duke University, Durham, North Carolina; Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, Psychology, & Neuroscience, King's College London, London, United Kingdom; PROMENTA, Department of Psychology, University of Oslo, Oslo, Norway
| | - Karen Sugden
- Department of Psychology & Neuroscience, Duke University, Durham, North Carolina
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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Davyson E, Shen X, Huider F, Adams M, Borges K, McCartney D, Barker L, Van Dongen J, Boomsma D, Weihs A, Grabe H, Kühn L, Teumer A, Völzke H, Zhu T, Kaprio J, Ollikainen M, David FS, Meinert S, Stein F, Forstner AJ, Dannlowski U, Kircher T, Tapuc A, Czamara D, Binder EB, Brückl T, Kwong A, Yousefi P, Wong C, Arseneault L, Fisher HL, Mill J, Cox S, Redmond P, Russ TC, van den Oord E, Aberg KA, Penninx B, Marioni RE, Wray NR, McIntosh AM. Antidepressant Exposure and DNA Methylation: Insights from a Methylome-Wide Association Study. medRxiv 2024:2024.05.01.24306640. [PMID: 38746357 PMCID: PMC11092700 DOI: 10.1101/2024.05.01.24306640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Importance Understanding antidepressant mechanisms could help design more effective and tolerated treatments. Objective Identify DNA methylation (DNAm) changes associated with antidepressant exposure. Design Case-control methylome-wide association studies (MWAS) of antidepressant exposure were performed from blood samples collected between 2006-2011 in Generation Scotland (GS). The summary statistics were tested for enrichment in specific tissues, gene ontologies and an independent MWAS in the Netherlands Study of Depression and Anxiety (NESDA). A methylation profile score (MPS) was derived and tested for its association with antidepressant exposure in eight independent cohorts, alongside prospective data from GS. Setting Cohorts; GS, NESDA, FTC, SHIP-Trend, FOR2107, LBC1936, MARS-UniDep, ALSPAC, E-Risk, and NTR. Participants Participants with DNAm data and self-report/prescription derived antidepressant exposure. Main Outcomes and Measures Whole-blood DNAm levels were assayed by the EPIC/450K Illumina array (9 studies, N exposed = 661, N unexposed = 9,575) alongside MBD-Seq in NESDA (N exposed = 398, N unexposed = 414). Antidepressant exposure was measured by self- report and/or antidepressant prescriptions. Results The self-report MWAS (N = 16,536, N exposed = 1,508, mean age = 48, 59% female) and the prescription-derived MWAS (N = 7,951, N exposed = 861, mean age = 47, 59% female), found hypermethylation at seven and four DNAm sites (p < 9.42x10 -8 ), respectively. The top locus was cg26277237 ( KANK1, p self-report = 9.3x10 -13 , p prescription = 6.1x10 -3 ). The self-report MWAS found a differentially methylated region, mapping to DGUOK-AS1 ( p adj = 5.0x10 -3 ) alongside significant enrichment for genes expressed in the amygdala, the "synaptic vesicle membrane" gene ontology and the top 1% of CpGs from the NESDA MWAS (OR = 1.39, p < 0.042). The MPS was associated with antidepressant exposure in meta-analysed data from external cohorts (N studies = 9, N = 10,236, N exposed = 661, f3 = 0.196, p < 1x10 -4 ). Conclusions and Relevance Antidepressant exposure is associated with changes in DNAm across different cohorts. Further investigation into these changes could inform on new targets for antidepressant treatments. 3 Key Points Question: Is antidepressant exposure associated with differential whole blood DNA methylation?Findings: In this methylome-wide association study of 16,536 adults across Scotland, antidepressant exposure was significantly associated with hypermethylation at CpGs mapping to KANK1 and DGUOK-AS1. A methylation profile score trained on this sample was significantly associated with antidepressant exposure (pooled f3 [95%CI]=0.196 [0.105, 0.288], p < 1x10 -4 ) in a meta-analysis of external datasets. Meaning: Antidepressant exposure is associated with hypermethylation at KANK1 and DGUOK-AS1 , which have roles in mitochondrial metabolism and neurite outgrowth. If replicated in future studies, targeting these genes could inform the design of more effective and better tolerated treatments for depression.
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Clifton NE, Lin JQ, Holt CE, O'Donovan MC, Mill J. Enrichment of the Local Synaptic Translatome for Genetic Risk Associated With Schizophrenia and Autism Spectrum Disorder. Biol Psychiatry 2024; 95:888-895. [PMID: 38103876 DOI: 10.1016/j.biopsych.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Genes that encode synaptic proteins or messenger RNA targets of the RNA-binding protein FMRP (fragile X messenger ribonucleoprotein) have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants that confer risk for these disorders. FMRP binds many transcripts with synaptic functions and is thought to regulate their local translation, a process that enables rapid and compartmentalized protein synthesis required for development and plasticity. METHODS We used summary statistics from large-scale genome-wide association studies of schizophrenia (74,776 cases, 101,023 controls) and ASD (18,381 cases, 27,969 controls) to test the hypothesis that the subset of synaptic genes that encode localized transcripts is more strongly associated with each disorder than nonlocalized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets. RESULTS Schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Schizophrenia association was related to FMRP interactions with messenger RNAs in somata, but not in dendrites, while ASD association was related to FMRP binding in either compartment. CONCLUSIONS Our data suggest that synaptic transcripts capable of local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but they do not characterize the associations attributed to current sets of FMRP targets.
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Affiliation(s)
- Nicholas E Clifton
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
| | - Julie Qiaojin Lin
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, King's College London, London, United Kingdom
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Jonathan Mill
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Patel V, Mill J, Okonkwo OC, Salamat S, Li L, Raife T. Global Energy Metabolism Deficit in Alzheimer Disease Brain. J Prev Alzheimers Dis 2024; 11:171-178. [PMID: 38230730 DOI: 10.14283/jpad.2023.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
BACKGROUND The understanding of Alzheimer's disease (AD) has been dominated by the amyloid hypothesis. However, therapies targeting beta-amyloid have largely failed, generating interest in other potential pathogenic factors including energy metabolism. OBJECTIVES To interrogate canonical energy metabolism pathways from human prefrontal cortical tissue samples obtained from necropsy comparing AD and control. DESIGN, SETTING, AND PARTICIPANTS Postmortem pre-frontal cortical tissue from 10 subjects histologically diagnosed with AD and 10 control (CTRL) subjects was subjected to untargeted metabolomics to interrogate energy metabolism pathways. The samples were matched by age, sex, and post-mortem interval. Metabolite Measurements: Untargeted metabolomics analyses were via Metabolon®. RESULTS Glucose-derived energy metabolites in the glycolytic and pentose phosphate pathway and the ketone body β-hydroxybutyrate were uniformly decreased in AD brain vs. CTRL brain. CONCLUSION This pilot study aimed to identify energy metabolism abnormalities using untargeted brain metabolomics in two independent subject cohorts. Our study revealed a pattern of global energy deficit in AD brain, supporting a growing body of evidence of deficient energy metabolism in AD.
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Affiliation(s)
- V Patel
- Viharkumar Patel, University of California Davis Department of Pathology, 4400 V Street Suite 1114, Sacramento, CA 95817, USA, E-mail:
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Vellame DS, Shireby G, MacCalman A, Dempster EL, Burrage J, Gorrie-Stone T, Schalkwyk LS, Mill J, Hannon E. Uncertainty quantification of reference-based cellular deconvolution algorithms. Epigenetics 2023; 18:2137659. [PMID: 36539387 PMCID: PMC9980651 DOI: 10.1080/15592294.2022.2137659] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/12/2022] [Indexed: 12/24/2022] Open
Abstract
The majority of epigenetic epidemiology studies to date have generated genome-wide profiles from bulk tissues (e.g., whole blood) however these are vulnerable to confounding from variation in cellular composition. Proxies for cellular composition can be mathematically derived from the bulk tissue profiles using a deconvolution algorithm; however, there is no method to assess the validity of these estimates for a dataset where the true cellular proportions are unknown. In this study, we describe, validate and characterize a sample level accuracy metric for derived cellular heterogeneity variables. The CETYGO score captures the deviation between a sample's DNA methylation profile and its expected profile given the estimated cellular proportions and cell type reference profiles. We demonstrate that the CETYGO score consistently distinguishes inaccurate and incomplete deconvolutions when applied to reconstructed whole blood profiles. By applying our novel metric to >6,300 empirical whole blood profiles, we find that estimating accurate cellular composition is influenced by both technical and biological variation. In particular, we show that when using a common reference panel for whole blood, less accurate estimates are generated for females, neonates, older individuals and smokers. Our results highlight the utility of a metric to assess the accuracy of cellular deconvolution, and describe how it can enhance studies of DNA methylation that are reliant on statistical proxies for cellular heterogeneity. To facilitate incorporating our methodology into existing pipelines, we have made it freely available as an R package (https://github.com/ds420/CETYGO).
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Affiliation(s)
| | - Gemma Shireby
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Ailsa MacCalman
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Emma L Dempster
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Tyler Gorrie-Stone
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
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Lin S, Hannon E, Reppell M, Waring JF, Smaoui N, Pivorunas V, Guay H, Chanchlani N, Bewshea C, Bai BYH, Kennedy NA, Goodhand JR, Mill J, Ahmad T. Whole blood DNA methylation changes are associated with anti-TNF drug concentration in patients with Crohn's disease. J Crohns Colitis 2023:jjad133. [PMID: 37551994 DOI: 10.1093/ecco-jcc/jjad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND AND AIMS Anti-TNF treatment failure in patients with inflammatory bowel disease (IBD) is common and frequently related to low drug concentrations. In order to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy, we sought to define epigenetic biomarkers in whole blood at baseline associated with anti-TNF drug concentrations at week 14. METHODS DNA methylation from 1,104 whole blood samples from 385 patients in the Personalised Anti-TNF Therapy in Crohn's disease (PANTS) study were assessed using the Illumina EPIC Beadchip (v1.0) at baseline, weeks 14, 30 and 54. We compared DNA methylation profiles in anti-TNF-treated patients who experienced primary non-response at week 14 and if they were assessed at subsequent time points, were not in remission at week 30 or 54 (infliximab n = 99, adalimumab n = 94), with patients who responded at week 14 and when assessed at subsequent time points, were in remission at week 30 or 54 (infliximab n = 99, adalimumab n = 93). RESULTS Overall, between baseline and week 14, we observed 4,999 differentially methylated probes (DMPs) annotated to 2376 genes following anti-TNF treatment. Pathway analysis identified 108 significant gene ontology terms enriched in biological processes related to immune system processes and responses.Epigenome-wide association (EWAS) analysis identified 323 DMPs annotated to 210 genes at baseline associated with higher anti-TNF drug concentrations at week 14. Of these, 125 DMPs demonstrated shared associations with other common traits (proportion of shared CpGs compared to DMPs) including body mass index (23.2%), followed by CRP (11.5%), smoking (7.4%), alcohol consumption per day (7.1%) and IBD type (6.8%). EWAS of primary non-response to anti-TNF identified 20 DMPs that were associated with both anti-TNF drug concentration and primary non-response to anti-TNF with a strong correlation of the coefficients (Spearman's rho = -0.94, p < 0.001). CONCLUSION Baseline DNA methylation profiles may be used as a predictor for anti-TNF drug concentration at week 14 to identify patients who may benefit from dose optimisation at the outset of anti-TNF therapy.
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Affiliation(s)
- Simeng Lin
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | | | | | | | | | | | - Neil Chanchlani
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Claire Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Benjamin Y H Bai
- Genomics of Inflammation and Immunity Group, Wellcome Sanger Institute, Hinxton, UK
- Postgraduate School of Life Sciences, University of Cambridge, Cambridge, UK
| | - Nicholas A Kennedy
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - James R Goodhand
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Tariq Ahmad
- Gastroenterology, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
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Murthy M, Rizzu P, Heutink P, Mill J, Lashley T, Bettencourt C. Epigenetic Age Acceleration in Frontotemporal Lobar Degeneration: A Comprehensive Analysis in the Blood and Brain. Cells 2023; 12:1922. [PMID: 37508584 PMCID: PMC10378390 DOI: 10.3390/cells12141922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/22/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Frontotemporal lobar degeneration (FTLD) includes a heterogeneous group of disorders pathologically characterized by the degeneration of the frontal and temporal lobes. In addition to major genetic contributors of FTLD such as mutations in MAPT, GRN, and C9orf72, recent work has identified several epigenetic modifications including significant differential DNA methylation in DLX1, and OTUD4 loci. As aging remains one of the major risk factors for FTLD, we investigated the presence of accelerated epigenetic aging in FTLD compared to controls. We calculated epigenetic age in both peripheral blood and brain tissues of multiple FTLD subtypes using several DNA methylation clocks, i.e., DNAmClockMulti, DNAmClockHannum, DNAmClockCortical, GrimAge, and PhenoAge, and determined age acceleration and its association with different cellular proportions and clinical traits. Significant epigenetic age acceleration was observed in the peripheral blood of both frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP) patients compared to controls with DNAmClockHannum, even after accounting for confounding factors. A similar trend was observed with both DNAmClockMulti and DNAmClockCortical in post-mortem frontal cortex tissue of PSP patients and in FTLD cases harboring GRN mutations. Our findings support that increased epigenetic age acceleration in the peripheral blood could be an indicator for PSP and to a smaller extent, FTD.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK (T.L.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Alector, Inc., South San Francisco, CA 94080, USA
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 5DW, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK (T.L.)
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK (T.L.)
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 1PJ, UK
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Fodder K, Murthy M, Rizzu P, Toomey CE, Hasan R, Humphrey J, Raj T, Lunnon K, Mill J, Heutink P, Lashley T, Bettencourt C. Brain DNA methylomic analysis of frontotemporal lobar degeneration reveals OTUD4 in shared dysregulated signatures across pathological subtypes. Acta Neuropathol 2023:10.1007/s00401-023-02583-z. [PMID: 37149835 DOI: 10.1007/s00401-023-02583-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/08/2023]
Abstract
Frontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, including frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP). Among the major FTLD pathological subgroups, FTLD with TDP-43 positive inclusions (FTLD-TDP) and FTLD with tau-positive inclusions (FTLD-tau) are the most common, representing about 90% of the cases. Although alterations in DNA methylation have been consistently associated with neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease, little is known for FTLD and its heterogeneous subgroups and subtypes. The main goal of this study was to investigate DNA methylation variation in FTLD-TDP and FTLD-tau. We used frontal cortex genome-wide DNA methylation profiles from three FTLD cohorts (142 FTLD cases and 92 controls), generated using the Illumina 450K or EPIC microarrays. We performed epigenome-wide association studies (EWAS) for each cohort followed by meta-analysis to identify shared differentially methylated loci across FTLD subgroups/subtypes. In addition, we used weighted gene correlation network analysis to identify co-methylation signatures associated with FTLD and other disease-related traits. Wherever possible, we also incorporated relevant gene/protein expression data. After accounting for a conservative Bonferroni multiple testing correction, the EWAS meta-analysis revealed two differentially methylated loci in FTLD, one annotated to OTUD4 (5'UTR-shore) and the other to NFATC1 (gene body-island). Of these loci, OTUD4 showed consistent upregulation of mRNA and protein expression in FTLD. In addition, in the three independent co-methylation networks, OTUD4-containing modules were enriched for EWAS meta-analysis top loci and were strongly associated with the FTLD status. These co-methylation modules were enriched for genes implicated in the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling. Altogether, our findings identified novel FTLD-associated loci, and support a role for DNA methylation as a mechanism involved in the dysregulation of biological processes relevant to FTLD, highlighting novel potential avenues for therapeutic development.
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Affiliation(s)
- Katherine Fodder
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Christina E Toomey
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- The Francis Crick Institute, London, UK
| | - Rahat Hasan
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Towfique Raj
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Alector, Inc., South San Francisco, CA, USA
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
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11
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Alameda L, Liu Z, Sham PC, Aas M, Trotta G, Rodriguez V, Di Forti M, Stilo SA, Kandaswamy R, Arango C, Arrojo M, Bernardo M, Bobes J, de Haan L, Del-Ben CM, Gayer-Anderson C, Sideli L, Jones PB, Jongsma HE, Kirkbride JB, La Cascia C, Lasalvia A, Tosato S, Llorca PM, Menezes PR, van Os J, Quattrone D, Rutten BP, Santos JL, Sanjuán J, Selten JP, Szöke A, Tarricone I, Tortelli A, Velthorst E, Morgan C, Dempster E, Hannon E, Burrage J, Dwir D, Arumuham A, Mill J, Murray RM, Wong CCY. Exploring the mediation of DNA methylation across the epigenome between childhood adversity and First Episode of Psychosis-findings from the EU-GEI study. Mol Psychiatry 2023; 28:2095-2106. [PMID: 37062770 DOI: 10.1038/s41380-023-02044-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/04/2023] [Accepted: 03/20/2023] [Indexed: 04/18/2023]
Abstract
ABTRACT Studies conducted in psychotic disorders have shown that DNA-methylation (DNAm) is sensitive to the impact of Childhood Adversity (CA). However, whether it mediates the association between CA and psychosis is yet to be explored. Epigenome wide association studies (EWAS) using the Illumina Infinium-Methylation EPIC array in peripheral blood tissue from 366 First-episode of psychosis and 517 healthy controls was performed. Adversity scores were created for abuse, neglect and composite adversity with the Childhood Trauma Questionnaire (CTQ). Regressions examining (I) CTQ scores with psychosis; (II) with DNAm EWAS level and (III) between DNAm and caseness, adjusted for a variety of confounders were conducted. Divide-Aggregate Composite-null Test for the composite null-hypothesis of no mediation effect was conducted. Enrichment analyses were conducted with missMethyl package and the KEGG database. Our results show that CA was associated with psychosis (Composite: OR = 1.68; p = <0.001; abuse: OR = 2.16; p < 0.001; neglect: OR = 2.27; p = <0.001). None of the CpG sites significantly mediated the adversity-psychosis association after Bonferroni correction (p < 8.1 × 10-8). However, 28, 34 and 29 differentially methylated probes associated with 21, 27, 20 genes passed a less stringent discovery threshold (p < 5 × 10-5) for composite, abuse and neglect respectively, with a lack of overlap between abuse and neglect. These included genes previously associated to psychosis in EWAS studies, such as PANK1, SPEG TBKBP1, TSNARE1 or H2R. Downstream gene ontology analyses did not reveal any biological pathways that survived false discovery rate correction. Although at a non-significant level, DNAm changes in genes previously associated with schizophrenia in EWAS studies may mediate the CA-psychosis association. These results and associated involved processes such as mitochondrial or histaminergic disfunction, immunity or neural signalling requires replication in well powered samples. The lack of overlap between mediating genes associated with abuse and neglect suggests differential biological trajectories linking CA subtypes and psychosis.
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Affiliation(s)
- Luis Alameda
- Service of General Psychiatry, Treatment and Early Intervention in Psychosis Program, Lausanne University Hospital (CHUV), Lausanne, Switzerland.
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK.
- Instituto de Investigación Sanitaria de Sevilla, IbiS, Hospital Universitario Virgen del Rocío, Department of Psychiatry, Universidad de Sevilla, Seville, Spain.
| | - Zhonghua Liu
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Pak C Sham
- Department of Psychiatry, State Key Laboratory of Brain and Cognitive Sciences, and Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Monica Aas
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Giulia Trotta
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Victoria Rodriguez
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
| | - Marta Di Forti
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Simona A Stilo
- Department of Mental Health and Addiction Services, ASP Crotone, Crotone, Italy
| | - Radhika Kandaswamy
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid, Spain
| | - Manuel Arrojo
- Department of Psychiatry, Psychiatric Genetic Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago de Compostela, Santiago, Spain
| | - Miguel Bernardo
- Barcelona Clinic Schizophrenia Unit, Neuroscience Institute, Hospital Clinic of Barcelona, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, Biomedical Research Networking Centre in Mental Health (CIBERSAM), Barcelona, Spain
| | - Julio Bobes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Department of Medicine, Psychiatry Area, School of Medicine, Universidad de Oviedo, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Oviedo, Spain
| | - Lieuwe de Haan
- Department of Psychiatry, Early Psychosis Section, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Cristina Marta Del-Ben
- Neuroscience and Behaviour Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Lucia Sideli
- LUMSA University, Department of Human Science and Department of Psychosis Studies, KCL, Rome, Italy
| | - Peter B Jones
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- CAMEO Early Intervention Service, Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK
| | - Hannah E Jongsma
- Psylife Group, Division of Psychiatry, University College London, London, UK
| | - James B Kirkbride
- Psylife Group, Division of Psychiatry, University College London, London, UK
| | - Caterina La Cascia
- Section of Psychiatry, Department of Biomedicine, Neuroscience and advanced Diagnostic (BiND), University of Palermo, Palermo, Italy
| | - Antonio Lasalvia
- Section of Psychiatry, Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Sarah Tosato
- Section of Psychiatry, Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | | | - Paulo Rossi Menezes
- Department of Preventive Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Jim van Os
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, South Limburg Mental Health Research and Teaching Network, Maastricht University Medical Centre, Maastricht, The Netherlands
- Department Psychiatry, Brain Centre Rudolf Magnus, Utrecht University Medical Centre, Utrecht, The Netherlands
| | - Diego Quattrone
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Bart P Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, South Limburg Mental Health Research and Teaching Network, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Jose Luis Santos
- Department of Psychiatry, Servicio de Psiquiatría Hos"ital "Virgen de"a Luz", C/Hermandad de Donantes de Sangre, 16002, Cuenca, Spain
| | - Julio Sanjuán
- Department of Psychiatry, School of Medicine, Universidad de Valencia, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), C/Avda. Blasco Ibáñez 15, 46010, Valencia, Spain
| | - Jean-Paul Selten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, South Limburg Mental Health Research and Teaching Network, Maastricht University Medical Centre, Maastricht, The Netherlands
- Rivierduinen Institute for Mental Health Care, Leiden, The Netherlands
| | - Andrei Szöke
- University of Paris Est Creteil, INSERM, IMRB, AP-HP, Hôpitaux Universitaires, H. Mondor, DMU IMPACT, Creteil, France
| | - Ilaria Tarricone
- Bologna Transcultural Psychosomatic Team (BoTPT), Department of Medical and Surgical Science, Alma Mater Studiorum Università di Bologna, Bologna, Italy
| | | | - Eva Velthorst
- GGZ (Mental Health Services) Noord Holland Noord, Heerhugowaard, the Netherlands
| | - Craig Morgan
- ESRC Centre for Society and Mental Health, King's College London, London, UK
| | - Emma Dempster
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Eilis Hannon
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Joe Burrage
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Daniella Dwir
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Atheeshaan Arumuham
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
- Psychiatric Imaging Group, MRC London Institute of Medical Sciences, London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Jonathan Mill
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Robin M Murray
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
| | - Chloe C Y Wong
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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Doherty T, Dempster E, Hannon E, Mill J, Poulton R, Corcoran D, Sugden K, Williams B, Caspi A, Moffitt TE, Delany SJ, Murphy TM. A comparison of feature selection methodologies and learning algorithms in the development of a DNA methylation-based telomere length estimator. BMC Bioinformatics 2023; 24:178. [PMID: 37127563 PMCID: PMC10152624 DOI: 10.1186/s12859-023-05282-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND The field of epigenomics holds great promise in understanding and treating disease with advances in machine learning (ML) and artificial intelligence being vitally important in this pursuit. Increasingly, research now utilises DNA methylation measures at cytosine-guanine dinucleotides (CpG) to detect disease and estimate biological traits such as aging. Given the challenge of high dimensionality of DNA methylation data, feature-selection techniques are commonly employed to reduce dimensionality and identify the most important subset of features. In this study, our aim was to test and compare a range of feature-selection methods and ML algorithms in the development of a novel DNA methylation-based telomere length (TL) estimator. We utilised both nested cross-validation and two independent test sets for the comparisons. RESULTS We found that principal component analysis in advance of elastic net regression led to the overall best performing estimator when evaluated using a nested cross-validation analysis and two independent test cohorts. This approach achieved a correlation between estimated and actual TL of 0.295 (83.4% CI [0.201, 0.384]) on the EXTEND test data set. Contrastingly, the baseline model of elastic net regression with no prior feature reduction stage performed less well in general-suggesting a prior feature-selection stage may have important utility. A previously developed TL estimator, DNAmTL, achieved a correlation of 0.216 (83.4% CI [0.118, 0.310]) on the EXTEND data. Additionally, we observed that different DNA methylation-based TL estimators, which have few common CpGs, are associated with many of the same biological entities. CONCLUSIONS The variance in performance across tested approaches shows that estimators are sensitive to data set heterogeneity and the development of an optimal DNA methylation-based estimator should benefit from the robust methodological approach used in this study. Moreover, our methodology which utilises a range of feature-selection approaches and ML algorithms could be applied to other biological markers and disease phenotypes, to examine their relationship with DNA methylation and predictive value.
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Affiliation(s)
- Trevor Doherty
- School of Biological, Health and Sports Sciences, Technological University Dublin, Dublin, Ireland.
- SFI Centre for Research Training in Machine Learning, Technological University Dublin, Dublin, Ireland.
| | - Emma Dempster
- 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
| | - Richie Poulton
- Department of Psychology, University of Otago, Dunedin, 9016, New Zealand
| | - David Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Ben Williams
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Avshalom Caspi
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Terrie E Moffitt
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Sarah Jane Delany
- School of Computer Science, Technological University Dublin, Dublin, Ireland
| | - Therese M Murphy
- School of Biological, Health and Sports Sciences, Technological University Dublin, Dublin, Ireland
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Nho K, Risacher SL, Apostolova L, Bice PJ, Brosch J, Deardorff R, Faber K, Farlow MR, Foroud T, Gao S, Rosewood T, Kim JP, Nudelman K, Yu M, Aisen P, Sperling R, Hooli B, Shcherbinin S, Svaldi D, Jack CR, Jagust WJ, Landau S, Vasanthakumar A, Waring JF, Doré V, Laws SM, Masters CL, Porter T, Rowe CC, Villemagne VL, Dumitrescu L, Hohman TJ, Libby JB, Mormino E, Buckley RF, Johnson K, Yang HS, Petersen RC, Ramanan VK, Vemuri P, Cohen AD, Fan KH, Kamboh MI, Lopez OL, Bennett DA, Ali M, Benzinger T, Cruchaga C, Hobbs D, De Jager PL, Fujita M, Jadhav V, Lamb BT, Tsai AP, Castanho I, Mill J, Weiner MW, Saykin AJ. Novel CYP1B1-RMDN2 Alzheimer's disease locus identified by genome-wide association analysis of cerebral tau deposition on PET. medRxiv 2023:2023.02.27.23286048. [PMID: 36993271 PMCID: PMC10055458 DOI: 10.1101/2023.02.27.23286048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Determining the genetic architecture of Alzheimer's disease (AD) pathologies can enhance mechanistic understanding and inform precision medicine strategies. Here, we performed a genome-wide association study of cortical tau quantified by positron emission tomography in 3,136 participants from 12 independent studies. The CYP1B1-RMDN2 locus was associated with tau deposition. The most significant signal was at rs2113389, which explained 4.3% of the variation in cortical tau, while APOE4 rs429358 accounted for 3.6%. rs2113389 was associated with higher tau and faster cognitive decline. Additive effects, but no interactions, were observed between rs2113389 and diagnosis, APOE4 , and Aβ positivity. CYP1B1 expression was upregulated in AD. rs2113389 was associated with higher CYP1B1 expression and methylation levels. Mouse model studies provided additional functional evidence for a relationship between CYP1B1 and tau deposition but not Aβ. These results may provide insight into the genetic basis of cerebral tau and novel pathways for therapeutic development in AD.
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14
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Pishva E, van den Hove DLA, Laroche V, Lvovs A, Roy A, Ortega G, Burrage J, Veidebaum T, Kanarik M, Mill J, Lesch KP, Harro J. Genome-wide DNA methylation analysis of aggressive behaviour: a longitudinal population-based study. J Child Psychol Psychiatry 2023. [PMID: 36929374 DOI: 10.1111/jcpp.13782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/25/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Human aggression is influenced by an interplay between genetic predisposition and experience across the life span. This interaction is thought to occur through epigenetic mechanisms, inducing differential gene expression, thereby moderating neuronal cell and circuit function, and thus shaping aggressive behaviour. METHODS Genome-wide DNA methylation (DNAm) levels were measured in peripheral blood obtained from 95 individuals participating in the Estonian Children Personality Behaviours and Health Study (ECPBHS) at 15 and 25 years of age. We examined the association between aggressive behaviour, as measured by Life History of Aggression (LHA) total score and DNAm levels both assessed at age 25. We further examined the pleiotropic effect of genetic variants regulating LHA-associated differentially methylated positions (DMPs) and multiple traits related to aggressive behaviours. Lastly, we tested whether the DNA methylomic loci identified in association with LHA at age 25 were also present at age 15. RESULTS We found one differentially methylated position (DMP) (cg17815886; p = 1.12 × 10-8 ) and five differentially methylated regions (DMRs) associated with LHA after multiple testing adjustments. The DMP annotated to the PDLIM5 gene, and DMRs resided in the vicinity of four protein-encoding genes (TRIM10, GTF2H4, SLC45A4, B3GALT4) and a long intergenic non-coding RNA (LINC02068). We observed evidence for the colocalization of genetic variants associated with top DMPs and general cognitive function, educational attainment and cholesterol levels. Notably, a subset of the DMPs associated with LHA at age 25 also displayed altered DNAm patterns at age 15 with high accuracy in predicting aggression. CONCLUSIONS Our findings highlight the potential role of DNAm in the development of aggressive behaviours. We observed pleiotropic genetic variants associated with identified DMPs, and various traits previously established to be relevant in shaping aggression in humans. The concordance of DNAm signatures in adolescents and young adults may have predictive value for inappropriate and maladaptive aggression later in life.
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Affiliation(s)
- Ehsan Pishva
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands.,College of Medicine and Health, University of Exeter Medical School, Exeter, UK
| | - Daniel L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands.,Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany
| | - Valentin Laroche
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Aneth Lvovs
- School of Natural Sciences and Health, Tallinn University, Tallinn, Estonia.,Chair of Neuropsychopharmacology, Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Arunima Roy
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany
| | - Gabriela Ortega
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany
| | - Joe Burrage
- College of Medicine and Health, University of Exeter Medical School, Exeter, UK
| | | | - Margus Kanarik
- Chair of Neuropsychopharmacology, Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Jonathan Mill
- College of Medicine and Health, University of Exeter Medical School, Exeter, UK
| | - Klaus-Peter Lesch
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands.,Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany
| | - Jaanus Harro
- Chair of Neuropsychopharmacology, Institute of Chemistry, University of Tartu, Tartu, Estonia
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15
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Nabais MF, Gadd DA, Hannon E, Mill J, McRae AF, Wray NR. An overview of DNA methylation-derived trait score methods and applications. Genome Biol 2023; 24:28. [PMID: 36797751 PMCID: PMC9936670 DOI: 10.1186/s13059-023-02855-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 01/17/2023] [Indexed: 02/18/2023] Open
Abstract
Microarray technology has been used to measure genome-wide DNA methylation in thousands of individuals. These studies typically test the associations between individual DNA methylation sites ("probes") and complex traits or diseases. The results can be used to generate methylation profile scores (MPS) to predict outcomes in independent data sets. Although there are many parallels between MPS and polygenic (risk) scores (PGS), there are key differences. Here, we review motivations, methods, and applications of DNA methylation-based trait prediction, with a focus on common diseases. We contrast MPS with PGS, highlighting where assumptions made in genetic modeling may not hold in epigenetic data.
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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
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - 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
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - 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.
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16
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Murthy M, Shireby G, Miki Y, Viré E, Lashley T, Warner TT, Mill J, Bettencourt C. Epigenetic age acceleration is associated with oligodendrocyte proportions in MSA and control brain tissue. Neuropathol Appl Neurobiol 2023; 49:e12872. [PMID: 36542090 PMCID: PMC10107510 DOI: 10.1111/nan.12872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/15/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
AIMS Epigenetic clocks are widely applied as surrogates for biological age in different tissues and/or diseases, including several neurodegenerative diseases. Despite white matter (WM) changes often being observed in neurodegenerative diseases, no study has investigated epigenetic ageing in white matter. METHODS We analysed the performances of two DNA methylation-based clocks, DNAmClockMulti and DNAmClockCortical , in post-mortem WM tissue from multiple subcortical regions and the cerebellum, and in oligodendrocyte-enriched nuclei. We also examined epigenetic ageing in control and multiple system atrophy (MSA) (WM and mixed WM and grey matter), as MSA is a neurodegenerative disease comprising pronounced WM changes and α-synuclein aggregates in oligodendrocytes. RESULTS Estimated DNA methylation (DNAm) ages showed strong correlations with chronological ages, even in WM (e.g., DNAmClockCortical , r = [0.80-0.97], p < 0.05). However, performances and DNAm age estimates differed between clocks and brain regions. DNAmClockMulti significantly underestimated ages in all cohorts except in the MSA prefrontal cortex mixed tissue, whereas DNAmClockCortical tended towards age overestimations. Pronounced age overestimations in the oligodendrocyte-enriched cohorts (e.g., oligodendrocyte-enriched nuclei, p = 6.1 × 10-5 ) suggested that this cell type ages faster. Indeed, significant positive correlations were observed between estimated oligodendrocyte proportions and DNAm age acceleration estimated by DNAmClockCortical (r > 0.31, p < 0.05), and similar trends were obtained with DNAmClockMulti . Although increased age acceleration was observed in MSA compared with controls, no significant differences were detected upon adjustment for possible confounders (e.g., cell-type proportions). CONCLUSIONS Our findings show that oligodendrocyte proportions positively influence epigenetic age acceleration across brain regions and highlight the need to further investigate this in ageing and neurodegeneration.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
| | - Gemma Shireby
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Yasuo Miki
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neuropathology, Institute of Brain ScienceHirosaki University Graduate School of MedicineHirosakiJapan
| | - Emmanuelle Viré
- UCL Institute of Prion Diseases, MRC Prion Unit at UCLUniversity College LondonLondonUK
| | - Tammaryn Lashley
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neurodegenerative Disease, Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of Neurology1 Wakefield StreetLondonWC1N 1PJUK
| | - Thomas T. Warner
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
- Reta Lila Weston InstituteUCL Queen Square Institute of NeurologyLondonUK
| | - Jonathan Mill
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Conceição Bettencourt
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neurodegenerative Disease, Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of Neurology1 Wakefield StreetLondonWC1N 1PJUK
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17
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Devall M, Soanes DM, Smith AR, Dempster EL, Smith RG, Burrage J, Iatrou A, Hannon E, Troakes C, Moore K, O'Neill P, Al-Sarraj S, Schalkwyk L, Mill J, Weedon M, Lunnon K. Genome-wide characterization of mitochondrial DNA methylation in human brain. Front Endocrinol (Lausanne) 2023; 13:1059120. [PMID: 36726473 PMCID: PMC9885148 DOI: 10.3389/fendo.2022.1059120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/05/2022] [Indexed: 01/17/2023] Open
Abstract
Background There is growing interest in the role of DNA methylation in regulating the transcription of mitochondrial genes, particularly in brain disorders characterized by mitochondrial dysfunction. Here, we present a novel approach to interrogate the mitochondrial DNA methylome at single base resolution using targeted bisulfite sequencing. We applied this method to investigate mitochondrial DNA methylation patterns in post-mortem superior temporal gyrus and cerebellum brain tissue from seven human donors. Results We show that mitochondrial DNA methylation patterns are relatively low but conserved, with peaks in DNA methylation at several sites, such as within the D-LOOP and the genes MT-ND2, MT-ATP6, MT-ND4, MT-ND5 and MT-ND6, predominantly in a non-CpG context. The elevated DNA methylation we observe in the D-LOOP we validate using pyrosequencing. We identify loci that show differential DNA methylation patterns associated with age, sex and brain region. Finally, we replicate previously reported differentially methylated regions between brain regions from a methylated DNA immunoprecipitation sequencing study. Conclusions We have annotated patterns of DNA methylation at single base resolution across the mitochondrial genome in human brain samples. Looking to the future this approach could be utilized to investigate the role of mitochondrial epigenetic mechanisms in disorders that display mitochondrial dysfunction.
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Affiliation(s)
- Matthew Devall
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Darren M Soanes
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Adam R Smith
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Emma L Dempster
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Rebecca G Smith
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Joe Burrage
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Artemis Iatrou
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Eilis Hannon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Claire Troakes
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Karen Moore
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Paul O'Neill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Safa Al-Sarraj
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Leonard Schalkwyk
- School of Biological Sciences, University of Essex, Essex, United Kingdom
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Michael Weedon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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18
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Imm JL, Harvey J, Creese B, Chouliaras L, Dempster E, Ballard CG, O'Brien JT, Aarsland D, Mill J, Pishva E, Lunnon K. A Role for Epigenetic Mechanisms in the Lewy Body Dementias. Alzheimers Dement 2022. [DOI: 10.1002/alz.064536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Dag Aarsland
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London London United Kingdom
| | | | - Ehsan Pishva
- University of Exeter Exeter United Kingdom
- Maastricht University Maastricht Netherlands
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19
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Wheildon G, Smith AR, Soanes D, Smith RG, Moore K, O'Neill P, Morgan K, Thomas AJ, Francis PT, Love S, Mill J, Pishva E, Lunnon K. Targeted bisulfite sequencing analysis of candidate genes associated with Alzheimer’s disease. Alzheimers Dement 2022. [DOI: 10.1002/alz.067703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | | | | | | | - Kevin Morgan
- University of Nottingham Nottingham United Kingdom
| | - Alan J Thomas
- Translational and Clinical Research Institute, Newcastle University Newcastle upon Tyne United Kingdom
| | | | - Seth Love
- University of Bristol Bristol United Kingdom
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20
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Weymouth LS, Kouhsar MP, Creese B, Bergh S, Wedatilake Y, Torkamani A, Smith AR, Selbaek G, Sweet R, Ballard CG, Mill J, Kofler J, Pishva E, Lunnon K. An Epigenome‐wide association study of psychosis in Alzheimer's disease dorsolateral prefrontal cortex. Alzheimers Dement 2022. [DOI: 10.1002/alz.065733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | - Sverre Bergh
- Norwegian National Advisory Unit on Aging and Health, Vestfold Hospital Trust Tønsberg Norway
- Centre for Old Age Psychiatric Research, Innlandet Hospital Trust Ottestad Norway
| | - Yehani Wedatilake
- Norwegian National Advisory Unit on Aging and Health, Vestfold Hospital Trust Tønsberg Norway
| | - Ali Torkamani
- Scripps Research Translational Institute La Jolla CA USA
| | | | - Geir Selbaek
- Norwegian National Advisory Unit on Aging and Health, Vestfold Hospital Trust Tønsberg Norway
- Centre for Old Age Psychiatric Research, Innlandet Hospital Trust Ottestad Norway
- Faculty of Medicine, University of Oslo Oslo Norway
- Oslo University Hospital Oslo Norway
| | | | | | | | - Julia Kofler
- University of Pittsburgh School of Medicine Pittsburgh PA USA
| | - Ehsan Pishva
- University of Exeter Exeter United Kingdom
- Maastricht University Maastricht Netherlands
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21
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Stevenson AJ, McCartney DL, Gadd DA, Shireby G, Hillary RF, King D, Tzioras M, Wrobel N, McCafferty S, Murphy L, McColl BW, Redmond P, Taylor AM, Harris SE, Russ TC, McIntosh AM, Mill J, Smith C, Deary IJ, Cox SR, Marioni RE, Spires‐Jones TL. A comparison of blood and brain-derived ageing and inflammation-related DNA methylation signatures and their association with microglial burdens. Eur J Neurosci 2022; 56:5637-5649. [PMID: 35362642 PMCID: PMC9525452 DOI: 10.1111/ejn.15661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/18/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022]
Abstract
Inflammation and ageing-related DNA methylation patterns in the blood have been linked to a variety of morbidities, including cognitive decline and neurodegenerative disease. However, it is unclear how these blood-based patterns relate to patterns within the brain and how each associates with central cellular profiles. In this study, we profiled DNA methylation in both the blood and in five post mortem brain regions (BA17, BA20/21, BA24, BA46 and hippocampus) in 14 individuals from the Lothian Birth Cohort 1936. Microglial burdens were additionally quantified in the same brain regions. DNA methylation signatures of five epigenetic ageing biomarkers ('epigenetic clocks'), and two inflammatory biomarkers (methylation proxies for C-reactive protein and interleukin-6) were compared across tissues and regions. Divergent associations between the inflammation and ageing signatures in the blood and brain were identified, depending on region assessed. Four out of the five assessed epigenetic age acceleration measures were found to be highest in the hippocampus (β range = 0.83-1.14, p ≤ 0.02). The inflammation-related DNA methylation signatures showed no clear variation across brain regions. Reactive microglial burdens were found to be highest in the hippocampus (β = 1.32, p = 5 × 10-4 ); however, the only association identified between the blood- and brain-based methylation signatures and microglia was a significant positive association with acceleration of one epigenetic clock (termed DNAm PhenoAge) averaged over all five brain regions (β = 0.40, p = 0.002). This work highlights a potential vulnerability of the hippocampus to epigenetic ageing and provides preliminary evidence of a relationship between DNA methylation signatures in the brain and differences in microglial burdens.
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Affiliation(s)
- Anna J. Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Gemma Shireby
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Declan King
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| | - Makis Tzioras
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| | - Nicola Wrobel
- Edinburgh Clinical Research FacilityWestern General HospitalEdinburghUK
| | - Sarah McCafferty
- Edinburgh Clinical Research FacilityWestern General HospitalEdinburghUK
| | - Lee Murphy
- Edinburgh Clinical Research FacilityWestern General HospitalEdinburghUK
| | - Barry W. McColl
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
| | - Paul Redmond
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
| | | | - Sarah E. Harris
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Tom C. Russ
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Alzheimer Scotland Dementia Research Centre, 7 George SquareUniversity of EdinburghEdinburghUK
- Division of PsychiatryUniversity of Edinburgh, Royal Edinburgh HospitalEdinburghUK
| | - Andrew M. McIntosh
- Division of PsychiatryUniversity of Edinburgh, Royal Edinburgh HospitalEdinburghUK
| | - Jonathan Mill
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Colin Smith
- Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Ian J. Deary
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Simon R. Cox
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
- Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
- Lothian Birth CohortsUniversity of EdinburghEdinburghUK
| | - Tara L. Spires‐Jones
- Centre for Discovery Brain SciencesUniversity of EdinburghEdinburghUK
- UK Dementia Research InstituteUniversity of EdinburghEdinburghUK
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22
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Tielbeek JJ, Uffelmann E, Williams BS, Colodro-Conde L, Gagnon É, Mallard TT, Levitt BE, Jansen PR, Johansson A, Sallis HM, Pistis G, Saunders GRB, Allegrini AG, Rimfeld K, Konte B, Klein M, Hartmann AM, Salvatore JE, Nolte IM, Demontis D, Malmberg ALK, Burt SA, Savage JE, Sugden K, Poulton R, Harris KM, Vrieze S, McGue M, Iacono WG, Mota NR, Mill J, Viana JF, Mitchell BL, Morosoli JJ, Andlauer TFM, Ouellet-Morin I, Tremblay RE, Côté SM, Gouin JP, Brendgen MR, Dionne G, Vitaro F, Lupton MK, Martin NG, Castelao E, Räikkönen K, Eriksson JG, Lahti J, Hartman CA, Oldehinkel AJ, Snieder H, Liu H, Preisig M, Whipp A, Vuoksimaa E, Lu Y, Jern P, Rujescu D, Giegling I, Palviainen T, Kaprio J, Harden KP, Munafò MR, Morneau-Vaillancourt G, Plomin R, Viding E, Boutwell BB, Aliev F, Dick DM, Popma A, Faraone SV, Børglum AD, Medland SE, Franke B, Boivin M, Pingault JB, Glennon JC, Barnes JC, Fisher SE, Moffitt TE, Caspi A, Polderman TJC, Posthuma D. Uncovering the genetic architecture of broad antisocial behavior through a genome-wide association study meta-analysis. Mol Psychiatry 2022; 27:4453-4463. [PMID: 36284158 PMCID: PMC10902879 DOI: 10.1038/s41380-022-01793-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/03/2022] [Accepted: 09/09/2022] [Indexed: 01/14/2023]
Abstract
Despite the substantial heritability of antisocial behavior (ASB), specific genetic variants robustly associated with the trait have not been identified. The present study by the Broad Antisocial Behavior Consortium (BroadABC) meta-analyzed data from 28 discovery samples (N = 85,359) and five independent replication samples (N = 8058) with genotypic data and broad measures of ASB. We identified the first significant genetic associations with broad ASB, involving common intronic variants in the forkhead box protein P2 (FOXP2) gene (lead SNP rs12536335, p = 6.32 × 10-10). Furthermore, we observed intronic variation in Foxp2 and one of its targets (Cntnap2) distinguishing a mouse model of pathological aggression (BALB/cJ strain) from controls (BALB/cByJ strain). Polygenic risk score (PRS) analyses in independent samples revealed that the genetic risk for ASB was associated with several antisocial outcomes across the lifespan, including diagnosis of conduct disorder, official criminal convictions, and trajectories of antisocial development. We found substantial genetic correlations of ASB with mental health (depression rg = 0.63, insomnia rg = 0.47), physical health (overweight rg = 0.19, waist-to-hip ratio rg = 0.32), smoking (rg = 0.54), cognitive ability (intelligence rg = -0.40), educational attainment (years of schooling rg = -0.46) and reproductive traits (age at first birth rg = -0.58, father's age at death rg = -0.54). Our findings provide a starting point toward identifying critical biosocial risk mechanisms for the development of ASB.
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Affiliation(s)
- Jorim J Tielbeek
- Center for Neurogenomics and Cognitive Research, Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands.
| | - Emil Uffelmann
- Center for Neurogenomics and Cognitive Research, Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Benjamin S Williams
- Department of Psychology and Neuroscience, Trinity College of Arts and Sciences, Duke University, 2020 West Main Street, Durham, NC, 27705, USA
| | - Lucía Colodro-Conde
- Psychiatric Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Éloi Gagnon
- Research Unit on Children's Psychosocial Maladjustment, École de psychologie, Université Laval, 2523 Allée des Bibliothèques, Quebec City, QC, G1V 0A6, Canada
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Brandt E Levitt
- Carolina Population Center, University of North Carolina at Chapel Hill, 123 Franklin St, Chapel Hill, NC, 27516, USA
| | - Philip R Jansen
- Center for Neurogenomics and Cognitive Research, Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Ada Johansson
- Department of Psychology, Faculty of Arts, Psychology, and Theology, Åbo Akademi University, Tuomiokirkontori 3, FI-20500, Turku, Finland
| | - Hannah M Sallis
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Road, Bristol, BS8 2BN, UK
| | - Giorgio Pistis
- Center for Psychiatric Epidemiology and Psychopathology, Department of Psychiatry, Lausanne University Hospital and University of Lausanne, Route de Cery 25, CH-1008, Prilly, Vaud, Switzerland
| | - Gretchen R B Saunders
- Department of Psychology, University of Minnesota, 75 E. River Road, Minneapolis, MN, 55455, USA
| | - Andrea G Allegrini
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, DeCrespigny Park, Denmark Hill, London, SE5 8AF, UK
| | - Kaili Rimfeld
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, DeCrespigny Park, Denmark Hill, London, SE5 8AF, UK
| | - Bettina Konte
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Marieke Klein
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Groteplein 10, 6500 HB, Nijmegen, The Netherlands
| | - Annette M Hartmann
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Jessica E Salvatore
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Ditte Demontis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000, Aarhus C, Aarhus, Denmark
| | - Anni L K Malmberg
- Department of Psychology and Logopedics, University of Helsinki, Haartmaninkatu 3, 00014, Helsinki, Finland
| | | | - Jeanne E Savage
- Center for Neurogenomics and Cognitive Research, Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Karen Sugden
- Department of Psychology and Neuroscience, Trinity College of Arts and Sciences, Duke University, 2020 West Main Street, Durham, NC, 27705, USA
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, Dunedin, New Zealand
| | - Kathleen Mullan Harris
- Department of Sociology, University of North Carolina at Chapel Hill, CB# 3210, 201 Hamilton Hall, Chapel Hill, NC, 27599, USA
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, 75 E. River Road, Minneapolis, MN, 55455, USA
| | - Matt McGue
- Department of Psychology, University of Minnesota, 75 E. River Road, Minneapolis, MN, 55455, USA
| | - William G Iacono
- Department of Psychology, University of Minnesota, 75 E. River Road, Minneapolis, MN, 55455, USA
| | - Nina Roth Mota
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Geert Groteplein 10, 6500 HB, Nijmegen, The Netherlands
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joana F Viana
- The Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Edgbaston, Birmingham, UK
| | - Brittany L Mitchell
- Genetic Epidemiology, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Jose J Morosoli
- Psychiatric Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Till F M Andlauer
- Department of Neurology, Technical University of Munich, 22 Ismaninger St., 81675, Munich, Germany
| | - Isabelle Ouellet-Morin
- Research Unit on Children's Psychosocial Maladjustment, École de criminologie, Université of Montreal, 3150 Rue Jean-Brillant, Montreal, QC, H3T 1N8, Canada
| | - Richard E Tremblay
- Research Unit on Children's Psychosocial Maladjustment, Département de pédiatrie et de psychologie, University of Montreal, 90 Avenue Vincent d'Indy, Montreal, QC, H2V 2S9, Canada
| | - Sylvana M Côté
- Research Unit on Children's Psychosocial Maladjustment, CHU Ste-Justine Research Center and Department of Social and Preventive Medicine, University of Montreal, 3175 Chemin de la Côte Ste-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Jean-Philippe Gouin
- Department of Psychology, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - Mara R Brendgen
- Research Unit on Children's Psychosocial Maladjustment, Département de psychologie, Université du Québec à Montréal, CP 8888 succursale Centre-ville, Montreal, QC, H3C 3P8, Canada
| | - Ginette Dionne
- Research Unit on Children's Psychosocial Maladjustment, École de psychologie, Université Laval, 2523 Allée des Bibliothèques, Quebec City, QC, G1V 0A6, Canada
| | - Frank Vitaro
- Research Unit on Children's Psychosocial Maladjustment, CHU Sainte-Justine Research Center and University of Montreal, 3175 Chemin de la Côte Ste-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Michelle K Lupton
- Genetic Epidemiology, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Nicholas G Martin
- Genetic Epidemiology, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Enrique Castelao
- Center for Psychiatric Epidemiology and Psychopathology, Department of Psychiatry, Lausanne University Hospital and University of Lausanne, Route de Cery 25, CH-1008, Prilly, Vaud, Switzerland
| | - Katri Räikkönen
- Department of Psychology and Logopedics, University of Helsinki, Haartmaninkatu 3, 00014, Helsinki, Finland
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, Tukholmankatu 8 B, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Haartmaninkatu 3, 00014, Helsinki, Finland
| | - Catharina A Hartman
- Interdisciplinary Center Psychopathology and Emotion Regulation (ICPE), University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation (ICPE), University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Hexuan Liu
- School of Criminal Justice, University of Cincinnati, 2840 Bearcat Way, Cincinnati, OH, 45221, USA
| | - Martin Preisig
- Center for Psychiatric Epidemiology and Psychopathology, Department of Psychiatry, Lausanne University Hospital and University of Lausanne, Route de Cery 25, CH-1008, Prilly, Vaud, Switzerland
| | - Alyce Whipp
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, PO Box 4, (Yliopistonkatu 3), 00014, Helsinki, Finland
| | - Eero Vuoksimaa
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, PO Box 4, (Yliopistonkatu 3), 00014, Helsinki, Finland
| | - Yi Lu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels Väg 12A, 171 77, Stockholm, Sweden
| | - Patrick Jern
- Department of Psychology, Faculty of Arts, Psychology, and Theology, Åbo Akademi University, Tuomiokirkontori 3, FI-20500, Turku, Finland
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Ina Giegling
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, PO Box 4, (Yliopistonkatu 3), 00014, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, PO Box 4, (Yliopistonkatu 3), 00014, Helsinki, Finland
| | - Kathryn Paige Harden
- Department of Psychology and Population Research Center, University of Texas at Austin, 108 E Dean Keeton Stop #A8000, Austin, TX, 78712, USA
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Road, Bristol, BS8 2BN, UK
| | - Geneviève Morneau-Vaillancourt
- Research Unit on Children's Psychosocial Maladjustment, École de psychologie, Université Laval, 2523 Allée des Bibliothèques, Quebec City, QC, G1V 0A6, Canada
| | - Robert Plomin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, DeCrespigny Park, Denmark Hill, London, SE5 8AF, UK
| | - Essi Viding
- Division of Psychology and Language Sciences, University College London, London, UK
| | - Brian B Boutwell
- School of Applied Sciences, University of Mississippi, John D. Bower School of Population Health, University of Mississippi Medical Center, 84 Dormitory Row West, University, MS, 38677, USA
| | - Fazil Aliev
- Department of Psychology, Virginia Commonwealth University, Box 842018, 806W Franklin St, Richmond, VA, 23284, USA
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, Box 842018, 806W Franklin St, Richmond, VA, 23284, USA
| | - Arne Popma
- Amsterdam UMC, VKC Psyche, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam, The Netherlands
| | - Stephen V Faraone
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, 8000, Aarhus C, Aarhus, Denmark
| | - Sarah E Medland
- Psychiatric Genetics, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaivour, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Michel Boivin
- Research Unit on Children's Psychosocial Maladjustment, École de psychologie, Université Laval, 2523 Allée des Bibliothèques, Quebec City, QC, G1V 0A6, Canada
| | - Jean-Baptiste Pingault
- Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Jeffrey C Glennon
- Conway Institute of Biomolecular and Biomedical Sciences, School of Medicine, University College Dublin, Dublin, Ireland
| | - J C Barnes
- School of Criminal Justice, University of Cincinnati, 2840 Bearcat Way, Cincinnati, OH, 45221, USA
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Wundtlaan 1, 6525 XD, Nijmegen, The Netherlands
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience, Trinity College of Arts and Sciences, Duke University, 2020 West Main Street, Durham, NC, 27705, USA
| | - Avshalom Caspi
- Department of Psychology and Neuroscience, Trinity College of Arts and Sciences, Duke University, 2020 West Main Street, Durham, NC, 27705, USA
| | - Tinca J C Polderman
- Amsterdam UMC, VKC Psyche, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam, The Netherlands
| | - Danielle Posthuma
- Center for Neurogenomics and Cognitive Research, Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
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23
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Sellers A, Hudson S, Ledger J, Moorehouse C, Young C, Groeber I, Knight B, Mill J, Allard J, Shankar R. Designing genetic studies for people with intellectual disabilities: Practical lessons from a pilot study. Policy Practice Intel Disabi 2022. [DOI: 10.1111/jppi.12445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | - Ian Groeber
- Cornwall Partnership NHS Foundation Trust Truro UK
| | - Bridget Knight
- NIHR Exeter Clinical Research Facility RD&E NHS Foundation Trust Exeter UK
- University of Exeter Medical School Exeter UK
| | | | - Jon Allard
- Cornwall Partnership NHS Foundation Trust Truro UK
| | - Rohit Shankar
- Cornwall Partnership NHS Foundation Trust Truro UK
- University of Exeter Medical School Exeter UK
- Cornwall Intellectual Disabilities Equitable Research (CIDER) University of Plymouth Medical School Truro UK
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24
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Shireby G, Dempster EL, Policicchio S, Smith RG, Pishva E, Chioza B, Davies JP, Burrage J, Lunnon K, Seiler Vellame D, Love S, Thomas A, Brookes K, Morgan K, Francis P, Hannon E, Mill J. DNA methylation signatures of Alzheimer's disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types. Nat Commun 2022; 13:5620. [PMID: 36153390 PMCID: PMC9509387 DOI: 10.1038/s41467-022-33394-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterized by the progressive accumulation of amyloid-beta and neurofibrillary tangles of tau in the neocortex. We profiled DNA methylation in two regions of the cortex from 631 donors, performing an epigenome-wide association study of multiple measures of AD neuropathology. We meta-analyzed our results with those from previous studies of DNA methylation in AD cortex (total n = 2013 donors), identifying 334 cortical differentially methylated positions (DMPs) associated with AD pathology including methylomic variation at loci not previously implicated in dementia. We subsequently profiled DNA methylation in NeuN+ (neuronal-enriched), SOX10+ (oligodendrocyte-enriched) and NeuN-/SOX10- (microglia- and astrocyte-enriched) nuclei, finding that the majority of DMPs identified in 'bulk' cortex tissue reflect DNA methylation differences occurring in non-neuronal cells. Our study highlights the power of utilizing multiple measures of neuropathology to identify epigenetic signatures of AD and the importance of characterizing disease-associated variation in purified cell-types.
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Affiliation(s)
- Gemma Shireby
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L Dempster
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Stefania Policicchio
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Rebecca G Smith
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Barry Chioza
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan P Davies
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joe Burrage
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Dorothea Seiler Vellame
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Seth Love
- Dementia Research Group, University of Bristol Medical School (Translational Health Sciences), Bristol, UK
| | - Alan Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Keeley Brookes
- Biosciences, School of Science & Technology, Nottingham Trent University, Nottingham, UK
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Paul Francis
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Eilis Hannon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK.
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25
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Pihlstrøm L, Shireby G, Geut H, Henriksen SP, Rozemuller AJM, Tunold JA, Hannon E, Francis P, Thomas AJ, Love S, Mill J, van de Berg WDJ, Toft M. Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology. Nat Commun 2022; 13:4932. [PMID: 35995800 PMCID: PMC9395387 DOI: 10.1038/s41467-022-32619-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are closely related progressive disorders with no available disease-modifying therapy, neuropathologically characterized by intraneuronal aggregates of misfolded α-synuclein. To explore the role of DNA methylation changes in PD and DLB pathogenesis, we performed an epigenome-wide association study (EWAS) of 322 postmortem frontal cortex samples and replicated results in an independent set of 200 donors. We report novel differentially methylated replicating loci associated with Braak Lewy body stage near TMCC2, SFMBT2, AKAP6 and PHYHIP. Differentially methylated probes were independent of known PD genetic risk alleles. Meta-analysis provided suggestive evidence for a differentially methylated locus within the chromosomal region affected by the PD-associated 22q11.2 deletion. Our findings elucidate novel disease pathways in PD and DLB and generate hypotheses for future molecular studies of Lewy body pathology.
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Affiliation(s)
- Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
| | - Gemma Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Hanneke Geut
- Amsterdam UMC, Vrije Universiteit, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Netherlands Brain Bank, Netherlands Institute of Neurosciences, Amsterdam, The Netherlands
| | | | - Annemieke J M Rozemuller
- Amsterdam UMC, Vrije Universiteit, Department of Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Jon-Anders Tunold
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Paul Francis
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Alan J Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Seth Love
- Dementia Research Group, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Wilma D J van de Berg
- Amsterdam UMC, Vrije Universiteit, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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26
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Washer SJ, Flynn R, Oguro‐Ando A, Hannon E, Burrage J, Jeffries A, Mill J, Dempster EL. Functional characterization of the schizophrenia associated gene AS3MT identifies a role in neuronal development. Am J Med Genet B Neuropsychiatr Genet 2022; 189:151-162. [PMID: 35719055 PMCID: PMC9546433 DOI: 10.1002/ajmg.b.32905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/05/2022] [Accepted: 05/28/2022] [Indexed: 11/06/2022]
Abstract
Genome-wide association studies (GWAS) have identified multiple genomic regions associated with schizophrenia, although many variants reside in noncoding regions characterized by high linkage disequilibrium (LD) making the elucidation of molecular mechanisms challenging. A genomic region on chromosome 10q24 has been consistently associated with schizophrenia with risk attributed to the AS3MT gene. Although AS3MT is hypothesized to play a role in neuronal development and differentiation, work to fully understand the function of this gene has been limited. In this study we explored the function of AS3MT using a neuronal cell line (SH-SY5Y). We confirm previous findings of isoform specific expression of AS3MT during SH-SY5Y differentiation toward neuronal fates. Using CRISPR-Cas9 gene editing we generated AS3MT knockout SH-SY5Y cell lines and used RNA-seq to identify significant changes in gene expression in pathways associated with neuronal development, inflammation, extracellular matrix formation, and RNA processing, including dysregulation of other genes strongly implicated in schizophrenia. We did not observe any morphological changes in cell size and neurite length following neuronal differentiation and MAP2 immunocytochemistry. These results provide novel insights into the potential role of AS3MT in brain development and identify pathways through which genetic variation in this region may confer risk for schizophrenia.
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Affiliation(s)
- Sam J. Washer
- University of Exeter College of Medicine and Health, University of ExeterExeterUK,Cellular Operations, Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUK
| | - Robert Flynn
- University of Exeter College of Medicine and Health, University of ExeterExeterUK
| | - Asami Oguro‐Ando
- University of Exeter College of Medicine and Health, University of ExeterExeterUK
| | - Eilis Hannon
- University of Exeter College of Medicine and Health, University of ExeterExeterUK
| | - Joe Burrage
- University of Exeter College of Medicine and Health, University of ExeterExeterUK
| | - Aaron Jeffries
- University of Exeter College of Medicine and Health, University of ExeterExeterUK
| | - Jonathan Mill
- University of Exeter College of Medicine and Health, University of ExeterExeterUK
| | - Emma L. Dempster
- University of Exeter College of Medicine and Health, University of ExeterExeterUK
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27
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Flynn R, Washer S, Jeffries AR, Andrayas A, Shireby G, Kumari M, Schalkwyk LC, Mill J, Hannon E. Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays. Hum Mol Genet 2022; 31:3181-3190. [PMID: 35567415 PMCID: PMC9476619 DOI: 10.1093/hmg/ddac112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/25/2022] [Accepted: 05/05/2022] [Indexed: 11/14/2022] Open
Abstract
Most epigenetic epidemiology to date has utilized microarrays to identify positions in the genome where variation in DNA methylation is associated with environmental exposures or disease. However, these profile less than 3% of DNA methylation sites in the human genome, potentially missing affected loci and preventing the discovery of disrupted biological pathways. Third generation sequencing technologies, including Nanopore sequencing, have the potential to revolutionise the generation of epigenetic data, not only by providing genuine genome-wide coverage but profiling epigenetic modifications direct from native DNA. Here we assess the viability of using Nanopore sequencing for epidemiology by performing a comparison with DNA methylation quantified using the most comprehensive microarray available, the Illumina EPIC array. We implemented a CRISPR-Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA methylation in three genomic regions to attempt to rediscover genomic positions that existing technologies have shown are differentially methylated in tobacco smokers. Using Nanopore sequencing reads, DNA methylation was quantified at 1779 CpGs across three regions, providing a finer resolution of DNA methylation patterns compared to the EPIC array. The correlation of estimated levels of DNA methylation between platforms was high. Furthermore, we identified 12 CpGs where hypomethylation was significantly associated with smoking status, including 10 within the AHRR gene. In summary, Nanopore sequencing is a valid option for identifying genomic loci where large differences in DNAm are associated with a phenotype and has the potential to advance our understanding of the role differential methylation plays in the aetiology of complex disease.
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Affiliation(s)
- Robert Flynn
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Sam Washer
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom.,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Aaron R Jeffries
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Alexandria Andrayas
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Gemma Shireby
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester CO3 3LG, United Kingdom
| | - Leonard C Schalkwyk
- School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, United Kingdom
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28
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Hop PJ, Zwamborn RA, Hannon E, Shireby GL, Nabais MF, Walker EM, van Rheenen W, van Vugt JJ, Dekker AM, Westeneng HJ, Tazelaar GH, van Eijk KR, Moisse M, Baird D, Khleifat AA, Iacoangeli A, Ticozzi N, Ratti A, Cooper-Knock J, Morrison KE, Shaw PJ, Basak AN, Chiò A, Calvo A, Moglia C, Canosa A, Brunetti M, Grassano M, Gotkine M, Lerner Y, Zabari M, Vourc’h P, Corcia P, Couratier P, Pardina JSM, Salas T, Dion P, Ross JP, Henderson RD, Mathers S, McCombe PA, Needham M, Nicholson G, Rowe DB, Pamphlett R, Mather KA, Sachdev PS, Furlong S, Garton FC, Henders AK, Lin T, Ngo ST, Steyn FJ, Wallace L, Williams KL, Neto MM, Cauchi RJ, Blair IP, Kiernan MC, Drory V, Povedano M, de Carvalho M, Pinto S, Weber M, Rouleau GA, Silani V, Landers JE, Shaw CE, Andersen PM, McRae AF, van Es MA, Pasterkamp RJ, Wray NR, McLaughlin RL, Hardiman O, Kenna KP, Tsai E, Runz H, Al-Chalabi A, van den Berg LH, Van Damme P, Mill J, Veldink JH. Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS. Sci Transl Med 2022; 14:eabj0264. [PMID: 35196023 PMCID: PMC10040186 DOI: 10.1126/scitranslmed.abj0264] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study meta-analysis in 9706 samples passing stringent quality control (6763 patients, 2943 controls). We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We then tested 39 DNA methylation-based proxies of putative ALS risk factors and found that high-density lipoprotein cholesterol, body mass index, white blood cell proportions, and alcohol intake were independently associated with ALS. Integration of these results with our latest genome-wide association study showed that cholesterol biosynthesis was potentially causally related to ALS. Last, DNA methylation at several DMPs and blood cell proportion estimates derived from DNA methylation data were associated with survival rate in patients, suggesting that they might represent indicators of underlying disease processes potentially amenable to therapeutic interventions.
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Affiliation(s)
- Paul J. Hop
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Ramona A.J. Zwamborn
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Gemma L. Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Marta F. Nabais
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Emma M. Walker
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Joke J.F.A. van Vugt
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Annelot M. Dekker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Gijs H.P. Tazelaar
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Kristel R. van Eijk
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Matthieu Moisse
- KU Leuven–University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven 3000, Belgium
- VIB, Center for Brain and Disease Research, Leuven 3000, Belgium
- University Hospitals Leuven, Department of Neurology, Leuven 3000, Belgium
| | - Denis Baird
- Translational Biology, Biogen, Boston, MA 02142, USA
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol BS8 2BN, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- National Institute for Health Research Biomedical Research Centre and Dementia Unit, South London and Maudsley NHS Foundation Trust and King’s College London, London SE5 8AZ, UK
| | - Nicola Ticozzi
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan 20149, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan 20122, Italy
| | - Antonia Ratti
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan 20149, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milano 20145, Italy
| | - Jonathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Karen E. Morrison
- School of Medicine, Dentistry, and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - A. Nazli Basak
- Koc University, School of Medicine, Translational Medicine Research Center, NDAL, Istanbul, 34450, Turkey
| | - Adriano Chiò
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Andrea Calvo
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Cristina Moglia
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Antonio Canosa
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Maura Brunetti
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
| | - Maurizio Grassano
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
| | - Marc Gotkine
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Yossef Lerner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Michal Zabari
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Patrick Vourc’h
- Service de Biochimie et Biologie moléculaire, CHU de Tours, Tours 37044, France
- UMR 1253, Université de Tours, Inserm, Tours 37044, France
| | - Philippe Corcia
- UMR 1253, Université de Tours, Inserm, Tours 37044, France
- Centre de référence sur la SLA, CHU de Tours, Tours 37044, France
| | - Philippe Couratier
- Centre de référence sur la SLA, CHRU de Limoges, Limoges 87042, France
- UMR 1094, Université de Limoges, Inserm, Limoges 87025, France
| | | | - Teresa Salas
- Department of Neurology, Hospital La Paz-Carlos III, Madrid 28046, Spain
| | - Patrick Dion
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC H3A 2B4, Canada
| | - Jay P. Ross
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Robert D. Henderson
- 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, University of Queensland, Brisbane, QLD 4019, 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
| | - Garth Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Dominic B. Rowe
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, University of Sydney, Sydney, NSW 2050, 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
| | - Perminder S. Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2031, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, UNSW, Randwick, NSW 2031, Australia
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | - Fleur C. Garton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Anjali K. Henders
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Shyuan T. Ngo
- Centre for Clinical Research, University of Queensland, Brisbane, QLD 4019, Australia
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Frederik J. Steyn
- Centre for Clinical Research, University of Queensland, Brisbane, QLD 4019, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Kelly L. Williams
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | | | | | | | - Ruben J. Cauchi
- Center for Molecular Medicine and Biobanking and Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta
| | - Ian P. Blair
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | - Matthew C. Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, NSW, 2050, Australia
- Department of Neurology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Vivian Drory
- Department of Neurology, Tel-Aviv Sourasky Medical Centre, Tel-Aviv 64239, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Monica Povedano
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
| | - Susana Pinto
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Guy A. Rouleau
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC H3A 2B4, Canada
| | - Vincenzo Silani
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan 20149, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan 20122, Italy
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Christopher E. Shaw
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Peter M. Andersen
- Department of Clinical Science, Umeå University, Umeå SE-901 85, Sweden
| | - Allan F. McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Michael A. van Es
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - R. Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, 3584 CX, Netherlands
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Russell L. McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Kevin P. Kenna
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, 3584 CX, Netherlands
| | - Ellen Tsai
- Translational Biology, Biogen, Boston, MA 02142, USA
| | - Heiko Runz
- Translational Biology, Biogen, Boston, MA 02142, USA
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- King’s College Hospital, Denmark Hill, London SE5 9RS, UK
| | - Leonard H. van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Philip Van Damme
- KU Leuven–University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven 3000, Belgium
- VIB, Center for Brain and Disease Research, Leuven 3000, Belgium
- University Hospitals Leuven, Department of Neurology, Leuven 3000, Belgium
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Jan H. Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
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Mill J, Jaroszynski D, Brunetti E, Maitrallain A. A REVIEW OF RECENT STUDIES INVOLVING THE DOSIMETRY AND FOCUSSING OF VERY HIGH ENERGY ELECTRONS FROM LINEAR ACCELERATORS AND LASER-PLASMA WAKEFIELD ACCELERATORS. Phys Med 2022. [DOI: 10.1016/s1120-1797(22)01624-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Belsky DW, Caspi A, Corcoran DL, Sugden K, Poulton R, Arseneault L, Baccarelli A, Chamarti K, Gao X, Hannon E, Harrington HL, Houts R, Kothari M, Kwon D, Mill J, Schwartz J, Vokonas P, Wang C, Williams BS, Moffitt TE. DunedinPACE, a DNA methylation biomarker of the pace of aging. eLife 2022; 11:e73420. [PMID: 35029144 PMCID: PMC8853656 DOI: 10.7554/elife.73420] [Citation(s) in RCA: 182] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/13/2021] [Indexed: 01/09/2023] Open
Abstract
Background Measures to quantify changes in the pace of biological aging in response to intervention are needed to evaluate geroprotective interventions for humans. Previously, we showed that quantification of the pace of biological aging from a DNA-methylation blood test was possible (Belsky et al., 2020). Here, we report a next-generation DNA-methylation biomarker of Pace of Aging, DunedinPACE (for Pace of Aging Calculated from the Epigenome). Methods We used data from the Dunedin Study 1972-1973 birth cohort tracking within-individual decline in 19 indicators of organ-system integrity across four time points spanning two decades to model Pace of Aging. We distilled this two-decade Pace of Aging into a single-time-point DNA-methylation blood-test using elastic-net regression and a DNA-methylation dataset restricted to exclude probes with low test-retest reliability. We evaluated the resulting measure, named DunedinPACE, in five additional datasets. Results DunedinPACE showed high test-retest reliability, was associated with morbidity, disability, and mortality, and indicated faster aging in young adults with childhood adversity. DunedinPACE effect-sizes were similar to GrimAge Clock effect-sizes. In analysis of incident morbidity, disability, and mortality, DunedinPACE and added incremental prediction beyond GrimAge. Conclusions DunedinPACE is a novel blood biomarker of the pace of aging for gerontology and geroscience. Funding This research was supported by US-National Institute on Aging grants AG032282, AG061378, AG066887, and UK Medical Research Council grant MR/P005918/1.
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Affiliation(s)
- Daniel W Belsky
- Department of Epidemiology & Butler Columbia Aging Center, Columbia UniversityNew YorkUnited States
| | - Avshalom Caspi
- Center for Genomic and Computational Biology, Duke UniversityDurhamUnited States
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke UniversityDurhamUnited States
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
| | - Richie Poulton
- Department of Psychology, University of OtagoOtagoNew Zealand
| | - Louise Arseneault
- Social, Genetic, and Developmental Psychiatry Centre, King's College LondonLondonUnited Kingdom
| | - Andrea Baccarelli
- Department of Environmental Health Sciences, Columbia UniversityNew YorkUnited States
| | - Kartik Chamarti
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
| | - Xu Gao
- Department of Occupational and Environmental Health, Peking UniversityBeijingChina
| | - Eilis Hannon
- Complex Disease Epigenetics Group, University of ExeterExeterUnited Kingdom
| | - Hona Lee Harrington
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
| | - Renate Houts
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
| | - Meeraj Kothari
- Robert N Butler Columbia Aging Center, Columbia UniversityBrooklynUnited States
| | - Dayoon Kwon
- Robert N Butler Columbia Aging Center, Columbia UniversityNew YorkUnited States
| | - Jonathan Mill
- Complex Disease Epigenetics Group, University of ExeterExeterUnited Kingdom
| | - Joel Schwartz
- Department of Environmental Health Sciences, Harvard TH Chan School of Public Health, Harvard UniversityBostonUnited States
| | - Pantel Vokonas
- Department of Medicine, VA Boston Healthcare SystemBostonUnited States
| | - Cuicui Wang
- Department of Environmental Health Sciences, Harvard TH Chan School of Public Health, Harvard UniversityBostonUnited States
| | - Benjamin S Williams
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience, Duke UniversityDurhamUnited States
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31
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van Rheenen W, van der Spek RAA, Bakker MK, van Vugt JJFA, Hop PJ, Zwamborn RAJ, de Klein N, Westra HJ, Bakker OB, Deelen P, Shireby G, Hannon E, Moisse M, Baird D, Restuadi R, Dolzhenko E, Dekker AM, Gawor K, Westeneng HJ, Tazelaar GHP, van Eijk KR, Kooyman M, Byrne RP, Doherty M, Heverin M, Al Khleifat A, Iacoangeli A, Shatunov A, Ticozzi N, Cooper-Knock J, Smith BN, Gromicho M, Chandran S, Pal S, Morrison KE, Shaw PJ, Hardy J, Orrell RW, Sendtner M, Meyer T, Başak N, van der Kooi AJ, Ratti A, Fogh I, Gellera C, Lauria G, Corti S, Cereda C, Sproviero D, D'Alfonso S, Sorarù G, Siciliano G, Filosto M, Padovani A, Chiò A, Calvo A, Moglia C, Brunetti M, Canosa A, Grassano M, Beghi E, Pupillo E, Logroscino G, Nefussy B, Osmanovic A, Nordin A, Lerner Y, Zabari M, Gotkine M, Baloh RH, Bell S, Vourc'h P, Corcia P, Couratier P, Millecamps S, Meininger V, Salachas F, Mora Pardina JS, Assialioui A, Rojas-García R, Dion PA, Ross JP, Ludolph AC, Weishaupt JH, Brenner D, Freischmidt A, Bensimon G, Brice A, Durr A, Payan CAM, Saker-Delye S, Wood NW, Topp S, Rademakers R, Tittmann L, Lieb W, Franke A, Ripke S, Braun A, Kraft J, Whiteman DC, Olsen CM, Uitterlinden AG, Hofman A, Rietschel M, Cichon S, Nöthen MM, Amouyel P, Traynor BJ, Singleton AB, Mitne Neto M, Cauchi RJ, Ophoff RA, Wiedau-Pazos M, Lomen-Hoerth C, van Deerlin VM, Grosskreutz J, Roediger A, Gaur N, Jörk A, Barthel T, Theele E, Ilse B, Stubendorff B, Witte OW, Steinbach R, Hübner CA, Graff C, Brylev L, Fominykh V, Demeshonok V, Ataulina A, Rogelj B, Koritnik B, Zidar J, Ravnik-Glavač M, Glavač D, Stević Z, Drory V, Povedano M, Blair IP, Kiernan MC, Benyamin B, Henderson RD, Furlong S, Mathers S, McCombe PA, Needham M, Ngo ST, Nicholson GA, Pamphlett R, Rowe DB, Steyn FJ, Williams KL, Mather KA, Sachdev PS, Henders AK, Wallace L, de Carvalho M, Pinto S, Petri S, Weber M, Rouleau GA, Silani V, Curtis CJ, Breen G, Glass JD, Brown RH, Landers JE, Shaw CE, Andersen PM, Groen EJN, van Es MA, Pasterkamp RJ, Fan D, Garton FC, McRae AF, Davey Smith G, Gaunt TR, Eberle MA, Mill J, McLaughlin RL, Hardiman O, Kenna KP, Wray NR, Tsai E, Runz H, Franke L, Al-Chalabi A, Van Damme P, van den Berg LH, Veldink JH. Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology. Nat Genet 2021; 53:1636-1648. [PMID: 34873335 PMCID: PMC8648564 DOI: 10.1038/s41588-021-00973-1] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 10/18/2021] [Indexed: 02/01/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a lifetime risk of one in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry genome-wide association study (GWAS) including 29,612 patients with ALS and 122,656 controls, which identified 15 risk loci. When combined with 8,953 individuals with whole-genome sequencing (6,538 patients, 2,415 controls) and a large cortex-derived expression quantitative trait locus (eQTL) dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, short tandem repeats or regulatory effects. ALS-associated risk loci were shared with multiple traits within the neurodegenerative spectrum but with distinct enrichment patterns across brain regions and cell types. Of the environmental and lifestyle risk factors obtained from the literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. The combination of all ALS-associated signals reveals a role for perturbations in vesicle-mediated transport and autophagy and provides evidence for cell-autonomous disease initiation in glutamatergic neurons.
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Affiliation(s)
- Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - Rick A A van der Spek
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mark K Bakker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Joke J F A van Vugt
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Paul J Hop
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ramona A J Zwamborn
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Niek de Klein
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Olivier B Bakker
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Gemma Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Matthieu Moisse
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Denis Baird
- Translational Biology, Biogen, Boston, MA, USA
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, UK
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | | | - Annelot M Dekker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Klara Gawor
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Gijs H P Tazelaar
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Kristel R van Eijk
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Maarten Kooyman
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ross P Byrne
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Mark Doherty
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Mark Heverin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- National Institute for Health Research Biomedical Research Centre and Dementia Unit, South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Nicola Ticozzi
- Department of Neurology, Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Bradley N Smith
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Marta Gromicho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Siddharthan Chandran
- Euan MacDonald Centre for Motor Neurone Disease Research, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
| | - Suvankar Pal
- Euan MacDonald Centre for Motor Neurone Disease Research, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
| | - Karen E Morrison
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - John Hardy
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Richard W Orrell
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Thomas Meyer
- Charité University Hospital, Humboldt University, Berlin, Germany
| | - Nazli Başak
- Koç University, School of Medicine, KUTTAM-NDAL, Istanbul, Turkey
| | | | - Antonia Ratti
- Department of Neurology, Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Isabella Fogh
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Giuseppe Lauria
- 3rd Neurology Unit, Motor Neuron Diseases Center, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', MIlan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Stefania Corti
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Daisy Sproviero
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Sandra D'Alfonso
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Gianni Sorarù
- Department of Neurosciences, University of Padova, Padova, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Massimiliano Filosto
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Alessandro Padovani
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Adriano Chiò
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Andrea Calvo
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Cristina Moglia
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Maura Brunetti
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Antonio Canosa
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Maurizio Grassano
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Ettore Beghi
- Laboratory of Neurological Diseases, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Elisabetta Pupillo
- Laboratory of Neurological Diseases, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giancarlo Logroscino
- Department of Clinical Research in Neurology, University of Bari at 'Pia Fondazione Card G. Panico' Hospital, Bari, Italy
| | - Beatrice Nefussy
- Neuromuscular Diseases Unit, Department of Neurology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Alma Osmanovic
- Department of Neurology, Hannover Medical School, Hannover, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), University Hospital Essen, Essen, Germany
| | - Angelica Nordin
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - Yossef Lerner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Center, Jerusalem, Israel
| | - Michal Zabari
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Center, Jerusalem, Israel
| | - Marc Gotkine
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Center, Jerusalem, Israel
| | - Robert H Baloh
- Center for Neural Science and Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurology, Neuromuscular Division, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shaughn Bell
- Center for Neural Science and Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurology, Neuromuscular Division, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Patrick Vourc'h
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, Tours, France
- UMR 1253, Université de Tours, Inserm, Tours, France
| | - Philippe Corcia
- UMR 1253, Université de Tours, Inserm, Tours, France
- Centre de référence sur la SLA, CHU de Tours, Tours, France
| | - Philippe Couratier
- Centre de référence sur la SLA, CHRU de Limoges, Limoges, France
- UMR 1094, Université de Limoges, Inserm, Limoges, France
| | - Stéphanie Millecamps
- ICM, Institut du Cerveau, Inserm, CNRS, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | | | - François Salachas
- ICM, Institut du Cerveau, Inserm, CNRS, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Département de Neurologie, Centre de référence SLA Ile de France, Hôpital de la Pitié-Salpêtrière, AP-HP, Paris, France
| | | | - Abdelilah Assialioui
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ricardo Rojas-García
- MND Clinic, Neurology Department, Hospital de la Santa Creu i Sant Pau de Barcelona, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Patrick A Dion
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Jay P Ross
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Jochen H Weishaupt
- Division of Neurodegeneration, Department of Neurology, University Medicine Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Brenner
- Division of Neurodegeneration, Department of Neurology, University Medicine Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Axel Freischmidt
- Department of Neurology, Ulm University, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Gilbert Bensimon
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpêtrière, UPMC Pharmacologie, AP-HP, Paris, France
- Pharmacologie Sorbonne Université, Paris, France
- Institut du Cerveau, Paris Brain Institute ICM, Paris, France
- Laboratoire de Biostatistique, Epidémiologie Clinique, Santé Publique Innovation et Méthodologie (BESPIM), CHU-Nîmes, Nîmes, France
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute, APHP, INSERM, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute, APHP, INSERM, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Christine A M Payan
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpêtrière, UPMC Pharmacologie, AP-HP, Paris, France
| | | | - Nicholas W Wood
- Department of Clinical and Movement Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Simon Topp
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL, USA
| | - Lukas Tittmann
- Popgen Biobank and Institute of Epidemiology, Christian Albrechts-University Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Popgen Biobank and Institute of Epidemiology, Christian Albrechts-University Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Alice Braun
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Julia Kraft
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - David C Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Catherine M Olsen
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Andre G Uitterlinden
- Department of Internal Medicine, Genetics Laboratory, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marcella Rietschel
- Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
- Central Institute of Mental Health, Mannheim, Germany
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, Bonn, Germany
- Division of Medical Genetics, University Hospital Basel and Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine INM-1, Research Center Juelich, Juelich, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Philippe Amouyel
- INSERM UMR1167-RID-AGE LabEx DISTALZ-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille, Centre Hospitalier of the University of Lille, Institut Pasteur de Lille, Lille, France
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | | | - Ruben J Cauchi
- Centre for Molecular Medicine and Biobanking and Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Roel A Ophoff
- University Medical Center Utrecht, Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, Utrecht, the Netherlands
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Martina Wiedau-Pazos
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Vivianna M van Deerlin
- Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Julian Grosskreutz
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
- Precision Neurology Unit, Department of Neurology, University Hospital Schleswig-Holstein, University of Luebeck, Luebeck, Germany
| | | | - Nayana Gaur
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Alexander Jörk
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Tabea Barthel
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Erik Theele
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Benjamin Ilse
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | | | - Otto W Witte
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Robert Steinbach
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | | | - Caroline Graff
- Department of Geriatric Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lev Brylev
- Department of Neurology, Bujanov Moscow Clinical Hospital, Moscow, Russia
- Moscow Research and Clinical Center for Neuropsychiatry of the Healthcare Department, Moscow, Russia
- Department of Functional Biochemistry of the Nervous System, Institute of Higher Nervous Activity and Neurophysiology Russian Academy of Sciences, Moscow, Russia
| | - Vera Fominykh
- Department of Neurology, Bujanov Moscow Clinical Hospital, Moscow, Russia
- Department of Functional Biochemistry of the Nervous System, Institute of Higher Nervous Activity and Neurophysiology Russian Academy of Sciences, Moscow, Russia
| | - Vera Demeshonok
- ALS-Care Center, 'GAOORDI', Medical Clinic of the St. Petersburg, St. Petersburg, Russia
| | - Anastasia Ataulina
- Department of Neurology, Bujanov Moscow Clinical Hospital, Moscow, Russia
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
- Biomedical Research Institute BRIS, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Koritnik
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Janez Zidar
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Metka Ravnik-Glavač
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Zorica Stević
- Clinic of Neurology, Clinical Center of Serbia, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vivian Drory
- Neuromuscular Diseases Unit, Department of Neurology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Monica Povedano
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Beben Benyamin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Australian Centre for Precision Health and Allied Health and Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Robert D Henderson
- Centre for Clinical Research, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, Victoria, Australia
| | - Pamela A McCombe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, Western Australia, Australia
- Notre Dame University, Fremantle, Western Australia, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
| | - Shyuan T Ngo
- Centre for Clinical Research, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Garth A Nicholson
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Dominic B Rowe
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- The School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Neuroscience Research Australia Institute, Randwick, New South Wales, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Neuropsychiatric Institute, the Prince of Wales Hospital, UNSW, Randwick, New South Wales, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Susana Pinto
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Susanne Petri
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Guy A Rouleau
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Vincenzo Silani
- Department of Neurology, Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Charles J Curtis
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Gerome Breen
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Jonathan D Glass
- Department Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Peter M Andersen
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - Ewout J N Groen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Michael A van Es
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Dongsheng Fan
- Department of Neurology, Third Hospital, Peking University, Beijing, China
| | - Fleur C Garton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, Bristol, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Russell L McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Kevin P Kenna
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Ellen Tsai
- Translational Biology, Biogen, Boston, MA, USA
| | - Heiko Runz
- Translational Biology, Biogen, Boston, MA, USA
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- King's College Hospital, London, UK
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Leonard H van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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Leung SK, Jeffries AR, Castanho I, Jordan BT, Moore K, Davies JP, Dempster EL, Bray NJ, O'Neill P, Tseng E, Ahmed Z, Collier DA, Jeffery ED, Prabhakar S, Schalkwyk L, Jops C, Gandal MJ, Sheynkman GM, Hannon E, Mill J. Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing. Cell Rep 2021; 37:110022. [PMID: 34788620 PMCID: PMC8609283 DOI: 10.1016/j.celrep.2021.110022] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 07/30/2021] [Accepted: 10/28/2021] [Indexed: 12/05/2022] Open
Abstract
Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community. There is widespread transcript diversity in the cortex and many novel transcripts Some genes display big differences in isoform number between human and mouse cortex There is evidence of differential transcript usage between human fetal and adult cortex There are many novel isoforms of genes associated with human brain disease
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Key Words
- isoform, transcript, expression, brain, cortex, mouse, human, adult, fetal, long-read sequencing, alternative splicing
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Affiliation(s)
| | | | - Isabel Castanho
- University of Exeter, Exeter, UK; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ben T Jordan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | | | | | | | | | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore
| | | | - Connor Jops
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; UVA Cancer Center, University of Virginia, Charlottesville, VA, USA
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33
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van Dongen J, Gordon SD, McRae AF, Odintsova VV, Mbarek H, Breeze CE, Sugden K, Lundgren S, Castillo-Fernandez JE, Hannon E, Moffitt TE, Hagenbeek FA, van Beijsterveldt CEM, Jan Hottenga J, Tsai PC, Min JL, Hemani G, Ehli EA, Paul F, Stern CD, Heijmans BT, Slagboom PE, Daxinger L, van der Maarel SM, de Geus EJC, Willemsen G, Montgomery GW, Reversade B, Ollikainen M, Kaprio J, Spector TD, Bell JT, Mill J, Caspi A, Martin NG, Boomsma DI. Identical twins carry a persistent epigenetic signature of early genome programming. Nat Commun 2021; 12:5618. [PMID: 34584077 PMCID: PMC8479069 DOI: 10.1038/s41467-021-25583-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/19/2021] [Indexed: 02/08/2023] Open
Abstract
Monozygotic (MZ) twins and higher-order multiples arise when a zygote splits during pre-implantation stages of development. The mechanisms underpinning this event have remained a mystery. Because MZ twinning rarely runs in families, the leading hypothesis is that it occurs at random. Here, we show that MZ twinning is strongly associated with a stable DNA methylation signature in adult somatic tissues. This signature spans regions near telomeres and centromeres, Polycomb-repressed regions and heterochromatin, genes involved in cell-adhesion, WNT signaling, cell fate, and putative human metastable epialleles. Our study also demonstrates a never-anticipated corollary: because identical twins keep a lifelong molecular signature, we can retrospectively diagnose if a person was conceived as monozygotic twin.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands.
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands.
| | - Scott D Gordon
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Hamdi Mbarek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | | | - Karen Sugden
- Department of Psychology and Neuroscience and Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Sara Lundgren
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | | | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience and Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Catharina E M van Beijsterveldt
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Josine L Min
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Erik A Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD, USA
| | - Franziska Paul
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
| | - Claudio D Stern
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Eco J C de Geus
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Bruno Reversade
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Medical Genetics Department, KOC University, School of Medicine, Istanbul, Turkey
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Avshalom Caspi
- Department of Psychology and Neuroscience and Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, Australia
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
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34
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Grodstein F, Lemos B, Yu L, Klein HU, Iatrou A, Buchman AS, Shireby GL, Mill J, Schneider JA, De Jager PL, Bennett DA. The association of epigenetic clocks in brain tissue with brain pathologies and common aging phenotypes. Neurobiol Dis 2021; 157:105428. [PMID: 34153464 PMCID: PMC8373772 DOI: 10.1016/j.nbd.2021.105428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022] Open
Abstract
Epigenetic clocks are calculated by combining DNA methylation states across select CpG sites to estimate biologic age, and have been noted as the most successful markers of biologic aging to date. Yet, limited research has considered epigenetic clocks calculated in brain tissue. We used DNA methylation states in dorsolateral prefrontal cortex specimens from 721 older participants of the Religious Orders Study and Rush Memory and Aging Project, to calculate DNA methylation age using four established epigenetic clocks: Hannum, Horvath, PhenoAge, GrimAge, and a new Cortical clock. The four established clocks were trained in blood samples (Hannum, PhenoAge, GrimAge) or using 51 human tissue and cell types (Horvath); the recent Cortical clock is the first trained in postmortem cortical tissue. Participants were recruited beginning in 1994 (Religious Orders Study) and 1997 (Memory and Aging Project), and followed annually with questionnaires and clinical evaluations; brain specimens were obtained for 80-90% of participants. Mean age at death was 88.0 (SD 6.7) years. We used linear regression, logistic regression, and linear mixed models, to examine relations of epigenetic clock ages to neuropathologic and clinical aging phenotypes, controlling for chronologic age, sex, education, and depressive symptomatology. Hannum, Horvath, PhenoAge and Cortical clock ages were related to pathologic diagnosis of Alzheimer's disease (AD), as well as to Aβ load (a hallmark pathology of Alzheimer's disease). However, associations were substantially stronger for the Cortical than other clocks; for example, each standard deviation (SD) increase in Hannum, Horvath, and PhenoAge clock age was related to approximately 30% greater likelihood of pathologic AD (all p < 0.05), while each SD increase in Cortical age was related to 90% greater likelihood of pathologic AD (odds ratio = 1.91, 95% confidence interval 1.38, 2.62). Moreover, Cortical age was significantly related to other AD pathology (eg, mean tau tangle density, p = 0.003), and to odds of neocortical Lewy body pathology (for each SD increase in Cortical age, odds ratio = 2.00, 95% confidence 1.27, 3.17), although no clocks were related to cerebrovascular neuropathology. Cortical age was the only epigenetic clock significantly associated with the clinical phenotypes examined, from dementia to cognitive decline (5 specific cognitive systems, and a global cognitive measure averaging 17 tasks) to Parkinsonian signs. Overall, our findings provide evidence of the critical necessity for bespoke clocks of brain aging for advancing research to understand, and eventually prevent, neurodegenerative diseases of aging.
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Affiliation(s)
- Francine Grodstein
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States of America.
| | - Bernardo Lemos
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, United States of America
| | - Lei Yu
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Artemis Iatrou
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America
| | - Aron S Buchman
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
| | - Gemma L Shireby
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America; Department of Pathology, Rush University Medical Center, Chicago, IL, United States of America
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States of America
| | - David A Bennett
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
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35
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Kouakou MR, Cameron D, Hannon E, Dempster EL, Mill J, Hill MJ, Bray NJ. Sites of active gene regulation in the prenatal frontal cortex and their role in neuropsychiatric disorders. Am J Med Genet B Neuropsychiatr Genet 2021; 186:376-388. [PMID: 34632689 DOI: 10.1002/ajmg.b.32877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 04/06/2021] [Accepted: 09/21/2021] [Indexed: 12/21/2022]
Abstract
Common genetic variation appears to largely influence risk for neuropsychiatric disorders through effects on gene regulation. It is therefore possible to shed light on the biology of these conditions by testing for enrichment of associated genetic variation within regulatory genomic regions operating in specific tissues or cell types. Here, we have used the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) to map open chromatin (an index of active regulatory genomic regions) in bulk tissue, NeuN+ and NeuN- nuclei from the prenatal human frontal cortex, and tested enrichment of single-nucleotide polymorphism (SNP) heritability for five neuropsychiatric disorders (autism spectrum disorder, attention deficit hyperactivity disorder [ADHD], bipolar disorder, major depressive disorder, and schizophrenia) within these regions. We observed significant enrichment of SNP heritability for ADHD, major depressive disorder, and schizophrenia within open chromatin regions (OCRs) mapped in bulk fetal frontal cortex, and for all five tested neuropsychiatric conditions when we restricted these sites to those overlapping histone modifications indicative of enhancers (H3K4me1) or promoters (H3K4me3) in fetal brain. SNP heritability for neuropsychiatric disorders was significantly enriched in OCRs identified in fetal frontal cortex NeuN- as well as NeuN+ nuclei overlapping fetal brain H3K4me1 or H3K4me3 sites. We additionally demonstrate the utility of our mapped OCRs for prioritizing potentially functional SNPs at genome-wide significant risk loci for neuropsychiatric disorders. Our data provide evidence for an early neurodevelopmental component to a range of neuropsychiatric conditions and highlight an important role for regulatory genomic regions active within both NeuN+ and NeuN- cells of the prenatal brain.
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Affiliation(s)
- Manuela R Kouakou
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Darren Cameron
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L Dempster
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Matthew J Hill
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
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36
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Min JL, Hemani G, Hannon E, Dekkers KF, Castillo-Fernandez J, Luijk R, Carnero-Montoro E, Lawson DJ, Burrows K, Suderman M, Bretherick AD, Richardson TG, Klughammer J, Iotchkova V, Sharp G, Al Khleifat A, Shatunov A, Iacoangeli A, McArdle WL, Ho KM, Kumar A, Söderhäll C, Soriano-Tárraga C, Giralt-Steinhauer E, Kazmi N, Mason D, McRae AF, Corcoran DL, Sugden K, Kasela S, Cardona A, Day FR, Cugliari G, Viberti C, Guarrera S, Lerro M, Gupta R, Bollepalli S, Mandaviya P, Zeng Y, Clarke TK, Walker RM, Schmoll V, Czamara D, Ruiz-Arenas C, Rezwan FI, Marioni RE, Lin T, Awaloff Y, Germain M, Aïssi D, Zwamborn R, van Eijk K, Dekker A, van Dongen J, Hottenga JJ, Willemsen G, Xu CJ, Barturen G, Català-Moll F, Kerick M, Wang C, Melton P, Elliott HR, Shin J, Bernard M, Yet I, Smart M, Gorrie-Stone T, Shaw C, Al Chalabi A, Ring SM, Pershagen G, Melén E, Jiménez-Conde J, Roquer J, Lawlor DA, Wright J, Martin NG, Montgomery GW, Moffitt TE, Poulton R, Esko T, Milani L, Metspalu A, Perry JRB, Ong KK, Wareham NJ, Matullo G, Sacerdote C, Panico S, Caspi A, Arseneault L, Gagnon F, Ollikainen M, Kaprio J, Felix JF, Rivadeneira F, Tiemeier H, van IJzendoorn MH, Uitterlinden AG, Jaddoe VWV, Haley C, McIntosh AM, Evans KL, Murray A, Räikkönen K, Lahti J, Nohr EA, Sørensen TIA, Hansen T, Morgen CS, Binder EB, Lucae S, Gonzalez JR, Bustamante M, Sunyer J, Holloway JW, Karmaus W, Zhang H, Deary IJ, Wray NR, Starr JM, Beekman M, van Heemst D, Slagboom PE, Morange PE, Trégouët DA, Veldink JH, Davies GE, de Geus EJC, Boomsma DI, Vonk JM, Brunekreef B, Koppelman GH, Alarcón-Riquelme ME, Huang RC, Pennell CE, van Meurs J, Ikram MA, Hughes AD, Tillin T, Chaturvedi N, Pausova Z, Paus T, Spector TD, Kumari M, Schalkwyk LC, Visscher PM, Davey Smith G, Bock C, Gaunt TR, Bell JT, Heijmans BT, Mill J, Relton CL. Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation. Nat Genet 2021; 53:1311-1321. [PMID: 34493871 PMCID: PMC7612069 DOI: 10.1038/s41588-021-00923-x] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/12/2021] [Indexed: 12/25/2022]
Abstract
Characterizing genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. In the present study, we describe results of DNAm quantitative trait locus (mQTL) analyses on 32,851 participants, identifying genetic variants associated with DNAm at 420,509 DNAm sites in blood. We present a database of >270,000 independent mQTLs, of which 8.5% comprise long-range (trans) associations. Identified mQTL associations explain 15-17% of the additive genetic variance of DNAm. We show that the genetic architecture of DNAm levels is highly polygenic. Using shared genetic control between distal DNAm sites, we constructed networks, identifying 405 discrete genomic communities enriched for genomic annotations and complex traits. Shared genetic variants are associated with both DNAm levels and complex diseases, but only in a minority of cases do these associations reflect causal relationships from DNAm to trait or vice versa, indicating a more complex genotype-phenotype map than previously anticipated.
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Affiliation(s)
- Josine L Min
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Koen F Dekkers
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | - René Luijk
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Elena Carnero-Montoro
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Gemma Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Biostatistics and Health Informatics, King's College London, London, UK
| | - Wendy L McArdle
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Karen M Ho
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Chronic Disease Epidemiology unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Soriano-Tárraga
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Eva Giralt-Steinhauer
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Karen Sugden
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Silva Kasela
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alexia Cardona
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Felix R Day
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Giovanni Cugliari
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Simonetta Guarrera
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Michael Lerro
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Richa Gupta
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pooja Mandaviya
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Toni-Kim Clarke
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Vanessa Schmoll
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Carlos Ruiz-Arenas
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Faisal I Rezwan
- Department of Computer Science, Aberystwyth University, Aberystwyth, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Tian Lin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Yvonne Awaloff
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Marine Germain
- INSERM UMR_S 1219, Bordeaux Population Health Center, University of Bordeaux, Bordeaux, France
| | - Dylan Aïssi
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Ramona Zwamborn
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Kristel van Eijk
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Annelot Dekker
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, the Netherlands
- CiiM and TWINCORE, Hannover Medical School and Helmholtz Centre for Infection Research, Hannover, Germany
| | - Guillermo Barturen
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
| | - Francesc Català-Moll
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - Martin Kerick
- Instituto de Parasitología y Biomedicina López Neyra, CSIC, Granada, Spain
| | - Carol Wang
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, Australia
| | - Phillip Melton
- Menzies Institute for Medical Research, College of Health and Medicine, University of Tasmania, Hobart, Australia
- School of Global Population Health, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jean Shin
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Manon Bernard
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Idil Yet
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Melissa Smart
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | | | - Chris Shaw
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Neurology, King's College Hospital, London, UK
| | - Ammar Al Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London, UK
- Department of Neurology, King's College Hospital, London, UK
- United Kingdom Dementia Research Institute, King's College London, London, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Jordi Jiménez-Conde
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Jaume Roquer
- Neurology Department, Hospital del Mar, Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain
| | - Deborah A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - John Wright
- Bradford Institute for Health Research, Bradford, UK
| | | | - Grant W Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Terrie E Moffitt
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - John R B Perry
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Ken K Ong
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, School of Clinical Medicine, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Carlotta Sacerdote
- Italian Institute for Genomic Medicine, Turin, Italy
- Piemonte Centre for Cancer Prevention, Turin, Italy
| | - Salvatore Panico
- Dipartimento Di Medicina Clinica E Chirurgia, Federico II University, Naples, Italy
| | - Avshalom Caspi
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University Medical School, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - France Gagnon
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Miina Ollikainen
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Department of Clinical, Educational and Health Psychology, Division on Psychology and Language Sciences, Faculty of Brain Sciences, University College London, London, UK
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Chris Haley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Alison Murray
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ellen A Nohr
- Research Unit for Gynaecology and Obstetrics, Institute of Clinical research, University of Southern Denmark, Odense, Denmark
- Centre of Women's, Family and Child Health, University of South-Eastern Norway, Kongsberg, Norway
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health (Section of Epidemiology), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Camilla S Morgen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Susanne Lucae
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Juan Ramon Gonzalez
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Sunyer
- ISGlobal, Barcelona Global Health Institute, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Diana van Heemst
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Eco J C de Geus
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, GRIAC Research Institute Groningen, Groningen, the Netherlands
| | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Universiteit Utrecht, Utrecht, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, the Netherlands
| | - Marta E Alarcón-Riquelme
- Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Craig E Pennell
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, Australia
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | | | | | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Tomas Paus
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, Canada
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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Abstract
Alzheimer's disease (AD) is a growing global healthcare epidemic. Owing to advances in technology, genome-scale studies of various layers of molecular information have been undertaken in recent years and robust variation in key loci have now been published and reproduced by others. This mini-symposium highlights four key areas of current research in the field of molecular biology in AD, including articles focused on large-scale genomic profiling, epigenetic research, integrative multi-omic approaches and how these can be appropriately modeled to address reverse causality. This mini-symposium provides a timely update on research focused on elucidating the molecular etiology of AD to date and highlights new methodological advances that could enable neuroscientists to identify novel therapeutic targets.
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Affiliation(s)
- Adam R Smith
- University of Exeter Medical School, Exeter University, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, Exeter University, Exeter, UK
| | - Katie Lunnon
- University of Exeter Medical School, Exeter University, Exeter, UK
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Gunasekara CJ, Hannon E, MacKay H, Coarfa C, McQuillin A, Clair DS, Mill J, Waterland RA. A machine learning case-control classifier for schizophrenia based on DNA methylation in blood. Transl Psychiatry 2021; 11:412. [PMID: 34341337 PMCID: PMC8329061 DOI: 10.1038/s41398-021-01496-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/07/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
Epigenetic dysregulation is thought to contribute to the etiology of schizophrenia (SZ), but the cell type-specificity of DNA methylation makes population-based epigenetic studies of SZ challenging. To train an SZ case-control classifier based on DNA methylation in blood, therefore, we focused on human genomic regions of systemic interindividual epigenetic variation (CoRSIVs), a subset of which are represented on the Illumina Human Methylation 450K (HM450) array. HM450 DNA methylation data on whole blood of 414 SZ cases and 433 non-psychiatric controls were used as training data for a classification algorithm with built-in feature selection, sparse partial least squares discriminate analysis (SPLS-DA); application of SPLS-DA to HM450 data has not been previously reported. Using the first two SPLS-DA dimensions we calculated a "risk distance" to identify individuals with the highest probability of SZ. The model was then evaluated on an independent HM450 data set on 353 SZ cases and 322 non-psychiatric controls. Our CoRSIV-based model classified 303 individuals as cases with a positive predictive value (PPV) of 80%, far surpassing the performance of a model based on polygenic risk score (PRS). Importantly, risk distance (based on CoRSIV methylation) was not associated with medication use, arguing against reverse causality. Risk distance and PRS were positively correlated (Pearson r = 0.28, P = 1.28 × 10-12), and mediational analysis suggested that genetic effects on SZ are partially mediated by altered methylation at CoRSIVs. Our results indicate two innate dimensions of SZ risk: one based on genetic, and the other on systemic epigenetic variants.
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Affiliation(s)
- Chathura J. Gunasekara
- grid.39382.330000 0001 2160 926XUSDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Eilis Hannon
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Harry MacKay
- grid.39382.330000 0001 2160 926XUSDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Cristian Coarfa
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Andrew McQuillin
- grid.83440.3b0000000121901201Division of Psychiatry, Faculty of Brain Sciences, University College London, London, UK
| | - David St. Clair
- grid.7107.10000 0004 1936 7291The Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Jonathan Mill
- grid.8391.30000 0004 1936 8024University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Robert A. Waterland
- grid.39382.330000 0001 2160 926XUSDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
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Wang Y, Hannon E, Grant OA, Gorrie-Stone TJ, Kumari M, Mill J, Zhai X, McDonald-Maier KD, Schalkwyk LC. DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy. BMC Genomics 2021; 22:484. [PMID: 34182928 PMCID: PMC8240370 DOI: 10.1186/s12864-021-07675-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 05/05/2021] [Indexed: 03/17/2023] Open
Abstract
Background Sex is an important covariate of epigenome-wide association studies due to its strong influence on DNA methylation patterns across numerous genomic positions. Nevertheless, many samples on the Gene Expression Omnibus (GEO) frequently lack a sex annotation or are incorrectly labelled. Considering the influence that sex imposes on DNA methylation patterns, it is necessary to ensure that methods for filtering poor samples and checking of sex assignment are accurate and widely applicable. Results Here we presented a novel method to predict sex using only DNA methylation beta values, which can be readily applied to almost all DNA methylation datasets of different formats (raw IDATs or text files with only signal intensities) uploaded to GEO. We identified 4345 significantly (p<0.01) sex-associated CpG sites present on both 450K and EPIC arrays, and constructed a sex classifier based on the two first principal components of the DNA methylation data of sex-associated probes mapped on sex chromosomes. The proposed method is constructed using whole blood samples and exhibits good performance across a wide range of tissues. We further demonstrated that our method can be used to identify samples with sex chromosome aneuploidy, this function is validated by five Turner syndrome cases and one Klinefelter syndrome case. Conclusions This proposed sex classifier not only can be used for sex predictions but also applied to identify samples with sex chromosome aneuploidy, and it is freely and easily accessible by calling the ‘estimateSex’ function from the newest wateRmelon Bioconductor package (https://github.com/schalkwyk/wateRmelon). Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-07675-2).
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Affiliation(s)
- Yucheng Wang
- School of Computer Science and Electronic Engineering, University of Essex, Wivenhoe Park, Colchester, UK
| | - Eilis Hannon
- Medical School, University of Exeter, Barrack Road, Exeter, UK
| | - Olivia A Grant
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
| | | | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Wivenhoe Park, Colchester, UK
| | - Jonathan Mill
- Medical School, University of Exeter, Barrack Road, Exeter, UK
| | - Xiaojun Zhai
- School of Computer Science and Electronic Engineering, University of Essex, Wivenhoe Park, Colchester, UK.
| | - Klaus D McDonald-Maier
- School of Computer Science and Electronic Engineering, University of Essex, Wivenhoe Park, Colchester, UK
| | - Leonard C Schalkwyk
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK
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Steg LC, Shireby GL, Imm J, Davies JP, Franklin A, Flynn R, Namboori SC, Bhinge A, Jeffries AR, Burrage J, Neilson GWA, Walker EM, Perfect LW, Price J, McAlonan G, Srivastava DP, Bray NJ, Cope EL, Jones KM, Allen ND, Pishva E, Dempster EL, Lunnon K, Mill J, Hannon E. Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons. Mol Brain 2021; 14:98. [PMID: 34174924 PMCID: PMC8236187 DOI: 10.1186/s13041-021-00810-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) and their differentiated neurons (iPSC-neurons) are a widely used cellular model in the research of the central nervous system. However, it is unknown how well they capture age-associated processes, particularly given that pluripotent cells are only present during the earliest stages of mammalian development. Epigenetic clocks utilize coordinated age-associated changes in DNA methylation to make predictions that correlate strongly with chronological age. It has been shown that the induction of pluripotency rejuvenates predicted epigenetic age. As existing clocks are not optimized for the study of brain development, we developed the fetal brain clock (FBC), a bespoke epigenetic clock trained in human prenatal brain samples in order to investigate more precisely the epigenetic age of iPSCs and iPSC-neurons. The FBC was tested in two independent validation cohorts across a total of 194 samples, confirming that the FBC outperforms other established epigenetic clocks in fetal brain cohorts. We applied the FBC to DNA methylation data from iPSCs and embryonic stem cells and their derived neuronal precursor cells and neurons, finding that these cell types are epigenetically characterized as having an early fetal age. Furthermore, while differentiation from iPSCs to neurons significantly increases epigenetic age, iPSC-neurons are still predicted as being fetal. Together our findings reiterate the need to better understand the limitations of existing epigenetic clocks for answering biological research questions and highlight a limitation of iPSC-neurons as a cellular model of age-related diseases.
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Affiliation(s)
- Leonard C Steg
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Gemma L Shireby
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Jennifer Imm
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Jonathan P Davies
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Alice Franklin
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Robert Flynn
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Seema C Namboori
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Akshay Bhinge
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Aaron R Jeffries
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Joe Burrage
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Grant W A Neilson
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Emma M Walker
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Leo W Perfect
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Grainne McAlonan
- Department of Forensic and Neurodevelopmental Sciences, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Behavioural and Developmental Psychiatry, South London and Maudsley NHS Foundation Trust, London, UK
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Nicholas J Bray
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Emma L Cope
- School of Biosciences, Cardiff University, Cardiff, UK
| | | | | | - Ehsan Pishva
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Emma L Dempster
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Katie Lunnon
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Jonathan Mill
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK
| | - Eilis Hannon
- College of Medicine and Health, University of Exeter, RILD Building Level 3, Barrack Rd, Exeter, UK.
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Seiler Vellame D, Castanho I, Dahir A, Mill J, Hannon E. Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify between-group differences in DNA methylation. BMC Genomics 2021; 22:446. [PMID: 34126923 PMCID: PMC8204428 DOI: 10.1186/s12864-021-07721-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The combination of sodium bisulfite treatment with highly-parallel sequencing is a common method for quantifying DNA methylation across the genome. The power to detect between-group differences in DNA methylation using bisulfite-sequencing approaches is influenced by both experimental (e.g. read depth, missing data and sample size) and biological (e.g. mean level of DNA methylation and difference between groups) parameters. There is, however, no consensus about the optimal thresholds for filtering bisulfite sequencing data with implications for the reproducibility of findings in epigenetic epidemiology. RESULTS We used a large reduced representation bisulfite sequencing (RRBS) dataset to assess the distribution of read depth across DNA methylation sites and the extent of missing data. To investigate how various study variables influence power to identify DNA methylation differences between groups, we developed a framework for simulating bisulfite sequencing data. As expected, sequencing read depth, group size, and the magnitude of DNA methylation difference between groups all impacted upon statistical power. The influence on power was not dependent on one specific parameter, but reflected the combination of study-specific variables. As a resource to the community, we have developed a tool, POWEREDBiSeq, which utilizes our simulation framework to predict study-specific power for the identification of DNAm differences between groups, taking into account user-defined read depth filtering parameters and the minimum sample size per group. CONCLUSIONS Our data-driven approach highlights the importance of filtering bisulfite-sequencing data by minimum read depth and illustrates how the choice of threshold is influenced by the specific study design and the expected differences between groups being compared. The POWEREDBiSeq tool, which can be applied to different types of bisulfite sequencing data (e.g. RRBS, whole genome bisulfite sequencing (WGBS), targeted bisulfite sequencing and amplicon-based bisulfite sequencing), can help users identify the level of data filtering needed to optimize power and aims to improve the reproducibility of bisulfite sequencing studies.
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Affiliation(s)
- Dorothea Seiler Vellame
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK.
| | - Isabel Castanho
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline-Avenue, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Aisha Dahir
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK.
| | - Eilis Hannon
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK.
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Smith RG, Pishva E, Shireby G, Smith AR, Roubroeks JAY, Hannon E, Wheildon G, Mastroeni D, Gasparoni G, Riemenschneider M, Giese A, Sharp AJ, Schalkwyk L, Haroutunian V, Viechtbauer W, van den Hove DLA, Weedon M, Brokaw D, Francis PT, Thomas AJ, Love S, Morgan K, Walter J, Coleman PD, Bennett DA, De Jager PL, Mill J, Lunnon K. A meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex. Nat Commun 2021; 12:3517. [PMID: 34112773 PMCID: PMC8192929 DOI: 10.1038/s41467-021-23243-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2021] [Indexed: 01/01/2023] Open
Abstract
Epigenome-wide association studies of Alzheimer's disease have highlighted neuropathology-associated DNA methylation differences, although existing studies have been limited in sample size and utilized different brain regions. Here, we combine data from six DNA methylomic studies of Alzheimer's disease (N = 1453 unique individuals) to identify differential methylation associated with Braak stage in different brain regions and across cortex. We identify 236 CpGs in the prefrontal cortex, 95 CpGs in the temporal gyrus and ten CpGs in the entorhinal cortex at Bonferroni significance, with none in the cerebellum. Our cross-cortex meta-analysis (N = 1408 donors) identifies 220 CpGs associated with neuropathology, annotated to 121 genes, of which 84 genes have not been previously reported at this significance threshold. We have replicated our findings using two further DNA methylomic datasets consisting of a further >600 unique donors. The meta-analysis summary statistics are available in our online data resource ( www.epigenomicslab.com/ad-meta-analysis/ ).
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Affiliation(s)
- Rebecca G Smith
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Gemma Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Adam R Smith
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Janou A Y Roubroeks
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Gregory Wheildon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Diego Mastroeni
- Banner ASU Neurodegenerative Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Gilles Gasparoni
- Department of Genetics, University of Saarland (UdS), Saarbruecken, Germany
| | - Matthias Riemenschneider
- Department of Psychiatry and Psychotherapy, Saarland University Hospital (UKS), Homburg, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Vahram Haroutunian
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- JJ Peters VA Medical Center, Bronx, NY, USA
| | - Wolfgang Viechtbauer
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Daniel L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
- Laboratory of Translational Neuroscience, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Würzburg, Germany
| | - Michael Weedon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Danielle Brokaw
- Banner ASU Neurodegenerative Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Paul T Francis
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Alan J Thomas
- Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, UK
| | - Seth Love
- Dementia Research Group, Institute of Clinical Neurosciences, School of Clinical Sciences, University of Bristol, Bristol, UK
| | - Kevin Morgan
- Human Genetics Group, University of Nottingham, Nottingham, UK
| | - Jörn Walter
- Department of Genetics, University of Saarland (UdS), Saarbruecken, Germany
| | - Paul D Coleman
- Banner ASU Neurodegenerative Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute, Columbia University Medical Center, New York, NY, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Katie Lunnon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK.
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van Dongen J, Hagenbeek FA, Suderman M, Roetman PJ, Sugden K, Chiocchetti AG, Ismail K, Mulder RH, Hafferty JD, Adams MJ, Walker RM, Morris SW, Lahti J, Küpers LK, Escaramis G, Alemany S, Jan Bonder M, Meijer M, Ip HF, Jansen R, Baselmans BML, Parmar P, Lowry E, Streit F, Sirignano L, Send TS, Frank J, Jylhävä J, Wang Y, Mishra PP, Colins OF, Corcoran DL, Poulton R, Mill J, Hannon E, Arseneault L, Korhonen T, Vuoksimaa E, Felix JF, Bakermans-Kranenburg MJ, Campbell A, Czamara D, Binder E, Corpeleijn E, Gonzalez JR, Grazuleviciene R, Gutzkow KB, Evandt J, Vafeiadi M, Klein M, van der Meer D, Ligthart L, Kluft C, Davies GE, Hakulinen C, Keltikangas-Järvinen L, Franke B, Freitag CM, Konrad K, Hervas A, Fernández-Rivas A, Vetro A, Raitakari O, Lehtimäki T, Vermeiren R, Strandberg T, Räikkönen K, Snieder H, Witt SH, Deuschle M, Pedersen NL, Hägg S, Sunyer J, Franke L, Kaprio J, Ollikainen M, Moffitt TE, Tiemeier H, van IJzendoorn MH, Relton C, Vrijheid M, Sebert S, Jarvelin MR, Caspi A, Evans KL, McIntosh AM, Bartels M, Boomsma DI. DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan. Mol Psychiatry 2021; 26:2148-2162. [PMID: 33420481 PMCID: PMC8263810 DOI: 10.1038/s41380-020-00987-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 11/04/2020] [Accepted: 12/04/2020] [Indexed: 01/06/2023]
Abstract
DNA methylation profiles of aggressive behavior may capture lifetime cumulative effects of genetic, stochastic, and environmental influences associated with aggression. Here, we report the first large meta-analysis of epigenome-wide association studies (EWAS) of aggressive behavior (N = 15,324 participants). In peripheral blood samples of 14,434 participants from 18 cohorts with mean ages ranging from 7 to 68 years, 13 methylation sites were significantly associated with aggression (alpha = 1.2 × 10-7; Bonferroni correction). In cord blood samples of 2425 children from five cohorts with aggression assessed at mean ages ranging from 4 to 7 years, 83% of these sites showed the same direction of association with childhood aggression (r = 0.74, p = 0.006) but no epigenome-wide significant sites were found. Top-sites (48 at a false discovery rate of 5% in the peripheral blood meta-analysis or in a combined meta-analysis of peripheral blood and cord blood) have been associated with chemical exposures, smoking, cognition, metabolic traits, and genetic variation (mQTLs). Three genes whose expression levels were associated with top-sites were previously linked to schizophrenia and general risk tolerance. At six CpGs, DNA methylation variation in blood mirrors variation in the brain. On average 44% (range = 3-82%) of the aggression-methylation association was explained by current and former smoking and BMI. These findings point at loci that are sensitive to chemical exposures with potential implications for neuronal functions. We hope these results to be a starting point for studies leading to applications as peripheral biomarkers and to reveal causal relationships with aggression and related traits.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Matthew Suderman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Peter J Roetman
- Curium-LUMC, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Oegstgeest, The Netherlands
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Khadeeja Ismail
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Rosa H Mulder
- Institute of Education and Child Studies, Leiden University, Leiden, The Netherlands
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jari Lahti
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland
- Department of Psychology and logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Leanne K Küpers
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Georgia Escaramis
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Department of Biomedical Science, Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain
- Research Group on Statistics, Econometrics and Health (GRECS), UdG, Girona, Spain
| | - Silvia Alemany
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Mandy Meijer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Hill F Ip
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rick Jansen
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Bart M L Baselmans
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Priyanka Parmar
- Center for Life Course Health Research, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
| | - Estelle Lowry
- Center for Life Course Health Research, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Queen's University Belfast, Belfast, UK
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Lea Sirignano
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Tabea S Send
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Juulia Jylhävä
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yunzhang Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Pashupati Prasad Mishra
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Olivier F Colins
- Curium-LUMC, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Oegstgeest, The Netherlands
- Department of Special Needs Education, Ghent University, Ghent, Belgium
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Tellervo Korhonen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Eero Vuoksimaa
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Janine F Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Elisabeth Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, 12 Executive Park Dr, Atlanta, GA, 30329, USA
| | - Eva Corpeleijn
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Juan R Gonzalez
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Regina Grazuleviciene
- Department of Environmental Sciences, Vytautas Magnus University, K. Donelaicio str. 58, 44248, Kaunas, Lithuania
| | - Kristine B Gutzkow
- Department of Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jorunn Evandt
- Department of Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Marina Vafeiadi
- Department of Social Medicine, University of Crete, Heraklion, Greece
| | - Marieke Klein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- University Medical Center Utrecht, UMC Utrecht Brain Center, Department of Psychiatry, Utrecht, The Netherlands
| | - Dennis van der Meer
- NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Lannie Ligthart
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Gareth E Davies
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD, 57108, USA
| | - Christian Hakulinen
- Department of Psychology and logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Barbara Franke
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department of Psychiatry, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Kerstin Konrad
- University Hospital, RWTH Aachen, Child Neuropsychology Section, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Aachen, Germany
- JARA-Brain Institute II, Molecular Neuroscience and Neuroimaging (INM-11), RWTH Aachen & Research Centre Juelich, Juelich, Germany
| | - Amaia Hervas
- Hospital Universitario Mutua de Terrassa, Child and Adolescent Mental Health Service, Barcelona, Spain
| | | | - Agnes Vetro
- Szeged University, Department of Pediatrics and Pediatrics health center, Child and Adolescent Psychiatry, Szeged, Hungary
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Robert Vermeiren
- Curium-LUMC, Department of Child and Adolescent Psychiatry, Leiden University Medical Center, Oegstgeest, The Netherlands
- Youz, Parnassia Group, The Hague, The Netherlands
| | - Timo Strandberg
- Helsinki University Central Hospital, Geriatrics, Helsinki, Finland
| | - Katri Räikkönen
- Department of Psychology and logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Michael Deuschle
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jordi Sunyer
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Social and Behavioral Science, Harvard TH Chan School of Public Health, Boston, USA
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, The Netherlands
- Department of Clinical, Educational and Health Psychology, UCL, University of London, London, UK
| | - Caroline Relton
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Sylvain Sebert
- Center for Life Course Health Research, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Section of Genomics of Common Disease, Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, Du Cane Road, London, W12 0NN, UK
| | - Marjo-Riitta Jarvelin
- Center for Life Course Health Research, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, P.O. Box 5000, 90014, Oulu, Finland
- MRC-PHE Centre for Environment and Health, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, Du Cane Road, London, W12 0NN, UK
| | - Avshalom Caspi
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Meike Bartels
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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van Heukelum S, Tulva K, Geers FE, van Dulm S, Ruisch IH, Mill J, Viana JF, Beckmann CF, Buitelaar JK, Poelmans G, Glennon JC, Vogt BA, Havenith MN, França ASC. A central role for anterior cingulate cortex in the control of pathological aggression. Curr Biol 2021; 31:2321-2333.e5. [PMID: 33857429 DOI: 10.1016/j.cub.2021.03.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/17/2021] [Accepted: 03/18/2021] [Indexed: 12/31/2022]
Abstract
Controlling aggression is a crucial skill in social species like rodents and humans and has been associated with anterior cingulate cortex (ACC). Here, we directly link the failed regulation of aggression in BALB/cJ mice to ACC hypofunction. We first show that ACC in BALB/cJ mice is structurally degraded: neuron density is decreased, with pervasive neuron death and reactive astroglia. Gene-set enrichment analysis suggested that this process is driven by neuronal degeneration, which then triggers toxic astrogliosis. cFos expression across ACC indicated functional consequences: during aggressive encounters, ACC was engaged in control mice, but not BALB/cJ mice. Chemogenetically activating ACC during aggressive encounters drastically suppressed pathological aggression but left species-typical aggression intact. The network effects of our chemogenetic perturbation suggest that this behavioral rescue is mediated by suppression of amygdala and hypothalamus and activation of mediodorsal thalamus. Together, these findings highlight the central role of ACC in curbing pathological aggression.
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Affiliation(s)
- Sabrina van Heukelum
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands.
| | - Kerli Tulva
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
| | - Femke E Geers
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
| | - Sanne van Dulm
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
| | - I Hyun Ruisch
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joana F Viana
- The Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Edgbaston, Birmingham, UK
| | - Christian F Beckmann
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
| | - Jan K Buitelaar
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
| | - Geert Poelmans
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jeffrey C Glennon
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands; Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Brent A Vogt
- Cingulum Neurosciences Institute, Manlius, NY, USA; Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, USA
| | - Martha N Havenith
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands; Zero-Noise Lab, Ernst Strüngmann Institute for Neuroscience, 60528 Frankfurt a.M., Germany
| | - Arthur S C França
- Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hannon E, Mansell G, Walker E, Nabais MF, Burrage J, Kepa A, Best-Lane J, Rose A, Heck S, Moffitt TE, Caspi A, Arseneault L, Mill J. Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology. PLoS Genet 2021; 17:e1009443. [PMID: 33739972 PMCID: PMC8011804 DOI: 10.1371/journal.pgen.1009443] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 03/31/2021] [Accepted: 02/23/2021] [Indexed: 02/01/2023] Open
Abstract
Most epigenome-wide association studies (EWAS) quantify DNA methylation (DNAm) in peripheral tissues such as whole blood to identify positions in the genome where variation is statistically associated with a trait or exposure. As whole blood comprises a mix of cell types, it is unclear whether trait-associated DNAm variation is specific to an individual cellular population. We collected three peripheral tissues (whole blood, buccal epithelial and nasal epithelial cells) from thirty individuals. Whole blood samples were subsequently processed using fluorescence-activated cell sorting (FACS) to purify five constituent cell-types (monocytes, granulocytes, CD4+ T cells, CD8+ T cells, and B cells). DNAm was profiled in all eight sample-types from each individual using the Illumina EPIC array. We identified significant differences in both the level and variability of DNAm between different sample types, and DNAm data-derived estimates of age and smoking were found to differ dramatically across sample types from the same individual. We found that for the majority of loci variation in DNAm in individual blood cell types was only weakly predictive of variance in DNAm measured in whole blood, although the proportion of variance explained was greater than that explained by either buccal or nasal epithelial samples. Covariation across sample types was much higher for DNAm sites influenced by genetic factors. Overall, we observe that DNAm variation in whole blood is additively influenced by a combination of the major blood cell types. For a subset of sites, however, variable DNAm detected in whole blood can be attributed to variation in a single blood cell type providing potential mechanistic insight about EWAS findings. Our results suggest that associations between whole blood DNAm and traits or exposures reflect differences in multiple cell types and our data will facilitate the interpretation of findings in epigenetic epidemiology. As epigenetic variation is cell-type specific, an ongoing challenge in epigenetic epidemiology is how to interpret studies performed using bulk tissue (for example, whole blood) which comprises a mix of different cell types. In this study, we identified major differences in DNA methylation (DNAm) across multiple peripheral tissues and different blood cell types, with each sample type being characterized by a unique signature across multiple genomic loci. We demonstrate how these differences influence commonly used prediction scores derived from DNAm data for age and tobacco smoking, with estimates for the same individual being highly variable across tissues and cell types. Our results enabled us to assess the extent to which variable DNAm in each individual blood cell type relates to variation measured in whole blood. We found that although individual blood cell types predict more of the variation in DNAm in whole blood compared to buccal and nasal epithelial cells, the actual proportion of variance explained is relatively small, except for at sites where DNAm is under genetic control. Our data indicate that for most sites variation in multiple blood cell types additively combines to drive variation in DNAm measured in whole blood. Of note, for a subset of sites, variation in DNAm detected in whole blood can be attributed to a specific blood cell type, potentially facilitating the interpretation of EWAS findings.
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Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Georgina Mansell
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Emma Walker
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Marta F Nabais
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Agnieszka Kepa
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Janis Best-Lane
- Section of Anaesthetics, Pain Medicine and Intensive Care Medicine, Department of Surgery and Cancer, Imperial College London and Imperial College Healthcare NHS Trust, London, United Kingdom
- Imperial Clinical Trials Unit, Imperial College London, London, United Kingdom
| | - Anna Rose
- BRC Flow Cytometry Platform, NIHR GSTT/KCL Comprehensive Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Suzanne Heck
- Biomedical Research Centre at Guy's and St Thomas' Hospitals and King's College London, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Terrie E Moffitt
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Psychology and Neuroscience, Duke University, Durham, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, United States of America
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, United States of America
| | - Avshalom Caspi
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
- Department of Psychology and Neuroscience, Duke University, Durham, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, United States of America
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, United States of America
| | - Louise Arseneault
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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47
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Shireby GL, Davies JP, Francis PT, Burrage J, Walker EM, Neilson GWA, Dahir A, Thomas AJ, Love S, Smith RG, Lunnon K, Kumari M, Schalkwyk LC, Morgan K, Brookes K, Hannon E, Mill J. Recalibrating the epigenetic clock: implications for assessing biological age in the human cortex. Brain 2021; 143:3763-3775. [PMID: 33300551 PMCID: PMC7805794 DOI: 10.1093/brain/awaa334] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
Human DNA methylation data have been used to develop biomarkers of ageing, referred to as ‘epigenetic clocks’, which have been widely used to identify differences between chronological age and biological age in health and disease including neurodegeneration, dementia and other brain phenotypes. Existing DNA methylation clocks have been shown to be highly accurate in blood but are less precise when used in older samples or in tissue types not included in training the model, including brain. We aimed to develop a novel epigenetic clock that performs optimally in human cortex tissue and has the potential to identify phenotypes associated with biological ageing in the brain. We generated an extensive dataset of human cortex DNA methylation data spanning the life course (n = 1397, ages = 1 to 108 years). This dataset was split into ‘training’ and ‘testing’ samples (training: n = 1047; testing: n = 350). DNA methylation age estimators were derived using a transformed version of chronological age on DNA methylation at specific sites using elastic net regression, a supervised machine learning method. The cortical clock was subsequently validated in a novel independent human cortex dataset (n = 1221, ages = 41 to 104 years) and tested for specificity in a large whole blood dataset (n = 1175, ages = 28 to 98 years). We identified a set of 347 DNA methylation sites that, in combination, optimally predict age in the human cortex. The sum of DNA methylation levels at these sites weighted by their regression coefficients provide the cortical DNA methylation clock age estimate. The novel clock dramatically outperformed previously reported clocks in additional cortical datasets. Our findings suggest that previous associations between predicted DNA methylation age and neurodegenerative phenotypes might represent false positives resulting from clocks not robustly calibrated to the tissue being tested and for phenotypes that become manifest in older ages. The age distribution and tissue type of samples included in training datasets need to be considered when building and applying epigenetic clock algorithms to human epidemiological or disease cohorts.
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Affiliation(s)
- Gemma L Shireby
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan P Davies
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Paul T Francis
- University of Exeter Medical School, University of Exeter, Exeter, UK.,Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma M Walker
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Grant W A Neilson
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Aisha Dahir
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Alan J Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Seth Love
- Dementia Research Group, Institute of Clinical Neurosciences, School of Clinical Sciences, University of Bristol, Bristol, UK
| | - Rebecca G Smith
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Keeley Brookes
- School of Science and Technology, Nottingham Trent University, Nottingham, 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
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48
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Smith AR, Smith RG, Macdonald R, Marzi SJ, Burrage J, Troakes C, Al-Sarraj S, Mill J, Lunnon K. The histone modification H3K4me3 is altered at the ANK1 locus in Alzheimer's disease brain. Future Sci OA 2021; 7:FSO665. [PMID: 33815817 PMCID: PMC8015672 DOI: 10.2144/fsoa-2020-0161] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/04/2020] [Indexed: 01/24/2023] Open
Abstract
Several epigenome-wide association studies of DNA methylation have highlighted altered DNA methylation in the ANK1 gene in Alzheimer's disease (AD) brain samples. However, no study has specifically examined ANK1 histone modifications in the disease. We use chromatin immunoprecipitation-qPCR to quantify tri-methylation at histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) in the ANK1 gene in entorhinal cortex from donors with high (n = 59) or low (n = 29) Alzheimer's disease pathology. We demonstrate decreased levels of H3K4me3, a marker of active gene transcription, with no change in H3K27me3, a marker of inactive genes. H3K4me3 is negatively correlated with DNA methylation in specific regions of the ANK1 gene. Our study suggests that the ANK1 gene shows altered epigenetic marks indicative of reduced gene activation in Alzheimer's disease.
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Affiliation(s)
- Adam R Smith
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Rebecca G Smith
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Ruby Macdonald
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Sarah J Marzi
- The Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Claire Troakes
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Safa Al-Sarraj
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
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Morales Ferez X, Mill J, Delso G, Sitges M, Doltra A, Loncaric F, Camara O, Bijnens B. 4D flow magnetic resonance imaging to assess left atrial haemodynamics in healthy and hypertrophic subjects. Eur Heart J Cardiovasc Imaging 2021. [DOI: 10.1093/ehjci/jeaa356.288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): - University, research centre and hospital foundation grants for the contracting of new research staff (FI 2020) - Spanish Ministry of Economy and Competitiveness Retos investigacion project
Introduction
The assessment of the left atrium (LA) haemodynamics is key to better understand the development of LA-related pathological processes. In this regard 4D flow magnetic resonance imaging (MRI) can provide complementary information to standard Doppler echocardiographic studies and identify complex blood flow patterns. Yet, until recently, the left atrium (LA) has been largely left aside in 4D flow MRI studies.
Purpose
We aimed at assessing the LA haemodynamics of healthy and hypertrophic cardiomyopathy (HCM) subjects with a qualitative visualization of flow patterns and deriving quantitative indices related to ventricular dysfunction from pulmonary veins (PV) and mitral valve (MV) velocity profiles.
Methods
Segmentation was performed directly over 4D flow angiograms. A total of 20 cases were processed, 11 healthy and 9 HCM subjects. 4D velocity matrices were masked with the segmented mask to isolate LA haemodynamics. Velocity profiles were then obtained in the PV and MV and integrated over planes perpendicular to the lumen of the vessels to create velocity spectrograms. Fourier spectral analysis was applied to the velocity curves to highlight differences that might go unnoticed in the time domain. In addition, the Q-Criterion was computed for vortex identification, visually inspecting both cohorts across the whole cardiac cycle.
Results
Fourier spectral analysis of the velocity curves suggested that overall, healthy patients have higher dynamic range of the velocity curves. It can be observed in Figure 1, that the usual E/A MV velocity pattern is preserved in 10 of the 11 healthy subjects while 5 of the HCM patients present significant alterations of said curve. In fact, patients 4, 6, 7 and 8 seem to present a 3 peaked MV velocity curve. The vortex analysis identified 3 main types of vortices in healthy subjects: a ‘filling’ systolic vortex (10/11) arising near the most dominant PV (usually the left superior PV) as seen in Figure 2; a conduit phase vortex (7/11), similar in nature to the preceding systolic vortex; and an E-wave vortex (9/11) attached to the LA ostium. Four of the HCM patients (out of the five with altered MV velocity profile) also showed a systolic vortex, but with more complex blood flow patterns and emerging far from the PVs. One of such vortices is shown in Figure 2, composed of two distinct eddies near the MV. The E-wave vortex was also observed but was less predominant than in healthy subjects (3/9).
Conclusions
4D Flow analysis of the LA is feasible and might hold promise in the understanding of the complex haemodynamics in ventricular dysfunction.
Abstract Figure. Velocity Spectrograms and Vortices
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Affiliation(s)
- X Morales Ferez
- University Pompeu Fabra, Physense, BCN Medtech, Department of Information and Communications Technologies, Barcelona, Spain
| | - J Mill
- University Pompeu Fabra, Physense, BCN Medtech, Department of Information and Communications Technologies, Barcelona, Spain
| | - G Delso
- GE Healthcare Spain, Barcelona, Spain
| | - M Sitges
- Cardiovascular Institute, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain, Institut d"investigacions biomèdiques august pi i sunyer (IDIBAPS), Barcelona, Spain
| | - A Doltra
- Cardiovascular Institute, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain, Institut d"investigacions biomèdiques august pi i sunyer (IDIBAPS), Barcelona, Spain
| | - F Loncaric
- Cardiovascular Institute, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain, Institut d"investigacions biomèdiques august pi i sunyer (IDIBAPS), Barcelona, Spain
| | - O Camara
- University Pompeu Fabra, Physense, BCN Medtech, Department of Information and Communications Technologies, Barcelona, Spain
| | - B Bijnens
- Institut d"investigacions biomèdiques august pi i sunyer (IDIBAPS), Barcelona, Spain, La Institució Catalana de Recerca i Estudis Avançats, (ICREA), Barcelona, Spain
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