1
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Fernández-Pérez I, Jiménez-Balado J, Macias-Gómez A, Suárez-Pérez A, Vallverdú-Prats M, Pérez-Giraldo A, Viles-García M, Peris-Subiza J, Vidal-Notari S, Giralt-Steinhauer E, Guisado-Alonso D, Esteller M, Rodriguez-Campello A, Jiménez-Conde J, Ois A, Cuadrado-Godia E. Blood DNA Methylation Analysis Reveals a Distinctive Epigenetic Signature of Vasospasm in Aneurysmal Subarachnoid Hemorrhage. Transl Stroke Res 2025; 16:715-727. [PMID: 38649590 DOI: 10.1007/s12975-024-01252-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/28/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
Vasospasm is a potentially preventable cause of poor prognosis in patients with aneurysmal subarachnoid hemorrhage (aSAH). Epigenetics might provide insight on its molecular mechanisms. We aimed to analyze the association between differential DNA methylation (DNAm) and development of vasospasm. We conducted an epigenome-wide association study in 282 patients with aSAH admitted to our hospital. DNAm was assessed with the EPIC Illumina chip (> 850 K CpG sites) in whole-blood samples collected at hospital admission. We identified differentially methylated positions (DMPs) at the CpG level using Cox regression models adjusted for potential confounders, and then we used the DMP results to find differentially methylated regions (DMRs) and enriched biological pathways. A total of 145 patients (51%) experienced vasospasm. In the DMP analysis, we identified 31 CpGs associated with vasospasm at p-value < 10-5. One of them (cg26189827) was significant at the genome-wide level (p-value < 10-8), being hypermethylated in patients with vasospasm and annotated to SUGCT gene, mainly expressed in arteries. Region analysis revealed 13 DMRs, some of them annotated to interesting genes such as POU5F1, HLA-DPA1, RUFY1, and CYP1A1. Functional enrichment analysis showed the involvement of biological processes related to immunity, inflammatory response, oxidative stress, endothelial nitric oxide, and apoptosis. Our findings show, for the first time, a distinctive epigenetic signature of vasospasm in aSAH, establishing novel links with essential biological pathways, including inflammation, immune responses, and oxidative stress. Although further validation is required, our results provide a foundation for future research into the complex pathophysiology of vasospasm.
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Affiliation(s)
- Isabel Fernández-Pérez
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Joan Jiménez-Balado
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain.
| | - Adrià Macias-Gómez
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Antoni Suárez-Pérez
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Marta Vallverdú-Prats
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | | | - Marc Viles-García
- Neuroradiology Department, Hospital del Mar, Barcelona, Catalunya, Spain
| | | | | | - Eva Giralt-Steinhauer
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Daniel Guisado-Alonso
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Research Institute Against Leukemia Josep Carreras, Badalona, Catalunya, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalunya, Spain
| | - Ana Rodriguez-Campello
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Jordi Jiménez-Conde
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Angel Ois
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
| | - Elisa Cuadrado-Godia
- Neurology Department, Hospital del Mar, Barcelona, Catalunya, Spain
- Neurovascular Research Group, Hospital del Mar Medical Research Institute, C/Dr. Aiguader, 88, 08003, Barcelona, Catalunya, Spain
- Pompeu Fabra University, Barcelona, Catalunya, Spain
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2
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Pagano L, Lagrotteria D, Facconi A, Saraceno C, Longobardi A, Bellini S, Ingannato A, Bagnoli S, Ducci T, Mingrino A, Laganà V, Paparazzo E, Borroni B, Maletta R, Nacmias B, Montesanto A, Ghidoni R. Evaluation of Illumina and Oxford Nanopore Sequencing for the Study of DNA Methylation in Alzheimer's Disease and Frontotemporal Dementia. Int J Mol Sci 2025; 26:4198. [PMID: 40362435 PMCID: PMC12071509 DOI: 10.3390/ijms26094198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 04/24/2025] [Accepted: 04/25/2025] [Indexed: 05/15/2025] Open
Abstract
DNA methylation is a critical epigenetic mechanism involved in numerous physiological processes. Alterations in DNA methylation patterns are associated with various brain disorders, including dementias such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). Investigating these alterations is essential for understanding the pathogenesis and progression of these disorders. Among the various methods for detecting DNA methylation, DNA sequencing is one of the most widely employed. Specifically, two main sequencing approaches are commonly used for DNA methylation analysis: bisulfite sequencing and single-molecule long-read sequencing. In this review, we compared the performances of CpG methylation detection obtained using two popular sequencing platforms, Illumina for bisulfite sequencing and Oxford Nanopore (ON) for long-read sequencing. Our comparison considers several factors, including accuracy, efficiency, genomic regions, costs, wet-lab protocols, and bioinformatics pipelines. We provide insights into the strengths and limitations of both methods with a particular focus on their application in research on AD and FTD.
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Affiliation(s)
- Lorenzo Pagano
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (L.P.); (A.F.); (C.S.); (A.L.); (S.B.); (B.B.)
| | - Davide Lagrotteria
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (D.L.); (E.P.); (A.M.)
| | - Alessandro Facconi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (L.P.); (A.F.); (C.S.); (A.L.); (S.B.); (B.B.)
| | - Claudia Saraceno
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (L.P.); (A.F.); (C.S.); (A.L.); (S.B.); (B.B.)
| | - Antonio Longobardi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (L.P.); (A.F.); (C.S.); (A.L.); (S.B.); (B.B.)
| | - Sonia Bellini
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (L.P.); (A.F.); (C.S.); (A.L.); (S.B.); (B.B.)
| | - Assunta Ingannato
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, 50139 Florence, Italy; (A.I.); (S.B.); (B.N.)
- IRCCS Fondazione Don Carlo Gnocchi, 50143 Florence, Italy
| | - Silvia Bagnoli
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, 50139 Florence, Italy; (A.I.); (S.B.); (B.N.)
- IRCCS Fondazione Don Carlo Gnocchi, 50143 Florence, Italy
| | - Tommaso Ducci
- Azienda Ospedaliero-Universitaria Careggi SOD Neurologia 1, 50100 Florence, Italy; (T.D.); (A.M.)
| | - Alessandra Mingrino
- Azienda Ospedaliero-Universitaria Careggi SOD Neurologia 1, 50100 Florence, Italy; (T.D.); (A.M.)
| | - Valentina Laganà
- Regional Neurogenetic Centre (CRN), Department of Primary Care, ASP Catanzaro, 88046 Lamezia Terme, Italy; (V.L.); (R.M.)
| | - Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (D.L.); (E.P.); (A.M.)
| | - Barbara Borroni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (L.P.); (A.F.); (C.S.); (A.L.); (S.B.); (B.B.)
- Department of Clinical and Experimental Sciences, University of Brescia, 25123 Brescia, Italy
| | - Raffaele Maletta
- Regional Neurogenetic Centre (CRN), Department of Primary Care, ASP Catanzaro, 88046 Lamezia Terme, Italy; (V.L.); (R.M.)
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, 50139 Florence, Italy; (A.I.); (S.B.); (B.N.)
- IRCCS Fondazione Don Carlo Gnocchi, 50143 Florence, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy; (D.L.); (E.P.); (A.M.)
| | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy; (L.P.); (A.F.); (C.S.); (A.L.); (S.B.); (B.B.)
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3
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Pathak GA, Pietrzak RH, Lacobelle A, Overstreet C, Wendt FR, Deak JD, Friligkou E, Nunez YZ, Montalvo-Ortiz JL, Levey DF, Kranzler HR, Gelernter J, Polimanti R. Epigenetic and genetic profiling of comorbidity patterns among substance dependence diagnoses. Mol Psychiatry 2025:10.1038/s41380-025-03031-y. [PMID: 40247127 DOI: 10.1038/s41380-025-03031-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 04/08/2025] [Accepted: 04/10/2025] [Indexed: 04/19/2025]
Abstract
This study investigated the genetic and epigenetic mechanisms underlying the comorbidity of five substance dependence diagnoses (SDs; alcohol, AD; cannabis, CaD; cocaine, CoD; opioid, OD; tobacco, TD). A latent class analysis (LCA) was performed on 22,668 individuals from six cohorts to identify comorbid DSM-IV SD patterns. In subsets of this sample, we tested SD-latent classes with respect to polygenic overlap of psychiatric and psychosocial traits in 7659 individuals of European descent and epigenome-wide changes in 886 individuals of African, European, and Admixed-American descents. The LCA identified four latent classes related to SD comorbidities: AD + TD, CoD + TD, AD + CoD + OD + TD (i.e., polysubstance addiction, PSU), and TD. In the epigenome-wide association analysis, SPATA4 cg02833127 was associated with CoD + TD, AD + TD, and PSU latent classes. AD + TD latent class was also associated with CpG sites located on ARID1B, NOTCH1, SERTAD4, and SIN3B, while additional epigenome-wide significant associations with CoD + TD latent class were observed in ANO6 and MOV10 genes. PSU-latent class was also associated with a differentially methylated region in LDB1. We also observed shared polygenic score (PGS) associations for PSU, AD + TD, and CoD + TD latent classes (i.e., attention-deficit hyperactivity disorder, anxiety, educational attainment, and schizophrenia PGS). In contrast, TD-latent class was exclusively associated with posttraumatic stress disorder-PGS. Other specific associations were observed for PSU-latent class (subjective wellbeing-PGS and neuroticism-PGS) and AD + TD-latent class (bipolar disorder-PGS). In conclusion, we identified shared and unique genetic and epigenetic mechanisms underlying SD comorbidity patterns. These findings highlight the importance of modeling the co-occurrence of SD diagnoses when investigating the molecular basis of addiction-related traits.
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Affiliation(s)
- Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Robert H Pietrzak
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
- Department of Social and Behavioral Sciences, Yale School of Public Health, New Haven, CT, USA
| | - AnnMarie Lacobelle
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Cassie Overstreet
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Frank R Wendt
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Joseph D Deak
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Eleni Friligkou
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Yaira Z Nunez
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Janitza L Montalvo-Ortiz
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Daniel F Levey
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Henry R Kranzler
- Center for Studies of Addiction, University of Pennsylvania Perelman School of Medicine and the Mental Illness Research, Education and Clinical Center, Crescenz VAMC, Philadelphia, PA, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
- U.S Department of Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA.
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4
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Liu H, Xie Y, Ji Y, Zhou Y, Xu J, Tang J, Liu N, Ding H, Qin W, Liu F, Yu C. Identification of genetic architecture shared between schizophrenia and Alzheimer's disease. Transl Psychiatry 2025; 15:150. [PMID: 40240757 PMCID: PMC12003746 DOI: 10.1038/s41398-025-03348-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 03/15/2025] [Accepted: 03/24/2025] [Indexed: 04/18/2025] Open
Abstract
Both schizophrenia (SCZ) and Alzheimer's disease (AD) are highly heritable brain disorders. Despite of the observed comorbidity and shared psychosis and cognitive decline between the two disorders, the genetic risk architecture shared by SCZ and AD remains largely unknown. Based on summary statistics of the currently available largest genome-wide association studies for SCZ (n = 130,644) and AD (n = 455,258) in individuals of European ancestry, we conducted conditional/conjunctional false discovery rate (FDR) analysis to enhance the statistical power for discovering more genetic associations with SCZ or AD and to detect the common genetic variants shared by both disorders. We found shared genetic architecture in SCZ conditioned on AD and vice versa across different levels of significance, indicating polygenic overlap. We found 268 (78 novel) SCZ-only and 125 (55 novel) AD-only SNPs at conditional FDR < 0.01, and 16 lead SNPs shared by SCZ and AD at conjunctional FDR < 0.05. Only half of the shared SNPs showed concordant effect direction, which was consistent with the modest genetic correlation (r = 0.097; P = 0.026) between the two disorders. This study provides evidence for polygenic overlap between SCZ and AD, suggesting the existence of the shared molecular genetic mechanisms, which may inform therapeutic targets that are applicable for both disorders.
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Affiliation(s)
- Huaigui Liu
- Department of Radiology, Tianjin Key Lab of Functional Imaging & Tianjin Institute of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yingying Xie
- Department of Radiology, Tianjin Key Lab of Functional Imaging & Tianjin Institute of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuan Ji
- Department of Radiology, Tianjin Key Lab of Functional Imaging & Tianjin Institute of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yujing Zhou
- Department of Radiology, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jiayuan Xu
- Department of Radiology, Tianjin Key Lab of Functional Imaging & Tianjin Institute of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Jie Tang
- Department of Radiology, Tianjin Key Lab of Functional Imaging & Tianjin Institute of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Nana Liu
- Department of Radiology, Tianjin Key Lab of Functional Imaging & Tianjin Institute of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Hao Ding
- School of Medical Imaging, Tianjin Medical University, Tianjin, China
| | - Wen Qin
- Department of Radiology, Tianjin Key Lab of Functional Imaging & Tianjin Institute of Radiology, Tianjin Medical University General Hospital, Tianjin, China.
| | - Feng Liu
- Department of Radiology, Tianjin Key Lab of Functional Imaging & Tianjin Institute of Radiology, Tianjin Medical University General Hospital, Tianjin, China.
| | - Chunshui Yu
- Department of Radiology, Tianjin Key Lab of Functional Imaging & Tianjin Institute of Radiology, Tianjin Medical University General Hospital, Tianjin, China.
- State Key Laboratory of Experimental Hematology, Tianjin, China.
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5
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Macías M, Alba-Linares JJ, Acha B, Blanco-Luquin I, Fernández AF, Álvarez-Jiménez J, Urdánoz-Casado A, Roldan M, Robles M, Cabezon-Arteta E, Alcolea D, de Gordoa JSR, Corroza J, Cabello C, Erro ME, Jericó I, Fraga MF, Mendioroz M. Advancing Personalized Medicine in Alzheimer's Disease: Liquid Biopsy Epigenomics Unveil APOE ε4-Linked Methylation Signatures. Int J Mol Sci 2025; 26:3419. [PMID: 40244264 PMCID: PMC11989983 DOI: 10.3390/ijms26073419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Revised: 03/31/2025] [Accepted: 04/03/2025] [Indexed: 04/18/2025] Open
Abstract
Recent studies show that patients with Alzheimer's disease (AD) harbor specific methylation marks in the brain that, if accessible, could be used as epigenetic biomarkers. Liquid biopsy enables the study of circulating cell-free DNA (cfDNA) fragments originated from dead cells, including neurons affected by neurodegenerative processes. Here, we isolated and epigenetically characterized plasma cfDNA from 35 patients with AD and 35 cognitively healthy controls by using the Infinium® MethylationEPIC BeadChip array. Bioinformatics analysis was performed to identify differential methylation positions (DMPs) and regions (DMRs), including APOE ε4 genotype stratified analysis. Plasma pTau181 (Simoa) and cerebrospinal fluid (CSF) core biomarkers (Fujirebio) were also measured and correlated with differential methylation marks. Validation was performed with bisulfite pyrosequencing and bisulfite cloning sequencing. Epigenome-wide cfDNA analysis identified 102 DMPs associated with AD status. Most DMPs correlated with clinical cognitive and functional tests including 60% for Mini-Mental State Examination (MMSE) and 80% for Global Deterioration Scale (GDS), and with AD blood and CSF biomarkers. In silico functional analysis connected 30 DMPs to neurological processes, identifying key regulators such as SPTBN4 and APOE genes. Several DMRs were annotated to genes previously reported to harbor epigenetic brain changes in AD (HKR1, ZNF154, HOXA5, TRIM40, ATG16L2, ADAMST2) and were linked to APOE ε4 genotypes. Notably, a DMR in the HKR1 gene, previously shown to be hypermethylated in the AD hippocampus, was validated in cfDNA from an orthogonal perspective. These results support the feasibility of studying cfDNA to identify potential epigenetic biomarkers in AD. Thus, liquid biopsy could improve non-invasive AD diagnosis and aid personalized medicine by detecting epigenetic brain markers in blood.
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Affiliation(s)
- Mónica Macías
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Juan José Alba-Linares
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN CSIC), 33940 El Entrego, Spain
- Health Research Institute of Asturias (ISPA FINBA), University of Oviedo, 33011 Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
- Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), 28029 Madrid, Spain
| | - Blanca Acha
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Idoia Blanco-Luquin
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Agustín F. Fernández
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN CSIC), 33940 El Entrego, Spain
- Health Research Institute of Asturias (ISPA FINBA), University of Oviedo, 33011 Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
- Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), 28029 Madrid, Spain
| | - Johana Álvarez-Jiménez
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Amaya Urdánoz-Casado
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Miren Roldan
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Maitane Robles
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Eneko Cabezon-Arteta
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Daniel Alcolea
- Department of Neurology, Institut d’Investigacions Biomèdiques Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas, CIBERNED, 28029 Madrid, Spain
| | - Javier Sánchez Ruiz de Gordoa
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Neurology Department, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Jon Corroza
- Neurology Department, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Carolina Cabello
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Neurology Department, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - María Elena Erro
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Neurology Department, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Ivonne Jericó
- Neurology Department, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Mario F. Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Nanomaterials and Nanotechnology Research Center (CINN CSIC), 33940 El Entrego, Spain
- Health Research Institute of Asturias (ISPA FINBA), University of Oviedo, 33011 Oviedo, Spain
- Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
- Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII), 28029 Madrid, Spain
- Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, 33006 Oviedo, Spain
| | - Maite Mendioroz
- Neuroepigenetics Unit, Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Neurology Department, Hospital Universitario de Navarra, Universidad Pública de Navarra, Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
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6
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Wei M, Chang R, Li C, Jiang Y, Zhang J. Caregiver-child interaction and early childhood development among preschool children in rural China: the possible role of blood epigenome-wide DNA methylation. BMC Genomics 2025; 26:329. [PMID: 40170191 PMCID: PMC11963332 DOI: 10.1186/s12864-025-11406-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 02/25/2025] [Indexed: 04/03/2025] Open
Abstract
BACKGROUND While the association between caregiver-child interaction and early childhood development (ECD) has been observed, the underlying biological mechanism remains to be elucidated. OBJECTIVE This study aimed to examine the potential role of epigenome-wide DNA methylation in the association between caregiver-child interaction and ECD among preschool children living in rural China. METHODS This study was conducted in a rural area in Central China. ECD was evaluated with the Gesell Development Diagnosis Scale (Chinese version), yielding a developmental quotient (DQ), i.e. global neurodevelopmental score (NDS). Caregiver-child interaction was assessed using the Brigance Parent-Child Interaction Scale. Of the 171 children aged 3-6 years who participated in ECD assessment and blood samples collection, a total of 64 were selected for epigenome-wide association study with Illumina Infinium MethylationEPIC v1.0 BeadChip array (850 K). The linear regression model in the R package "CpGassoc"was applied to identify CpG sites associated with global NDS and caregiver-child interaction. The causal inference test (CIT) was utilized to explore the potential mediation effect of DNA methylation. RESULTS Our epigenome-wide DNA methylation analysis revealed 844 CpG sites significantly associated with children's global NDS (PFDR<0.05), while no CpG sites were found to be directly related to caregiver-child interaction after FDR correction. Mediation analysis indicated that 395 CpG sites mediated the association between caregiver-child interaction and children's ECD before FDR correction; and among the genes with top 20 CpG sites, genes CFAP45 (cg07740897), PCDH9 (cg20666533), LAMC3 (cg14447608), FAM19A5 (cg13192640), PRKG1 (cg09071556), PLEKHG5 (cg05151739), TCERG1 (cg09189322), and MTRR (cg08075506) have been reported to be associated with neurodevelopment and related diseases. CONCLUSIONS Blood DNA methylation may mediate the association between caregiver-child interaction and ECD in preschool children. This provides population-level epigenetic evidence supporting parenting interventions for vulnerable preschool children who experience poor caregiver-child interaction, aiming to ensure optimal early development potential. However, future studies in diverse populations are needed to validate these findings.
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Affiliation(s)
- Mengna Wei
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rui Chang
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Division of Child Healthcare, Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chunan Li
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yanfen Jiang
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jianduan Zhang
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Hubei, 430030, Wuhan, China.
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7
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Laroche VT, Cavill R, Kouhsar M, Reijnders RA, Harvey J, Smith AR, Imm J, Koetsier J, Weymouth L, MacBean L, Pegoraro G, Eijssen L, Creese B, Kenis G, Tijms BM, van den Hove D, Lunnon K, Pishva E. Epigenomic subtypes of late-onset Alzheimer's disease reveal distinct microglial signatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.15.643144. [PMID: 40166175 PMCID: PMC11957029 DOI: 10.1101/2025.03.15.643144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Growing evidence suggests that clinical, pathological, and genetic heterogeneity in late-onset Alzheimer's disease contributes to variable therapeutic outcomes, potentially explaining many trial failures. Advances in molecular subtyping through proteomic and transcriptomic profiling reveal distinct patient subgroups, highlighting disease complexity beyond amyloid-beta plaques and tau tangles. This insight underscores the need to expand molecular subtyping across new molecular layers, to identify novel drug targets for different patient subgroups. In this study, we analyzed genome-wide DNA methylation data from three independent postmortem brain cohorts (n = 831) to identify epigenetic subtypes of late-onset Alzheimer's disease. Unsupervised clustering approaches were employed to identify distinct DNA methylation patterns, with subsequent cross-cohort validation to ensure robustness and reproducibility. To explore the cell-type specificity of the identified epigenomic subtypes, we characterized their methylation signatures utilizing DNA methylation profiles derived from purified brain cells. Transcriptomic data from bulk and single-cell RNA sequencing were integrated to examine the functional impact of epigenetic subtypes on gene expression profiles. Finally, we performed statistical analyses to investigate associations between these DNA methylation-defined subtypes and clinical or neuropathological features, aiming to elucidate their biological significance and clinical implications. We identified two distinct epigenomic subtypes of late-onset Alzheimer's disease, each defined by reproducible DNA methylation patterns across three cohorts. Both subtypes exhibit cell-type-specific DNA methylation profiles. Subtype 1 and subtype 2 show significant microglial methylation enrichment, with odds ratios (OR) of 1.6 and 1.3, respectively. The minimal overlap between them suggests distinct microglial states. Additionally, subtype 2 displays strong neuronal (OR = 1.6) and oligodendrocyte (OR = 3.6) enrichment. Bulk transcriptomic analyses further highlighted divergent biological mechanisms underpinning these subtypes, with subtype 1 enriched for immune-related processes, and subtype 2 characterized predominantly by neuronal and synaptic functional pathways. Single-cell transcriptional profiling of microglia revealed subtype-specific inflammatory states: subtype 1 represented a state of chronic innate immune hyperactivation with impaired resolution, while subtype 2 exhibited a more dynamic inflammatory profile balancing pro-inflammatory signaling with reparative and regulatory mechanisms. This study highlights the molecular heterogeneity of late-onset Alzheimer's disease by identifying two epigenetic subtypes with distinct cell-type-specific DNA methylation patterns. Their alignment with previously defined molecular classifications underscores their relevance in disease pathogenesis. By linking these subtypes to inflammatory microglial activity, our findings provide a foundation for future precision medicine approaches in Alzheimer's research and treatment.
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Affiliation(s)
- Valentin T. Laroche
- Department of Psychiatry and Neuropsychology, Mental Health and Neuroscience Research Institute (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Rachel Cavill
- Department of Advanced Computing Sciences, Faculty of Science and Engineering (FSE), Maastricht University, Maastricht, The Netherlands
| | - Morteza Kouhsar
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Rick A. Reijnders
- Department of Psychiatry and Neuropsychology, Mental Health and Neuroscience Research Institute (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Joshua Harvey
- 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
| | - Jennifer Imm
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Jarno Koetsier
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Luke Weymouth
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Lachlan MacBean
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Giulia Pegoraro
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Lars Eijssen
- Department of Psychiatry and Neuropsychology, Mental Health and Neuroscience Research Institute (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Byron Creese
- Department of Life Sciences, Brunel University, London, UK
| | - Gunter Kenis
- Department of Psychiatry and Neuropsychology, Mental Health and Neuroscience Research Institute (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Betty M. Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
| | - Daniel van den Hove
- Department of Psychiatry and Neuropsychology, Mental Health and Neuroscience Research Institute (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, Mental Health and Neuroscience Research Institute (MHeNs), Maastricht University, Maastricht, The Netherlands
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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Ramirez P, Sun W, Dehkordi SK, Zare H, Pascarella G, Carninci P, Fongang B, Bieniek KF, Frost B. Nanopore Long-Read Sequencing Unveils Genomic Disruptions in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.02.01.578450. [PMID: 38370753 PMCID: PMC10871260 DOI: 10.1101/2024.02.01.578450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Studies in laboratory models and postmortem human brain tissue from patients with Alzheimer's disease have revealed disruption of basic cellular processes such as DNA repair and epigenetic control as drivers of neurodegeneration. While genomic alterations in regions of the genome that are rich in repetitive sequences, often termed "dark regions," are difficult to resolve using traditional sequencing approaches, long-read technologies offer promising new avenues to explore previously inaccessible regions of the genome. In the current study, we leverage nanopore-based long-read whole-genome sequencing of DNA extracted from postmortem human frontal cortex at early and late stages of Alzheimer's disease, as well as age-matched controls, to analyze retrotransposon insertion events, non-allelic homologous recombination (NAHR), structural variants and DNA methylation within retrotransposon loci and other repetitive/dark regions of the human genome. Interestingly, we find that retrotransposon insertion events and repetitive element-associated NAHR are particularly enriched within centromeric and pericentromeric regions of DNA in the aged human brain, and that ribosomal DNA (rDNA) is subject to a high degree of NAHR compared to other regions of the genome. We detect a trending increase in potential somatic retrotransposition events of the small interfering nuclear element (SINE) AluY in late-stage Alzheimer's disease, and differential changes in methylation within repetitive elements and retrotransposons according to disease stage. Taken together, our analysis provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, NAHR, structural variants, and DNA methylation in the aged brain, and points toward transposable elements, centromeric/pericentromeric regions and rDNA as hotspots for genomic variation.
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Affiliation(s)
- Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
- Brown University, Providence, Rhode Island
| | - Wenyan Sun
- Barshop Institute for Longevity and Aging Studies
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
- Clinical Neuroscience Research Center, Department of Neurosurgery, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Shiva Kazempour Dehkordi
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | | | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Kevin F. Bieniek
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases
- Department of Pathology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
- Brown University, Providence, Rhode Island
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Kunkle BW, Chen XS, Martin ER, Wang L. Blood DNA methylation signature for incident dementia: Evidence from longitudinal cohorts. Alzheimers Dement 2025; 21:e14496. [PMID: 40133250 PMCID: PMC11936765 DOI: 10.1002/alz.14496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 11/26/2024] [Accepted: 12/01/2024] [Indexed: 03/27/2025]
Abstract
INTRODUCTION Distinguishing between molecular changes that precede dementia onset and those resulting from the disease is challenging with cross-sectional studies. METHODS We studied blood DNA methylation (DNAm) differences and incident dementia in two large longitudinal cohorts: the Offspring cohort of the Framingham Heart Study (FHS) and the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. We analyzed blood DNAm samples from > 1000 cognitively unimpaired subjects. RESULTS Meta-analysis identified 44 CpGs and 44 differentially methylated regions consistently associated with time to dementia in both cohorts. Our integrative analysis identified early processes in dementia, such as immune responses and metabolic dysfunction. Furthermore, we developed a methylation-based risk score, which successfully predicted future cognitive decline in an independent validation set, even after accounting for age, sex, apolipoprotein E ε4, years of education, baseline diagnosis, and baseline Mini-Mental State Examination score. DISCUSSION DNAm offers a promising source as a biomarker for dementia risk assessment. HIGHLIGHTS Blood DNA methylation (DNAm) differences at individual CpGs and differentially methylated regions are significantly associated with incident dementia. Pathway analysis revealed DNAm differences associated with incident dementia are significantly enriched in biological pathways involved in immune responses and metabolic processes. Out-of-sample validation analysis demonstrated that a methylation-based risk score successfully predicted future cognitive decline in an independent dataset, even after accounting for age, sex, apolipoprotein E ε4, years of education, baseline diagnosis, and baseline Mini-Mental State Examination score.
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Affiliation(s)
- Wei Zhang
- Division of BiostatisticsDepartment of Public Health SciencesMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Juan I. Young
- Dr. John T. Macdonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Lissette Gomez
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Michael A. Schmidt
- Dr. John T. Macdonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - David Lukacsovich
- Division of BiostatisticsDepartment of Public Health SciencesMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Brian W. Kunkle
- Dr. John T. Macdonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - X. Steven Chen
- Division of BiostatisticsDepartment of Public Health SciencesMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- Sylvester Comprehensive Cancer CenterMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Eden R. Martin
- Dr. John T. Macdonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Lily Wang
- Division of BiostatisticsDepartment of Public Health SciencesMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- Dr. John T. Macdonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- Sylvester Comprehensive Cancer CenterMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
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10
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Davyson E, Shen X, Huider F, Adams MJ, Borges K, McCartney DL, Barker LF, van Dongen J, Boomsma DI, Weihs A, Grabe HJ, 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 ASF, Yousefi P, Wong CCY, Arseneault L, Fisher HL, Mill J, Cox SR, Redmond P, Russ TC, van den Oord EJCG, Aberg KA, Penninx BWJH, Marioni RE, Wray NR, McIntosh AM. Insights from a methylome-wide association study of antidepressant exposure. Nat Commun 2025; 16:1908. [PMID: 39994233 PMCID: PMC11850842 DOI: 10.1038/s41467-024-55356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 12/09/2024] [Indexed: 02/26/2025] Open
Abstract
This study tests the association of whole-blood DNA methylation and antidepressant exposure in 16,531 individuals from Generation Scotland (GS), using self-report and prescription-derived measures. We identify 8 associations and a high concordance of results between self-report and prescription-derived measures. Sex-stratified analyses observe nominally significant increased effect estimates in females for four CpGs. There is observed enrichment for genes expressed in the Amygdala and annotated to synaptic vesicle membrane ontology. Two CpGs (cg15071067; DGUOK-AS1 and cg26277237; KANK1) show correlation between DNA methylation with the time in treatment. There is a significant overlap in the top 1% of CpGs with another independent methylome-wide association study of antidepressant exposure. Finally, a methylation profile score trained on this sample shows a significant association with antidepressant exposure in a meta-analysis of eight independent external datasets. In this large investigation of antidepressant exposure and DNA methylation, we demonstrate robust associations which warrant further investigation to inform on the design of more effective and tolerated treatments for depression.
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Affiliation(s)
- E Davyson
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - X Shen
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - F Huider
- Complex Trait Genetics, Center of Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Biological Psychiatry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - M J Adams
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - K Borges
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - D L McCartney
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - L F Barker
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
| | - J van Dongen
- Complex Trait Genetics, Center of Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Department of Biological Psychiatry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, Research Institute, Amsterdam, The Netherlands
| | - D I Boomsma
- Complex Trait Genetics, Center of Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development, Research Institute, Amsterdam, The Netherlands
| | - A Weihs
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475, Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17489, Greifswald, Germany
| | - H J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475, Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, 17489, Greifswald, Germany
| | - L Kühn
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475, Greifswald, Germany
| | - A Teumer
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17489, Greifswald, Germany
| | - H Völzke
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, 17489, Greifswald, Germany
- Department SHIP/Clinical-Epidemiological Research, Institute for Community Medicine, University Medicine Greifswald, 17475, Greifswald, Germany
| | - T Zhu
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - J Kaprio
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - M Ollikainen
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - F S David
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
| | - S Meinert
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
- Institute for Translational Neuroscience, University of Münster, Münster, Germany
| | - F Stein
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior, University of Marburg, Marburg, Germany
| | - A J Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | - U Dannlowski
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - T Kircher
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior, University of Marburg, Marburg, Germany
| | - A Tapuc
- Max Planck School of Cognition, Leipzig, Germany
- Max-Planck-Institute of Psychiatry, Department Genes and Environment, Munich, Germany
| | - D Czamara
- Max-Planck-Institute of Psychiatry, Department Genes and Environment, Munich, Germany
| | - E B Binder
- Max-Planck-Institute of Psychiatry, Department Genes and Environment, Munich, Germany
| | - T Brückl
- Max-Planck-Institute of Psychiatry, Department Genes and Environment, Munich, Germany
| | - A S F Kwong
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - P Yousefi
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, Bristol, UK
| | - C C Y Wong
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - L Arseneault
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - H L Fisher
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- ESRC Centre for Society and Mental Health, King's College London, London, UK
| | - J Mill
- Department of Clinical & Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - S R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - P Redmond
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - T C Russ
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
- Neuroprogressive and Dementia Network, NHS Research Scotland, Scotland, UK
| | - E J C G van den Oord
- Center for Biomarker Research and Precision Medicine (BPM), Virginia Commonwealth University, Virginia, USA
| | - K A Aberg
- Center for Biomarker Research and Precision Medicine (BPM), Virginia Commonwealth University, Virginia, USA
| | - B W J H Penninx
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - R E Marioni
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - N R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - A M McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
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11
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Han S, Cho SA, Choi W, Eilbeck K, Coon H, Nho K, Lee Y. Interaction of genetic variants and methylation in transcript-level expression regulation in Alzheimer's disease by multi-omics data analysis. BMC Genomics 2025; 26:170. [PMID: 39979805 PMCID: PMC11844006 DOI: 10.1186/s12864-025-11362-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 02/13/2025] [Indexed: 02/22/2025] Open
Abstract
BACKGROUND Alzheimer's disease (AD) presents a significant public health problem and major cause of dementia. Not only genetic but epigenetic factors contribute to complex and heterogeneous molecular mechanisms underlying AD risk; in particular, single nucleotide polymorphisms (SNPs) and DNA methylation can lead to dysregulation of gene expression in the AD brain. Each of these regulators has been independently studied well in AD progression, however, their interactive roles, particularly when they are located differently, still remains unclear. Here, we aimed to explore the interplay between SNPs and DNA methylation in regulating transcript expression levels in the AD brain through an integrative analysis of whole-genome sequencing, RNA-seq, and methylation data measured from the dorsolateral prefrontal cortex. RESULTS We identified 179 SNP-methylation combination pairs that showed statistically significant interactions associated with the expression of 67 transcripts (63 unique genes), enriched in functional pathways, including immune-related and post-synaptic assembly pathways. Particularly, a number of HLA family genes (HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DRB5, HLA-DPA1, HLA-K, HLA-DQB1, and HLA-DMA) were observed as having expression changes associated with the interplay. CONCLUSIONS Our findings especially implicate immune-related pathways as targets of these regulatory interactions. SNP-methylation interactions may thus contribute to the molecular complexity underlying immune-related pathogenies in AD patients. Our study provides a new molecular knowledge in the context of the interplay between genetic and epigenetic regulations, in that it concerns transcript expression status in AD.
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Affiliation(s)
- Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Soo-Ah Cho
- The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea
| | - Wongyung Choi
- The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hilary Coon
- Department of Psychiatry & Huntsman Mental Health Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences and Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Younghee Lee
- The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826, South Korea.
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12
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Oatman SR, Reddy JS, Atashgaran A, Wang X, Min Y, Quicksall Z, Vanelderen F, Carrasquillo MM, Liu CC, Yamazaki Y, Nguyen TT, Heckman M, Zhao N, DeTure M, Murray ME, Bu G, Kanekiyo T, Dickson DW, Allen M, Ertekin-Taner N. Integrative Epigenomic Landscape of Alzheimer's Disease Brains Reveals Oligodendrocyte Molecular Perturbations Associated with Tau. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.12.637140. [PMID: 40027794 PMCID: PMC11870448 DOI: 10.1101/2025.02.12.637140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Alzheimer's disease (AD) brains are characterized by neuropathologic and biochemical changes that are highly variable across individuals. Capturing epigenetic factors that associate with this variability can reveal novel biological insights into AD pathophysiology. We conducted an epigenome-wide association study of DNA methylation (DNAm) in 472 AD brains with neuropathologic measures (Braak stage, Thal phase, and cerebral amyloid angiopathy score) and brain biochemical levels of five proteins (APOE, amyloid-β (Aβ)40, Aβ42, tau, and p-tau) core to AD pathogenesis. Using a novel regional methylation (rCpGm) approach, we identified 5,478 significant associations, 99.7% of which were with brain tau biochemical measures. Of the tau-associated rCpGms, 93 had concordant associations in external datasets comprising 1,337 brain samples. Integrative transcriptome-methylome analyses uncovered 535 significant gene expression associations for these 93 rCpGms. Genes with concurrent transcriptome-methylome perturbations were enriched in oligodendrocyte marker genes, including known AD risk genes such as BIN1 , myelination genes MYRF, MBP and MAG previously implicated in AD, as well as novel genes like LDB3 . We further annotated the top oligodendrocyte genes in an additional 6 brain single cell and 2 bulk transcriptome datasets from AD and two other tauopathies, Pick's disease and progressive supranuclear palsy (PSP). Our findings support consistent rCpGm and gene expression associations with these tauopathies and tau-related phenotypes in both bulk brain tissue and oligodendrocyte clusters. In summary, we uncover the integrative epigenomic landscape of AD and demonstrate tau-related oligodendrocyte gene perturbations as a common potential pathomechanism across different tauopathies.
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Hüls A, Liu J, Konwar C, Conneely KN, Levey AI, Lah JJ, Wingo AP, Wingo TS. Epigenome-wide association study of cerebrospinal fluid-based biomarkers of Alzheimer's disease in cognitively normal individuals. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.02.04.25321657. [PMID: 39974053 PMCID: PMC11838696 DOI: 10.1101/2025.02.04.25321657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
INTRODUCTION Cerebrospinal fluid (CSF) biomarkers of Alzheimer's disease (AD) are reliable predictors of future AD risk. We investigated whether pre-clinical changes in AD CSF biomarkers are reflected in blood DNA methylation (DNAm) levels in cognitively normal participants. METHODS We profiled blood-based DNAm with the EPIC array in participants without a diagnosis of cognitive impairment in the Emory Healthy Brain Study (EHBS; N=495) and ADNI (N=122). Their CSF Aβ42, tTau, and pTau levels were quantified using Elecsys immunoassays. We conducted epigenome-wide association studies to assess associations between DNAm and CSF biomarkers of AD. RESULTS In EHBS, no loci were Bonferroni-significant after adjusting for confounding factors. In ADNI, two loci were significant, but they were not replicated in EHBS. There was little agreement between the top loci from EHBS and ADNI. DISCUSSION Our study showed little evidence of an association between differential blood-based DNAm and pre-clinical AD CSF biomarkers.
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Affiliation(s)
- Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
- Ganagarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA, 30322
| | - Jiaqi Liu
- Department of Psychiatry, University of California, Davis, Sacramento, CA USA, 95816
| | - Chaini Konwar
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver BC V5Z 4H4, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC Canada V5Z 4H4
| | - Karen N. Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA, 95816
| | - Allan I. Levey
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA USA, 30322
- Department of Neurology, Emory University School of Medicine, Atlanta, GA USA, 30322
| | - James J. Lah
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA USA, 30322
- Department of Neurology, Emory University School of Medicine, Atlanta, GA USA, 30322
| | - Aliza P. Wingo
- Department of Psychiatry, University of California, Davis, Sacramento, CA USA, 95816
- Division of Mental Health, Northern California VA, Sacramento, CA USA, 95816
| | - Thomas S. Wingo
- Department of Neurology, University of California, Davis, Sacramento, CA USA, 95816
- Alzheimer’s Disease Research Center, University of California, Davis, Sacramento, USA, 95816
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14
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Newell ME, Aravindan A, Babbrah A, Halden RU. Epigenetic Biomarkers Driven by Environmental Toxins Associated with Alzheimer's Disease, Parkinson's Disease, and Amyotrophic Lateral Sclerosis in the United States: A Systematic Review. TOXICS 2025; 13:114. [PMID: 39997929 PMCID: PMC11860158 DOI: 10.3390/toxics13020114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2024] [Revised: 01/18/2025] [Accepted: 01/28/2025] [Indexed: 02/26/2025]
Abstract
Environmental toxins and epigenetic changes have been linked to neurodegenerative diseases, including Alzheimer's Disease (AD), Parkinson's Disease (PD), and amyotrophic lateral sclerosis (ALS). This paper aimed to (i) identify environmental toxins associated with AD, PD, and ALS, (ii) locate potential industrial sources of toxins in the United States (U.S.), and (iii) assess epigenetic changes driven by exposure to toxins reported by patients. Environmental factors and epigenetic biomarkers of neurodegeneration were compiled from 69 studies in the literature using Preferred Reporting Items for Systematic Reviews and Meta Analyses (PRISMA) and geographic information system approaches. Some 127 environmental toxins have been associated or putatively associated with AD, PD, or ALS, with four toxic metals (As, Cd, Mn, and Hg) common to all three of these neurodegenerative diseases. Environmental toxins associated with epigenetic changes (e.g., DNA methylation) in patients include air pollutants, metals, and organic chemicals (e.g., pesticides, mycotoxins, and cyanotoxins). Geographic analysis showed that study locations (e.g., U.S., Europe, and East Asia) were selected by researchers based on convenience of access rather than exposure risk and disease prevalence. We conclude that several toxins and epigenetic markers shared among neurodegenerative diseases could serve as attractive future targets guiding environmental quality improvements and aiding in early disease detection.
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Affiliation(s)
- Melanie Engstrom Newell
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Center for Environmental Health Engineering, Tempe, AZ 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | - Anumitha Aravindan
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Center for Environmental Health Engineering, Tempe, AZ 85287, USA
- Barrett, The Honors College, Arizona State University, Tempe, AZ 85287, USA
| | - Ayesha Babbrah
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Center for Environmental Health Engineering, Tempe, AZ 85287, USA
- Barrett, The Honors College, Arizona State University, Tempe, AZ 85287, USA
| | - Rolf U. Halden
- Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Biodesign Center for Environmental Health Engineering, Tempe, AZ 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
- Barrett, The Honors College, Arizona State University, Tempe, AZ 85287, USA
- School of Sustainable Engineering and The Built Environment, Arizona State University, Tempe, AZ 85287, USA
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15
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Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs improve discovery of DNA methylation associations with complex traits. Nat Commun 2025; 16:368. [PMID: 39753567 PMCID: PMC11698866 DOI: 10.1038/s41467-024-55698-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 12/18/2024] [Indexed: 01/06/2025] Open
Abstract
We have developed the regionalpcs method, an approach for summarizing gene-level methylation. regionalpcs addresses the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease. In contrast to averaging, regionalpcs uses principal components analysis to capture complex methylation patterns across gene regions. Our method demonstrates a 54% improvement in sensitivity over averaging in simulations, providing a robust framework for identifying subtle epigenetic variations. Applying regionalpcs to Alzheimer's disease brain methylation data, combined with cell type deconvolution, we uncover 838 differentially methylated genes associated with neuritic plaque burden-significantly outperforming conventional methods. Integrating methylation quantitative trait loci with genome-wide association studies identified 17 genes with potential causal roles in Alzheimer's disease risk, including MS4A4A and PICALM. Available in the Bioconductor package regionalpcs, our approach facilitates a deeper understanding of the epigenetic landscape in Alzheimer's disease and opens avenues for research into complex diseases.
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Affiliation(s)
- Tiffany Eulalio
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
| | - Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Olivier Gevaert
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, Stanford, CA, USA
| | - Michael D Greicius
- Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA, USA
| | | | - Daniel Nachun
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Stephen B Montgomery
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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16
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Weymouth L, Smith AR, Lunnon K. DNA Methylation in Alzheimer's Disease. Curr Top Behav Neurosci 2025; 69:149-178. [PMID: 39455499 DOI: 10.1007/7854_2024_530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2024]
Abstract
To date, DNA methylation is the best characterized epigenetic modification in Alzheimer's disease. Involving the addition of a methyl group to the fifth carbon of the cytosine pyrimidine base, DNA methylation is generally thought to be associated with the silencing of gene expression. It has been hypothesized that epigenetics may mediate the interaction between genes and the environment in the manifestation of Alzheimer's disease, and therefore studies investigating DNA methylation could elucidate novel disease mechanisms. This chapter comprehensively reviews epigenomic studies, undertaken in human brain tissue and purified brain cell types, focusing on global methylation levels, candidate genes, epigenome wide approaches, and recent meta-analyses. We discuss key differentially methylated genes and pathways that have been highlighted to date, with a discussion on how new technologies and the integration of multiomic data may further advance the field.
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Affiliation(s)
- Luke Weymouth
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Adam R Smith
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
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17
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Cocoș R, Popescu BO. Scrutinizing neurodegenerative diseases: decoding the complex genetic architectures through a multi-omics lens. Hum Genomics 2024; 18:141. [PMID: 39736681 DOI: 10.1186/s40246-024-00704-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 12/10/2024] [Indexed: 01/01/2025] Open
Abstract
Neurodegenerative diseases present complex genetic architectures, reflecting a continuum from monogenic to oligogenic and polygenic models. Recent advances in multi-omics data, coupled with systems genetics, have significantly refined our understanding of how these data impact neurodegenerative disease mechanisms. To contextualize these genetic discoveries, we provide a comprehensive critical overview of genetic architecture concepts, from Mendelian inheritance to the latest insights from oligogenic and omnigenic models. We explore the roles of common and rare genetic variants, gene-gene and gene-environment interactions, and epigenetic influences in shaping disease phenotypes. Additionally, we emphasize the importance of multi-omics layers including genomic, transcriptomic, proteomic, epigenetic, and metabolomic data in elucidating the molecular mechanisms underlying neurodegeneration. Special attention is given to missing heritability and the contribution of rare variants, particularly in the context of pleiotropy and network pleiotropy. We examine the application of single-cell omics technologies, transcriptome-wide association studies, and epigenome-wide association studies as key approaches for dissecting disease mechanisms at tissue- and cell-type levels. Our review introduces the OmicPeak Disease Trajectory Model, a conceptual framework for understanding the genetic architecture of neurodegenerative disease progression, which integrates multi-omics data across biological layers and time points. This review highlights the critical importance of adopting a systems genetics approach to unravel the complex genetic architecture of neurodegenerative diseases. Finally, this emerging holistic understanding of multi-omics data and the exploration of the intricate genetic landscape aim to provide a foundation for establishing more refined genetic architectures of these diseases, enhancing diagnostic precision, predicting disease progression, elucidating pathogenic mechanisms, and refining therapeutic strategies for neurodegenerative conditions.
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Affiliation(s)
- Relu Cocoș
- Department of Medical Genetics, 'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania.
- Genomics Research and Development Institute, Bucharest, Romania.
| | - Bogdan Ovidiu Popescu
- Department of Clinical Neurosciences, 'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania.
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18
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Ramirez AM, Bertholim-Nasciben L, Moura S, Coombs LE, Rajabli F, DeRosa BA, Whitehead PG, Adams LD, Starks TD, Mena P, Illannes-Manrique M, Tejada SJ, Byrd GS, Caban-Holt A, Cuccaro M, McInerney K, Cornejo-Olivas M, Feliciano-Astacio B, Wang L, Robayo MC, Xu W, Jin F, Pericak-Vance MA, Griswold AJ, Dykxhoorn DM, Young JI, Vance JM. Ancestral Genomic Functional Differences in Oligodendroglia: Implications for Alzheimer's Disease. RESEARCH SQUARE 2024:rs.3.rs-5338140. [PMID: 39678342 PMCID: PMC11643296 DOI: 10.21203/rs.3.rs-5338140/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Background This study aims to elucidate ancestry-specific changes to the genomic regulatory architecture in induced pluripotent stem cell (iPSC)-derived oligodendroglia, focusing on their implications for Alzheimer's disease (AD). This work addresses the lack of diversity in previous iPSC studies by including ancestries that contribute to African American (European/African) and Hispanic/Latino populations (Amerindian/African/European). Methods We generated 12 iPSC lines-four African, four Amerindian, and four European- from both AD patients and non-cognitively impaired individuals, with varying APOE genotypes (APOE3/3 and APOE4/4). These lines were differentiated into neural spheroids containing oligodendrocyte lineage cells. Single-nuclei RNA sequencing and ATAC sequencing were employed to analyze transcriptional and chromatin accessibility profiles, respectively. Differential gene expression, chromatin accessibility, and Hi-C analyses were conducted, followed by pathway analysis to interpret the results. Results We identified ancestry-specific differences in gene expression and chromatin accessibility. Notably, numerous AD GWAS-associated genes were differentially expressed across ancestries. The largest number of differentially expressed genes (DEGs) were found in European vs. Amerindian and African vs. Amerindian iPSC-derived oligodendrocyte progenitor cells (OPCs). Pathway analysis of APOE4/4 carriers vs APOE3/3 carriers exhibited upregulation of a large number of disease and metabolic pathways in APOE4/4 individuals of all ancestries. Of particular interest was that APOE4/4 carriers had significantly upregulated cholesterol biosynthesis genes relative to APOE3/3 individuals across all ancestries, strongest in iOPCs. Comparison of iOPC and iOL transcriptome data with corresponding human frontal cortex data demonstrated a high correlation (R2 > 0.85). Conclusions This research emphasizes the importance of including diverse ancestries in AD research to uncover critical gene expression differences between populations and ancestries that may influence disease susceptibility and therapeutic interventions. The upregulation of cholesterol biosynthesis genes in APOE4/4 carriers of all three ancestries supports the concept that APOE4 may produce disease effects early in life, which could have therapeutic implications as we move forward towards specific therapy for APOE4 carriers. These findings and the high correlation between brain and iPSC-derived OPC and OL transcriptomes support the relevance of this approach as a model for disease study.
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Affiliation(s)
- Aura M Ramirez
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | | | - Sofia Moura
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Lauren E Coombs
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Farid Rajabli
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Brooke A DeRosa
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Patrice G Whitehead
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Larry D Adams
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Takiyah D Starks
- Wake Forest School of Medicine: Wake Forest University School of Medicine
| | - Pedro Mena
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | | | - Sergio J Tejada
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Goldie S Byrd
- Wake Forest School of Medicine: Wake Forest University School of Medicine
| | - Allison Caban-Holt
- Wake Forest School of Medicine: Wake Forest University School of Medicine
| | - Michael Cuccaro
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Katalina McInerney
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Mario Cornejo-Olivas
- Universidad Científica del Sur Facultad de Ciencias de la Salud: Universidad Cientifica del Sur Facultad de Ciencias de la Salud
| | | | - Liyong Wang
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Maria C Robayo
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Wanying Xu
- Case Western Reserve University School of Medicine
| | - Fulai Jin
- Case Western Reserve University School of Medicine
| | | | - Anthony J Griswold
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Derek M Dykxhoorn
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Juan I Young
- University of Miami Miller School of Medicine: University of Miami School of Medicine
| | - Jeffery M Vance
- University of Miami Miller School of Medicine: University of Miami School of Medicine
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19
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Opsasnick LA, Zhao W, Schmitz LL, Ratliff SM, Faul JD, Zhou X, Needham BL, Smith JA. Epigenome-wide association study of long-term psychosocial stress in older adults. Epigenetics 2024; 19:2323907. [PMID: 38431869 PMCID: PMC10913704 DOI: 10.1080/15592294.2024.2323907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Long-term psychosocial stress is strongly associated with negative physical and mental health outcomes, as well as adverse health behaviours; however, little is known about the role that stress plays on the epigenome. One proposed mechanism by which stress affects DNA methylation is through health behaviours. We conducted an epigenome-wide association study (EWAS) of cumulative psychosocial stress (n = 2,689) from the Health and Retirement Study (mean age = 70.4 years), assessing DNA methylation (Illumina Infinium HumanMethylationEPIC Beadchip) at 789,656 CpG sites. For identified CpG sites, we conducted a formal mediation analysis to examine whether smoking, alcohol use, physical activity, and body mass index (BMI) mediate the relationship between stress and DNA methylation. Nine CpG sites were associated with psychosocial stress (all p < 9E-07; FDR q < 0.10). Additionally, health behaviours and/or BMI mediated 9.4% to 21.8% of the relationship between stress and methylation at eight of the nine CpGs. Several of the identified CpGs were in or near genes associated with cardiometabolic traits, psychosocial disorders, inflammation, and smoking. These findings support our hypothesis that psychosocial stress is associated with DNA methylation across the epigenome. Furthermore, specific health behaviours mediate only a modest percentage of this relationship, providing evidence that other mechanisms may link stress and DNA methylation.
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Affiliation(s)
- Lauren A. Opsasnick
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Lauren L. Schmitz
- Robert M. La Follette School of Public Affairs, University of Wisconsin-Madison, Madison, WI, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Belinda L. Needham
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
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20
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Behl T, Kyada A, Roopashree R, Nathiya D, Arya R, Kumar MR, Khalid M, Gulati M, Sachdeva M, Fareed M, Patra PK, Agrawal A, Wal P, Gasmi A. Epigenetic biomarkers in Alzheimer's disease: Diagnostic and prognostic relevance. Ageing Res Rev 2024; 102:102556. [PMID: 39490904 DOI: 10.1016/j.arr.2024.102556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 10/22/2024] [Accepted: 10/22/2024] [Indexed: 11/05/2024]
Abstract
Alzheimer's disease (AD) is a leading cause of cognitive decline in the aging population, presenting a critical need for early diagnosis and effective prognostic tools. Epigenetic modifications, including DNA methylation, histone modifications, and non-coding RNAs, have emerged as promising biomarkers for AD due to their roles in regulating gene expression and potential for reversibility. This review examines the current landscape of epigenetic biomarkers in AD, emphasizing their diagnostic and prognostic relevance. DNA methylation patterns in genes such as APP, PSEN1, and PSEN2 are highlighted for their strong associations with AD pathology. Alterations in DNA methylation at specific CpG sites have been consistently observed in AD patients, suggesting their utility in early detection. Histone modifications, such as acetylation and methylation, also play a crucial role in chromatin remodelling and gene expression regulation in AD. Dysregulated histone acetylation and methylation have been linked to AD progression, making these modifications valuable biomarkers. Non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), further contribute to the epigenetic regulation in AD. miRNAs can modulate gene expression post-transcriptionally and have been found in altered levels in AD, while lncRNAs can influence chromatin structure and gene expression. The presence of these non-coding RNAs in biofluids like blood and cerebrospinal fluid positions them as accessible and minimally invasive biomarkers. Technological advancements in detecting and quantifying epigenetic modifications have propelled the field forward. Techniques such as next-generation sequencing, bisulfite sequencing, and chromatin immunoprecipitation assays offer high sensitivity and specificity, enabling the detailed analysis of epigenetic changes in clinical samples. These tools are instrumental in translating epigenetic research into clinical practice. This review underscores the potential of epigenetic biomarkers to enhance the early diagnosis and prognosis of AD, paving the way for personalized therapeutic strategies and improved patient outcomes. The integration of these biomarkers into clinical workflows promises to revolutionize AD management, offering hope for better disease monitoring and intervention.
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Affiliation(s)
- Tapan Behl
- Amity School of Pharmaceutical Sciences, Amity University, Punjab 140306, India.
| | - Ashishkumar Kyada
- Marwadi University Research Center, Department of Pharmaceutical Sciences, Faculty of Health Sciences, Marwadi University, Rajkot, Gujarat 360003, India
| | - R Roopashree
- Department of Chemistry and Biochemistry, School of Sciences, JAIN (Deemed to be University), Bangalore, Karnataka, India
| | - Deepak Nathiya
- Department of Pharmacy Practice, Institute of Pharmacy, NIMS University, Jaipur, India
| | - Renu Arya
- Chandigarh Pharmacy College, Chandigarh Group of Colleges-Jhanjeri, Mohali, Punjab 140307, India
| | - M Ravi Kumar
- Department of Basic Science & Humanities, Raghu Engineering College, Visakhapatnam, India
| | - Mohammad Khalid
- Department of pharmacognosy, College of pharmacy, Prince Sattam Bin Abdulaziz University Alkharj, Saudi Arabia
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 1444411, India; ARCCIM, Faculty of Health, University of Technology Sydney, Ultimo, NSW 20227, Australia
| | - Monika Sachdeva
- Fatima College of Health Sciences, Al Ain, United Arab Emirates
| | - Mohammad Fareed
- Department of Basic Medical Sciences, College of Medicine, AlMaarefa University, P.O. Box No. 71666, Riyadh 11597, Saudi Arabia
| | - Pratap Kumar Patra
- School of Pharmacy & Life Sciences, Centurion University of Technology & Managemnet, Bhubaneswar, Odisha 752050, India
| | - Ankur Agrawal
- Jai Institute of Pharmaceutical Sciences and Research, Gwalior, Madhya Pradesh 474001, India
| | - Pranay Wal
- PSIT-Pranveer Singh Institute of Technology, Pharmacy, NH-19, Bhauti Road, Kanpur, UP 209305, India
| | - Amin Gasmi
- Société Francophone de Nutrithérapie et de Nutrigénétique Appliquée, Villeurbanne, France; International Institute of Nutrition and Micronutrition Sciences, Saint-Étienne, France
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21
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays. Epigenetics 2024; 19:2333660. [PMID: 38564759 PMCID: PMC10989698 DOI: 10.1080/15592294.2024.2333660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer's Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Juan I. Young
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Brian Kunkle
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eden R. Martin
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Kunkle BW, Chen X, Martin ER, Wang L. Blood DNA Methylation Signature for Incident Dementia: Evidence from Longitudinal Cohorts. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.11.03.24316667. [PMID: 39649611 PMCID: PMC11623760 DOI: 10.1101/2024.11.03.24316667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2024]
Abstract
INTRODUCTION Distinguishing between molecular changes that precede dementia onset and those resulting from the disease is challenging with cross-sectional studies. METHODS We studied blood DNA methylation (DNAm) differences and incident dementia in two large longitudinal cohorts: the Offspring cohort of the Framingham Heart Study (FHS) and the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. We analyzed blood DNAm samples from over 1,000 cognitively unimpaired subjects. RESULTS Meta-analysis identified 44 CpGs and 44 differentially methylated regions consistently associated with time to dementia in both cohorts. Our integrative analysis identified early processes in dementia, such as immune responses and metabolic dysfunction. Furthermore, we developed a Methylation-based Risk Score, which successfully predicted future cognitive decline in an independent validation set, even after accounting for age, sex, APOE ε4, years of education, baseline diagnosis, and baseline MMSE score. DISCUSSION DNA methylation offers a promising source of biomarker for early detection of dementia.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian W. Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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Alves VC, Carro E, Figueiro-Silva J. Unveiling DNA methylation in Alzheimer's disease: a review of array-based human brain studies. Neural Regen Res 2024; 19:2365-2376. [PMID: 38526273 PMCID: PMC11090417 DOI: 10.4103/1673-5374.393106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/05/2023] [Indexed: 03/26/2024] Open
Abstract
The intricacies of Alzheimer's disease pathogenesis are being increasingly illuminated by the exploration of epigenetic mechanisms, particularly DNA methylation. This review comprehensively surveys recent human-centered studies that investigate whole genome DNA methylation in Alzheimer's disease neuropathology. The examination of various brain regions reveals distinctive DNA methylation patterns that associate with the Braak stage and Alzheimer's disease progression. The entorhinal cortex emerges as a focal point due to its early histological alterations and subsequent impact on downstream regions like the hippocampus. Notably, ANK1 hypermethylation, a protein implicated in neurofibrillary tangle formation, was recurrently identified in the entorhinal cortex. Further, the middle temporal gyrus and prefrontal cortex were shown to exhibit significant hypermethylation of genes like HOXA3, RHBDF2, and MCF2L, potentially influencing neuroinflammatory processes. The complex role of BIN1 in late-onset Alzheimer's disease is underscored by its association with altered methylation patterns. Despite the disparities across studies, these findings highlight the intricate interplay between epigenetic modifications and Alzheimer's disease pathology. Future research efforts should address methodological variations, incorporate diverse cohorts, and consider environmental factors to unravel the nuanced epigenetic landscape underlying Alzheimer's disease progression.
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Affiliation(s)
- Victoria Cunha Alves
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- PhD Program in Neuroscience, Autonoma de Madrid University, Madrid, Spain
- Neurotraumatology and Subarachnoid Hemorrhage Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
| | - Eva Carro
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Neurobiology of Alzheimer's Disease Unit, Functional Unit for Research Into Chronic Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Joana Figueiro-Silva
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
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24
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Pathak GA, Pietrzak RH, Lacobelle A, Overstreet C, Wendt FR, Deak JD, Friligkou E, Nunez Y, Montalvo-Ortiz JL, Levey DF, Kranzler HR, Gelernter J, Polimanti R. Epigenetic and Genetic Profiling of Comorbidity Patterns among Substance Dependence Diagnoses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.10.08.24315111. [PMID: 39417130 PMCID: PMC11482987 DOI: 10.1101/2024.10.08.24315111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Objective This study investigated the genetic and epigenetic mechanisms underlying the comorbidity patterns of five substance dependence diagnoses (SDs; alcohol, AD; cannabis, CaD; cocaine, CoD; opioid, OD; tobacco, TD). Methods A latent class analysis (LCA) was performed on 31,197 individuals (average age 42±11 years; 49% females) from six cohorts to identify comorbid DSM-IV SD patterns. In subsets of this sample, we tested SD-latent classes with respect to polygenic burden of psychiatric and behavioral traits and epigenome-wide changes in three population groups. Results An LCA identified four latent classes related to SD comorbidities: AD+TD, CoD+TD, AD+CoD+OD+TD (i.e., polysubstance use, PSU), and TD. In the epigenome-wide association analysis, SPATA4 cg02833127 was associated with CoD+TD, AD+TD, and PSU latent classes. AD+TD latent class was also associated with CpG sites located on ARID1B , NOTCH1 , SERTAD4, and SIN3B , while additional epigenome-wide significant associations with CoD+TD latent class were observed in ANO6 and MOV10 genes. PSU-latent class was also associated with a differentially methylated region in LDB1 . We also observed shared polygenic score (PGS) associations for PSU, AD+TD, and CoD+TD latent classes (i.e., attention-deficit hyperactivity disorder, anxiety, educational attainment, and schizophrenia PGS). In contrast, TD-latent class was exclusively associated with posttraumatic stress disorder-PGS. Other specific associations were observed for PSU-latent class (subjective wellbeing-PGS and neuroticism-PGS) and AD+TD-latent class (bipolar disorder-PGS). Conclusions We identified shared and unique genetic and epigenetic mechanisms underlying SD comorbidity patterns. These findings highlight the importance of modeling the co-occurrence of SD diagnoses when investigating the molecular basis of addiction-related traits.
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Bao J, Lee BN, Wen J, Kim M, Mu S, Yang S, Davatzikos C, Long Q, Ritchie MD, Shen L. Employing Informatics Strategies in Alzheimer's Disease Research: A Review from Genetics, Multiomics, and Biomarkers to Clinical Outcomes. Annu Rev Biomed Data Sci 2024; 7:391-418. [PMID: 38848574 PMCID: PMC11525791 DOI: 10.1146/annurev-biodatasci-102423-121021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Alzheimer's disease (AD) is a critical national concern, affecting 5.8 million people and costing more than $250 billion annually. However, there is no available cure. Thus, effective strategies are in urgent need to discover AD biomarkers for disease early detection and drug development. In this review, we study AD from a biomedical data scientist perspective to discuss the four fundamental components in AD research: genetics (G), molecular multiomics (M), multimodal imaging biomarkers (B), and clinical outcomes (O) (collectively referred to as the GMBO framework). We provide a comprehensive review of common statistical and informatics methodologies for each component within the GMBO framework, accompanied by the major findings from landmark AD studies. Our review highlights the potential of multimodal biobank data in addressing key challenges in AD, such as early diagnosis, disease heterogeneity, and therapeutic development. We identify major hurdles in AD research, including data scarcity and complexity, and advocate for enhanced collaboration, data harmonization, and advanced modeling techniques. This review aims to be an essential guide for understanding current biomedical data science strategies in AD research, emphasizing the need for integrated, multidisciplinary approaches to advance our understanding and management of AD.
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Affiliation(s)
- Jingxuan Bao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA;
| | - Brian N Lee
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA;
| | - Junhao Wen
- Laboratory of AI and Biomedical Science (LABS), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
| | - Mansu Kim
- AI Graduate School, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Shizhuo Mu
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA;
| | - Shu Yang
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA;
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Qi Long
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA;
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA;
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA;
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Lukacsovich D, O’Shea D, Huang H, Zhang W, Young J, Chen XS, Dietrich ST, Kunkle B, Martin E, Wang L. MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease. Database (Oxford) 2024; 2024:baae061. [PMID: 39028752 PMCID: PMC11259044 DOI: 10.1093/database/baae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/08/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder with a significant impact on aging populations. DNA methylation (DNAm) alterations have been implicated in both the aging processes and the development of AD. Given that AD affects more women than men, it is also important to explore DNAm changes that occur specifically in each sex. We created MIAMI-AD, a comprehensive knowledgebase containing manually curated summary statistics from 98 published tables in 38 studies, all of which included at least 100 participants. MIAMI-AD enables easy browsing, querying, and downloading DNAm associations at multiple levels-at individual CpG, gene, genomic regions, or genome-wide, in one or multiple studies. Moreover, it also offers tools to perform integrative analyses, such as comparing DNAm associations across different phenotypes or tissues, as well as interactive visualizations. Using several use case examples, we demonstrated that MIAMI-AD facilitates our understanding of age-associated CpGs in AD and the sex-specific roles of DNAm in AD. This open-access resource is freely available to the research community, and all the underlying data can be downloaded. MIAMI-AD facilitates integrative explorations to better understand the interplay between DNAm across aging, sex, and AD. Database URL: https://miami-ad.org/.
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Affiliation(s)
- David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
| | - Deirdre O’Shea
- Department of Neurology, Comprehensive Center for Brain Health, University of Miami, Miller School of Medicine, 7700 W Camino Real, Boca Raton, FL 33433, USA
| | - Hanchen Huang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
| | - Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
| | - Juan Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, 1475 NW 12th Ave, Miami, FL 33136, USA
| | - Sven-Thorsten Dietrich
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Eden Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, 1501 NW 10th Ave, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, 1475 NW 12th Ave, Miami, FL 33136, USA
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27
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Yadav B, Singh D, Mantri S, Rishi V. Genome-wide Methylation Dynamics and Context-dependent Gene Expression Variability in Differentiating Preadipocytes. J Endocr Soc 2024; 8:bvae121. [PMID: 38966711 PMCID: PMC11222978 DOI: 10.1210/jendso/bvae121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Indexed: 07/06/2024] Open
Abstract
Obesity, characterized by the accumulation of excess fat, is a complex condition resulting from the combination of genetic and epigenetic factors. Recent studies have found correspondence between DNA methylation and cell differentiation, suggesting a role of the former in cell fate determination. There is a lack of comprehensive understanding concerning the underpinnings of preadipocyte differentiation, specifically when cells are undergoing terminal differentiation (TD). To gain insight into dynamic genome-wide methylation, 3T3 L1 preadipocyte cells were differentiated by a hormone cocktail. The genomic DNA was isolated from undifferentiated cells and 4 hours, 2 days postdifferentiated cells, and 15 days TD cells. We employed whole-genome bisulfite sequencing (WGBS) to ascertain global genomic DNA methylation alterations at single base resolution as preadipocyte cells differentiate. The genome-wide distribution of DNA methylation showed similar overall patterns in pre-, post-, and terminally differentiated adipocytes, according to WGBS analysis. DNA methylation decreases at 4 hours after differentiation initiation, followed by methylation gain as cells approach TD. Studies revealed novel differentially methylated regions (DMRs) associated with adipogenesis. DMR analysis suggested that though DNA methylation is global, noticeable changes are observed at specific sites known as "hotspots." Hotspots are genomic regions rich in transcription factor (TF) binding sites and exhibit methylation-dependent TF binding. Subsequent analysis indicated hotspots as part of DMRs. The gene expression profile of key adipogenic genes in differentiating adipocytes is context-dependent, as we found a direct and inverse relationship between promoter DNA methylation and gene expression.
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Affiliation(s)
- Binduma Yadav
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
- Regional Center for Biotechnology, Faridabad, Haryana 160014, India
| | - Dalwinder Singh
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
- Department of Anatomy and Cell Biology, Western University, London, Ontario N6A 5C1, Canada
| | - Shrikant Mantri
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
| | - Vikas Rishi
- Nutritional Biotechnology, National Agri-Food Biotechnology Institute, Mohali, Punjab 140306, India
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Blanc J, Berg JJ. Testing for differences in polygenic scores in the presence of confounding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.12.532301. [PMID: 36993707 PMCID: PMC10055004 DOI: 10.1101/2023.03.12.532301] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Polygenic scores have become an important tool in human genetics, enabling the prediction of individuals' phenotypes from their genotypes. Understanding how the pattern of differences in polygenic score predictions across individuals intersects with variation in ancestry can provide insights into the evolutionary forces acting on the trait in question, and is important for understanding health disparities. However, because most polygenic scores are computed using effect estimates from population samples, they are susceptible to confounding by both genetic and environmental effects that are correlated with ancestry. The extent to which this confounding drives patterns in the distribution of polygenic scores depends on patterns of population structure in both the original estimation panel and in the prediction/test panel. Here, we use theory from population and statistical genetics, together with simulations, to study the procedure of testing for an association between polygenic scores and axes of ancestry variation in the presence of confounding. We use a general model of genetic relatedness to describe how confounding in the estimation panel biases the distribution of polygenic scores in a way that depends on the degree of overlap in population structure between panels. We then show how this confounding can bias tests for associations between polygenic scores and important axes of ancestry variation in the test panel. Specifically, for any given test, there exists a single axis of population structure in the GWAS panel that needs to be controlled for in order to protect the test. Based on this result, we propose a new approach for directly estimating this axis of population structure in the GWAS panel. We then use simulations to compare the performance of this approach to the standard approach in which the principal components of the GWAS panel genotypes are used to control for stratification.
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Affiliation(s)
- Jennifer Blanc
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Jeremy J. Berg
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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Jiménez-Balado J, Fernández-Pérez I, Gallego-Fábrega C, Lazcano U, Soriano-Tárraga C, Vallverdú-Prats M, Mola-Caminal M, Rey-Álvarez L, Macias-Gómez A, Suárez-Pérez A, Giralt-Steinhauer E, Rodríguez-Campello A, Cuadrado-Godia E, Ois Á, Esteller M, Roquer J, Fernández-Cadenas I, Jiménez-Conde J. DNA methylation and stroke prognosis: an epigenome-wide association study. Clin Epigenetics 2024; 16:75. [PMID: 38845005 PMCID: PMC11155152 DOI: 10.1186/s13148-024-01690-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND AND AIMS Stroke is the leading cause of adult-onset disability. Although clinical factors influence stroke outcome, there is a significant variability among individuals that may be attributed to genetics and epigenetics, including DNA methylation (DNAm). We aimed to study the association between DNAm and stroke prognosis. METHODS AND RESULTS To that aim, we conducted a two-phase study (discovery-replication and meta-analysis) in Caucasian patients with ischemic stroke from two independent centers (BasicMar [discovery, N = 316] and St. Pau [replication, N = 92]). Functional outcome was assessed using the modified Rankin Scale (mRS) at three months after stroke, being poor outcome defined as mRS > 2. DNAm was determined using the 450K and EPIC BeadChips in whole-blood samples collected within the first 24 h. We searched for differentially methylated positions (DMPs) in 370,344 CpGs, and candidates below p-value < 10-5 were subsequently tested in the replication cohort. We then meta-analyzed DMP results from both cohorts and used them to identify differentially methylated regions (DMRs). After doing the epigenome-wide association study, we found 29 DMPs at p-value < 10-5 and one of them was replicated: cg24391982, annotated to thrombospondin-2 (THBS2) gene (p-valuediscovery = 1.54·10-6; p-valuereplication = 9.17·10-4; p-valuemeta-analysis = 6.39·10-9). Besides, four DMRs were identified in patients with poor outcome annotated to zinc finger protein 57 homolog (ZFP57), Arachidonate 12-Lipoxygenase 12S Type (ALOX12), ABI Family Member 3 (ABI3) and Allantoicase (ALLC) genes (p-value < 1·10-9 in all cases). DISCUSSION Patients with poor outcome showed a DMP at THBS2 and four DMRs annotated to ZFP57, ALOX12, ABI3 and ALLC genes. This suggests an association between stroke outcome and DNAm, which may help identify new stroke recovery mechanisms.
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Affiliation(s)
- Joan Jiménez-Balado
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain.
| | - Isabel Fernández-Pérez
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
- Medicine Department, Autonomous University of Barcelona, Barcelona, Spain
| | | | - Uxue Lazcano
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Biscaia, Spain
| | - Carolina Soriano-Tárraga
- Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Marta Vallverdú-Prats
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Marina Mola-Caminal
- Unit of Medical Epidemiology, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Lucía Rey-Álvarez
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Adrià Macias-Gómez
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Antoni Suárez-Pérez
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Eva Giralt-Steinhauer
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Ana Rodríguez-Campello
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
- Medicine Department, DCEXS-Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Elisa Cuadrado-Godia
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
- Medicine Department, DCEXS-Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Ángel Ois
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
- Medicine Department, DCEXS-Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Jaume Roquer
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain
| | | | - Jordi Jiménez-Conde
- Neurovascular Research Group, Department of Neurology, Hospital del Mar Research Institute, C/ del Dr. Aiguader, 88, 08003, Barcelona, Spain.
- Medicine Department, DCEXS-Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain.
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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 : THE PREPRINT SERVER FOR HEALTH SCIENCES 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] [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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Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs: improved discovery of DNA methylation associations with complex traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.590171. [PMID: 38746367 PMCID: PMC11092597 DOI: 10.1101/2024.05.01.590171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We have developed the regional principal components (rPCs) method, a novel approach for summarizing gene-level methylation. rPCs address the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease (AD). In contrast to traditional averaging, rPCs leverage principal components analysis to capture complex methylation patterns across gene regions. Our method demonstrated a 54% improvement in sensitivity over averaging in simulations, offering a robust framework for identifying subtle epigenetic variations. Applying rPCs to the AD brain methylation data in ROSMAP, combined with cell type deconvolution, we uncovered 838 differentially methylated genes associated with neuritic plaque burden-significantly outperforming conventional methods. Integrating methylation quantitative trait loci (meQTL) with genome-wide association studies (GWAS) identified 17 genes with potential causal roles in AD, including MS4A4A and PICALM. Our approach is available in the Bioconductor package regionalpcs, opening avenues for research and facilitating a deeper understanding of the epigenetic landscape in complex diseases.
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Affiliation(s)
- Tiffany Eulalio
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Olivier Gevaert
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Michael D Greicius
- Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
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Yang T, Li C, Wei Q, Pang D, Cheng Y, Huang J, Lin J, Xiao Y, Jiang Q, Wang S, Shang H. Genome-wide DNA methylation analysis related to ALS patient progression and survival. J Neurol 2024; 271:2672-2683. [PMID: 38372747 DOI: 10.1007/s00415-024-12222-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/20/2024]
Abstract
BACKGROUND Epigenetics contributes to the pathogenesis of amyotrophic lateral sclerosis (ALS). We aimed to characterize the DNA methylation profiles associated with clinical heterogeneity in disease progression and survival among patients. METHODS We included a cohort of 41 patients with sporadic ALS, with a median follow-up of 86.9 months, and 27 rigorously matched healthy controls. Blood-based genome-wide DNA methylation analysis was conducted. RESULTS A total of 948 progression rate-associated differentially methylated positions, 298 progression rate-associated differentially methylated regions (R-DMRs), 590 survival time-associated DMPs, and 197 survival time-associated DMRs (S-DMRs) were identified, using complementary grouping strategies. Enrichment analysis of differentially methylated genes highlighted the involvement of synapses and axons in ALS progression and survival. Clinical analysis revealed a positive correlation between the average methylation levels of the R-DMR in PRDM8 and disease progression rate (r = 0.479, p = 0.002). Conversely, there was an inverse correlation between the average methylation levels of the R-DMR in ANKRD33 and disease progression rate (r = - 0.476, p = 0.002). In addition, patients with higher methylation levels within the S-DMR of ZNF696 experienced longer survival (p = 0.016), while those with elevated methylation levels in the S-DMR of RAI1 had shorter survival (p = 0.006). CONCLUSION DNA methylation holds promise as a potential biomarker for tracking disease progression and predicting survival outcome and also offers targets for precision medicine.
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Affiliation(s)
- Tianmi Yang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yangfan Cheng
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Junyu Lin
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yi Xiao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Qirui Jiang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Shichan Wang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China.
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Cevik SE, Skaar DA, Jima DD, Liu AJ, Østbye T, Whitson HE, Jirtle RL, Hoyo C, Planchart A. DNA methylation of imprint control regions associated with Alzheimer's disease in non-Hispanic Blacks and non-Hispanic Whites. Clin Epigenetics 2024; 16:58. [PMID: 38658973 PMCID: PMC11043040 DOI: 10.1186/s13148-024-01672-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/13/2024] [Indexed: 04/26/2024] Open
Abstract
Alzheimer's disease (AD) prevalence is twice as high in non-Hispanic Blacks (NHBs) as in non-Hispanic Whites (NHWs). The objective of this study was to determine whether aberrant methylation at imprint control regions (ICRs) is associated with AD. Differentially methylated regions (DMRs) were bioinformatically identified from whole-genome bisulfite sequenced DNA derived from brain tissue of 9 AD (5 NHBs and 4 NHWs) and 8 controls (4 NHBs and 4 NHWs). We identified DMRs located within 120 regions defined as candidate ICRs in the human imprintome ( https://genome.ucsc.edu/s/imprintome/hg38.AD.Brain_track ). Eighty-one ICRs were differentially methylated in NHB-AD, and 27 ICRs were differentially methylated in NHW-AD, with two regions common to both populations that are proximal to the inflammasome gene, NLRP1, and a known imprinted gene, MEST/MESTIT1. These findings indicate that early developmental alterations in DNA methylation of regions regulating genomic imprinting may contribute to AD risk and that this epigenetic risk differs between NHBs and NHWs.
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Affiliation(s)
- Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - David A Skaar
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Andy J Liu
- Department of Neurology, School of Medicine, Duke University, Durham, NC, USA
| | - Truls Østbye
- Department of Family Medicine and Community Health, Duke University, Durham, NC, USA
| | - Heather E Whitson
- Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
- Duke Center for the Study of Aging and Human Development, Durham, NC, USA
- Duke/UNC Alzheimer's Disease Research Center (ADRC), Durham, NC, USA
| | - Randy L Jirtle
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Cathrine Hoyo
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
| | - Antonio Planchart
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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He M, Zhao N, Satten GA. MIDASim: a fast and simple simulator for realistic microbiome data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.23.533996. [PMID: 36993431 PMCID: PMC10055388 DOI: 10.1101/2023.03.23.533996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Background Advances in sequencing technology has led to the discovery of associations between the human microbiota and many diseases, conditions, and traits. With the increasing availability of microbiome data, many statistical methods have been developed for studying these associations. The growing number of newly developed methods highlights the need for simple, rapid, and reliable methods to simulate realistic microbiome data, which is essential for validating and evaluating the performance of these methods. However, generating realistic microbiome data is challenging due to the complex nature of microbiome data, which feature correlation between taxa, sparsity, overdispersion, and compositionality. Current methods for simulating microbiome data are deficient in their ability to capture these important features of microbiome data, or can require exorbitant computational time. Methods We develop MIDASim ( MI crobiome DA ta Sim ulator), a fast and simple approach for simulating realistic microbiome data that reproduces the distributional and correlation structure of a template microbiome dataset. MIDASim is a two-step approach. The first step generates correlated binary indicators that represent the presence-absence status of all taxa, and the second step generates relative abundances and counts for the taxa that are considered to be present in step 1, utilizing a Gaussian copula to account for the taxon-taxon correlations. In the second step, MIDASim can operate in both a nonparametric and parametric mode. In the nonparametric mode, the Gaussian copula uses the empirical distribution of relative abundances for the marginal distributions. In the parametric mode, an inverse generalized gamma distribution is used in place of the empirical distribution. Results We demonstrate improved performance of MIDASim relative to other existing methods using gut and vaginal data. MIDASim showed superior performance by PER-MANOVA and in terms of alpha diversity and beta dispersion in either parametric or nonparametric mode. We also show how MIDASim in parametric mode can be used to assess the performance of methods for finding differentially abundant taxa in a compositional model. Conclusions MIDASim is easy to implement, flexible and suitable for most microbiome data simulation situations. MIDASim has three major advantages. First, MIDASim performs better in reproducing the distributional features of real data compared to other methods at both presence-absence level and relative-abundance level. MIDASim-simulated data are more similar to the template data than competing methods, as quantified using a variety of measures. Second, MIDASim makes few distributional assumptions for the relative abundances, and thus can easily accommodate complex distributional features in real data. Third, MIDASim is computationally efficient and can be used to simulate large microbiome datasets.
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Giannini LAA, Boers RG, van der Ende EL, Poos JM, Jiskoot LC, Boers JB, van IJcken WFJ, Dopper EG, Pijnenburg YAL, Seelaar H, Meeter LH, van Rooij JGJ, Scheper W, Gribnau J, van Swieten JC. Distinctive cell-free DNA methylation characterizes presymptomatic genetic frontotemporal dementia. Ann Clin Transl Neurol 2024; 11:744-756. [PMID: 38481040 DOI: 10.1002/acn3.51997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE Methylation of plasma cell-free DNA (cfDNA) has potential as a marker of brain damage in neurodegenerative diseases such as frontotemporal dementia (FTD). Here, we study methylation of cfDNA in presymptomatic and symptomatic carriers of genetic FTD pathogenic variants, next to healthy controls. METHODS cfDNA was isolated from cross-sectional plasma of 10 presymptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), 10 symptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), and 9 healthy controls. Genome-wide methylation of cfDNA was determined using a high-resolution sequencing technique (MeD-seq). Cumulative scores based on the identified differentially methylated regions (DMRs) were estimated for presymptomatic carriers (vs. controls and symptomatic carriers), and reevaluated in a validation cohort (8 presymptomatic: 3 C9orf72, 3 GRN, and 2 MAPT; 26 symptomatic: 7 C9orf72, 6 GRN, 12 MAPT, and 1 TARDBP; 13 noncarriers from genetic FTD families). RESULTS Presymptomatic carriers showed a distinctive methylation profile compared to healthy controls and symptomatic carriers. Cumulative DMR scores in presymptomatic carriers enabled to significantly differentiate presymptomatic carriers from healthy controls (p < 0.001) and symptomatic carriers (p < 0.001). In the validation cohort, these scores differentiated presymptomatic carriers from symptomatic carriers (p ≤ 0.007) only. Transcription-start-site methylation in presymptomatic carriers, generally associated with gene downregulation, was enriched for genes involved in ubiquitin-dependent processes, while gene body methylation, generally associated with gene upregulation, was enriched for genes involved in neuronal cell processes. INTERPRETATION A distinctive methylation profile of cfDNA characterizes the presymptomatic stage of genetic FTD, and could reflect neuronal death in this stage.
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Affiliation(s)
- Lucia A A Giannini
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Emma L van der Ende
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Jackie M Poos
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lize C Jiskoot
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elise G Dopper
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Harro Seelaar
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lieke H Meeter
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wiep Scheper
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Human Genetics, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - John C van Swieten
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
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Domínguez-Barragán J, Fernández-Sanlés A, Hernáez Á, Llauradó-Pont J, Marrugat J, Robinson O, Tzoulaki I, Elosua R, Lassale C. Blood DNA methylation signature of diet quality and association with cardiometabolic traits. Eur J Prev Cardiol 2024; 31:191-202. [PMID: 37793095 PMCID: PMC10809172 DOI: 10.1093/eurjpc/zwad317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023]
Abstract
AIMS Diet quality might influence cardiometabolic health through epigenetic changes, but this has been little investigated in adults. Our aims were to identify cytosine-phosphate-guanine (CpG) dinucleotides associated with diet quality by conducting an epigenome-wide association study (EWAS) based on blood DNA methylation (DNAm) and to assess how diet-related CpGs associate with inherited susceptibility to cardiometabolic traits: body mass index (BMI), systolic blood pressure (SBP), triglycerides, type 2 diabetes (T2D), and coronary heart disease (CHD). METHODS AND RESULTS Meta-EWAS including 5274 participants in four cohorts from Spain, the USA, and the UK. We derived three dietary scores (exposures) to measure adherence to a Mediterranean diet, to a healthy plant-based diet, and to the Dietary Approaches to Stop Hypertension. Blood DNAm (outcome) was assessed with the Infinium arrays Human Methylation 450K BeadChip and MethylationEPIC BeadChip. For each diet score, we performed linear EWAS adjusted for age, sex, blood cells, smoking and technical variables, and BMI in a second set of models. We also conducted Mendelian randomization analyses to assess the potential causal relationship between diet-related CpGs and cardiometabolic traits. We found 18 differentially methylated CpGs associated with dietary scores (P < 1.08 × 10-7; Bonferroni correction), of which 12 were previously associated with cardiometabolic traits. Enrichment analysis revealed overrepresentation of diet-associated genes in pathways involved in inflammation and cardiovascular disease. Mendelian randomization analyses suggested that genetically determined methylation levels corresponding to lower diet quality at cg02079413 (SNORA54), cg02107842 (MAST4), and cg23761815 (SLC29A3) were causally associated with higher BMI and at cg05399785 (WDR8) with greater SBP, and methylation levels associated with higher diet quality at cg00711496 (PRMT1) with lower BMI, T2D risk, and CHD risk and at cg0557921 (AHRR) with lower CHD risk. CONCLUSION Diet quality in adults was related to differential methylation in blood at 18 CpGs, some of which related to cardiometabolic health.
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Affiliation(s)
- Jorge Domínguez-Barragán
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
| | - Alba Fernández-Sanlés
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 7HB, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Álvaro Hernáez
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo 0463, Norway
- Blanquerna School of Health Sciences, Universitat Ramon Llull, 08025 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
| | - Joana Llauradó-Pont
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
| | - Jaume Marrugat
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Oliver Robinson
- μedical Research Council Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Ioanna Tzoulaki
- Centre for Systems Biology, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Roberto Elosua
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic—Central University of Catalunya, Ctra. de Roda, 70, 08500 Vic, Spain
| | - Camille Lassale
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003, Barcelona, Spain
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Cheng Y, Li B, Zhang X, Aouizerat BE, Zhao H, Xu K. Reply to: Genetic differentiation at probe SNPs leads to spurious results in meQTL discovery. Commun Biol 2023; 6:1296. [PMID: 38129596 PMCID: PMC10739901 DOI: 10.1038/s42003-023-05646-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Affiliation(s)
- Youshu Cheng
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA
- VA Connecticut Healthcare System, US Department of Veterans Affairs, West Haven, CT, USA
| | - Boyang Li
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA
- VA Connecticut Healthcare System, US Department of Veterans Affairs, West Haven, CT, USA
| | - Xinyu Zhang
- VA Connecticut Healthcare System, US Department of Veterans Affairs, West Haven, CT, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, NY, USA
- Department of Oral and Maxillofacial Surgery, New York University, New York, NY, USA
| | - Hongyu Zhao
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA.
- VA Connecticut Healthcare System, US Department of Veterans Affairs, West Haven, CT, USA.
| | - Ke Xu
- VA Connecticut Healthcare System, US Department of Veterans Affairs, West Haven, CT, USA.
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.
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Reed EG, Keller-Norrell PR. Minding the Gap: Exploring Neuroinflammatory and Microglial Sex Differences in Alzheimer's Disease. Int J Mol Sci 2023; 24:17377. [PMID: 38139206 PMCID: PMC10743742 DOI: 10.3390/ijms242417377] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Research into Alzheimer's Disease (AD) describes a link between AD and the resident immune cells of the brain, the microglia. Further, this suspected link is thought to have underlying sex effects, although the mechanisms of these effects are only just beginning to be understood. Many of these insights are the result of policies put in place by funding agencies such as the National Institutes of Health (NIH) to consider sex as a biological variable (SABV) and the move towards precision medicine due to continued lackluster therapeutic options. The purpose of this review is to provide an updated assessment of the current research that summarizes sex differences and the research pertaining to microglia and their varied responses in AD.
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Affiliation(s)
- Erin G. Reed
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44242, USA
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Lukacsovich D, O’Shea D, Huang H, Zhang W, Young JI, Steven Chen X, Dietrich ST, Kunkle B, Martin ER, Wang L. MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.04.23299412. [PMID: 38105943 PMCID: PMC10723513 DOI: 10.1101/2023.12.04.23299412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder with a significant impact on aging populations. DNA methylation (DNAm) alterations have been implicated in both the aging processes and the development of AD. Given that AD affects more women than men, it is also important to explore DNAm changes that occur specifically in each sex. We created MIAMI-AD, a comprehensive knowledge base containing manually curated summary statistics from 97 published tables in 37 studies, all of which included at least 100 participants. MIAMI-AD enables easy browsing, querying, and downloading DNAm associations at multiple levels - at individual CpG, gene, genomic regions, or genome-wide, in one or multiple studies. Moreover, it also offers tools to perform integrative analyses, such as comparing DNAm associations across different phenotypes or tissues, as well as interactive visualizations. Using several use case examples, we demonstrated that MIAMI-AD facilitates our understanding of age-associated CpGs in AD and the sex-specific roles of DNAm in AD. This open-access resource is freely available to the research community, and all the underlying data can be downloaded. MIAMI-AD (https://miami-ad.org/) facilitates integrative explorations to better understand the interplay between DNAm across aging, sex, and AD.
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Affiliation(s)
- David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Deirdre O’Shea
- Department of Neurology, Comprehensive Center for Brain Health, University of Miami Miller School of Medicine, Boca Raton, FL, 33433
| | - Hanchen Huang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Sven-Thorsten Dietrich
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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Macías M, Acha B, Corroza J, Urdánoz-Casado A, Roldan M, Robles M, Sánchez-Ruiz de Gordoa J, Erro ME, Jericó I, Blanco-Luquin I, Mendioroz M. Liquid Biopsy in Alzheimer's Disease Patients Reveals Epigenetic Changes in the PRLHR Gene. Cells 2023; 12:2679. [PMID: 38067107 PMCID: PMC10705731 DOI: 10.3390/cells12232679] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
In recent years, new DNA methylation variants have been reported in genes biologically relevant to Alzheimer's disease (AD) in human brain tissue. However, this AD-specific epigenetic information remains brain-locked and unreachable during patients' lifetimes. In a previous methylome performed in the hippocampus of 26 AD patients and 12 controls, we found higher methylation levels in AD patients in the promoter region of PRLHR, a gene involved in energy balance regulation. Our aim was to further characterize PRLHR's role in AD and to evaluate if the liquid biopsy technique would provide life access to this brain information in a non-invasive way. First, we extended the methylation mapping of PRLHR and validated previous methylome results via bisulfite cloning sequencing. Next, we observed a positive correlation between PRLHR methylation levels and AD-related neuropathological changes and a decreased expression of PRLHR in AD hippocampus. Then, we managed to replicate the hippocampal methylation differences in plasma cfDNA from an additional cohort of 35 AD patients and 35 controls. The isolation of cfDNA from the plasma of AD patients may constitute a source of potential epigenetic biomarkers to aid AD clinical management.
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Affiliation(s)
- Mónica Macías
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Blanca Acha
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Jon Corroza
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - Amaya Urdánoz-Casado
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Miren Roldan
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Maitane Robles
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Javier Sánchez-Ruiz de Gordoa
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - María Elena Erro
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - Ivonne Jericó
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - Idoia Blanco-Luquin
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Maite Mendioroz
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays. RESEARCH SQUARE 2023:rs.3.rs-3068938. [PMID: 37461726 PMCID: PMC10350239 DOI: 10.21203/rs.3.rs-3068938/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays. RESEARCH SQUARE 2023:rs.3.rs-3068938. [PMID: 37461726 PMCID: PMC10350239 DOI: 10.21203/rs.3.rs-3068938/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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Hu X, Logan JG, Kwon Y, Lima JAC, Jacobs DR, Duprez D, Brumback L, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Blackwell TW, Papanicolaou G, Mitchell GF, Rich SS, Rotter JI, Van Den Berg DJ, Chirinos JA, Hughes TM, Garrett-Bakelman FE, Manichaikul A. Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA. Sci Rep 2023; 13:17680. [PMID: 37848499 PMCID: PMC10582077 DOI: 10.1038/s41598-023-44806-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
Despite the prognostic value of arterial stiffness (AS) and pulsatile hemodynamics (PH) for cardiovascular morbidity and mortality, epigenetic modifications that contribute to AS/PH remain unknown. To gain a better understanding of the link between epigenetics (DNA methylation) and AS/PH, we examined the relationship of eight measures of AS/PH with CpG sites and co-methylated regions using multi-ancestry participants from Trans-Omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA) with sample sizes ranging from 438 to 874. Epigenome-wide association analysis identified one genome-wide significant CpG (cg20711926-CYP1B1) associated with aortic augmentation index (AIx). Follow-up analyses, including gene set enrichment analysis, expression quantitative trait methylation analysis, and functional enrichment analysis on differentially methylated positions and regions, further prioritized three CpGs and their annotated genes (cg23800023-ETS1, cg08426368-TGFB3, and cg17350632-HLA-DPB1) for AIx. Among these, ETS1 and TGFB3 have been previously prioritized as candidate genes. Furthermore, both ETS1 and HLA-DPB1 have significant tissue correlations between Whole Blood and Aorta in GTEx, which suggests ETS1 and HLA-DPB1 could be potential biomarkers in understanding pathophysiology of AS/PH. Overall, our findings support the possible role of epigenetic regulation via DNA methylation of specific genes associated with AIx as well as identifying potential targets for regulation of AS/PH.
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Affiliation(s)
- Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jeongok G Logan
- School of Nursing, University of Virginia, Charlottesville, VA, USA
| | - Younghoon Kwon
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joao A C Lima
- Department of Internal Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David R Jacobs
- Division of Epidemiology, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Daniel Duprez
- Cardiovascular Division, University of Minnesota, Minneapolis, MN, USA
| | - Lyndia Brumback
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Elaine Cornell
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yongmei Liu
- Division of Cardiology, Department of Medicine, Duke University, Durham, NC, USA
| | - Russell P Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA
| | - Thomas W Blackwell
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - George Papanicolaou
- Epidemiology Branch, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David J Van Den Berg
- Department of Preventive Medicine and Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Julio A Chirinos
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy M Hughes
- Department of Internal Medicine - Section of Gerontology and Geriatric Medicine, and Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, Department of Medicine, University of Virginia, 1340 Jefferson Park Ave., Pinn hall 6054, Charlottesville, VA, 22908, USA.
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
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Magrin C, Bellafante M, Sola M, Piovesana E, Bolis M, Cascione L, Napoli S, Rinaldi A, Papin S, Paganetti P. Tau protein modulates an epigenetic mechanism of cellular senescence in human SH-SY5Y neuroblastoma cells. Front Cell Dev Biol 2023; 11:1232963. [PMID: 37842084 PMCID: PMC10569482 DOI: 10.3389/fcell.2023.1232963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/21/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: Progressive Tau deposition in neurofibrillary tangles and neuropil threads is the hallmark of tauopathies, a disorder group that includes Alzheimer's disease. Since Tau is a microtubule-associated protein, a prevalent concept to explain the pathogenesis of tauopathies is that abnormal Tau modification contributes to dissociation from microtubules, assembly into multimeric β-sheets, proteotoxicity, neuronal dysfunction and cell loss. Tau also localizes in the cell nucleus and evidence supports an emerging function of Tau in DNA stability and epigenetic modulation. Methods: To better characterize the possible role of Tau in regulation of chromatin compaction and subsequent gene expression, we performed a bioinformatics analysis of transcriptome data obtained from Tau-depleted human neuroblastoma cells. Results: Among the transcripts deregulated in a Tau-dependent manner, we found an enrichment of target genes for the polycomb repressive complex 2. We further describe decreased cellular amounts of the core components of the polycomb repressive complex 2 and lower histone 3 trimethylation in Tau deficient cells. Among the de-repressed polycomb repressive complex 2 target gene products, IGFBP3 protein was found to be linked to increased senescence induction in Tau-deficient cells. Discussion: Our findings propose a mechanism for Tau-dependent epigenetic modulation of cell senescence, a key event in pathologic aging.
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Affiliation(s)
- Claudia Magrin
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, PhD Program in Neurosciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Martina Bellafante
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
| | - Martina Sola
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, PhD Program in Neurosciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Ester Piovesana
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, PhD Program in Neurosciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Marco Bolis
- Functional Cancer Genomics Laboratory, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milano, Italy
- Lymphoma and Genomics Research Program, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
| | - Luciano Cascione
- Lymphoma and Genomics Research Program, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sara Napoli
- Lymphoma and Genomics Research Program, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
| | - Andrea Rinaldi
- Lymphoma and Genomics Research Program, Institute of Oncology Research, Università Della Svizzera Italiana, Bellinzona, Switzerland
| | - Stéphanie Papin
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
| | - Paolo Paganetti
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Cantonale Ospedaliero, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, PhD Program in Neurosciences, Università Della Svizzera Italiana, Lugano, Switzerland
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Wang X, Liu L, Jiang X, Saredy J, Xi H, Cueto R, Sigler D, Khan M, Wu S, Ji Y, Snyder NW, Hu W, Yang X, Wang H. Identification of methylation-regulated genes modulating microglial phagocytosis in hyperhomocysteinemia-exacerbated Alzheimer's disease. Alzheimers Res Ther 2023; 15:164. [PMID: 37789414 PMCID: PMC10546779 DOI: 10.1186/s13195-023-01311-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Hyperhomocysteinemia (HHcy) has been linked to development of Alzheimer's disease (AD) neuropathologically characterized by the accumulation of amyloid β (Aβ). Microglia (MG) play a crucial role in uptake of Aβ fibrils, and its dysfunction worsens AD. However, the effect of HHcy on MG Aβ phagocytosis remains unstudied. METHODS We isolated MG from the cerebrum of HHcy mice with genetic cystathionine-β-synthase deficiency (Cbs-/-) and performed bulk RNA-seq. We performed meta-analysis over transcriptomes of Cbs-/- mouse MG, human and mouse AD MG, MG Aβ phagocytosis model, human AD methylome, and GWAS AD genes. RESULTS HHcy and hypomethylation conditions were identified in Cbs-/- mice. Through Cbs-/- MG transcriptome analysis, 353 MG DEGs were identified. Phagosome formation and integrin signaling pathways were found suppressed in Cbs-/- MG. By analyzing MG transcriptomes from 4 AD patient and 7 mouse AD datasets, 409 human and 777 mouse AD MG DEGs were identified, of which 37 were found common in both species. Through further combinatory analysis with transcriptome from MG Aβ phagocytosis model, we identified 130 functional-validated Aβ phagocytic AD MG DEGs (20 in human AD, 110 in mouse AD), which reflected a compensatory activation of Aβ phagocytosis. Interestingly, we identified 14 human Aβ phagocytic AD MG DEGs which represented impaired MG Aβ phagocytosis in human AD. Finally, through a cascade of meta-analysis of transcriptome of AD MG, functional phagocytosis, HHcy MG, and human AD brain methylome dataset, we identified 5 HHcy-suppressed phagocytic AD MG DEGs (Flt1, Calponin 3, Igf1, Cacna2d4, and Celsr) which were reported to regulate MG/MΦ migration and Aβ phagocytosis. CONCLUSIONS We established molecular signatures for a compensatory response of Aβ phagocytosis activation in human and mouse AD MG and impaired Aβ phagocytosis in human AD MG. Our discoveries suggested that hypomethylation may modulate HHcy-suppressed MG Aβ phagocytosis in AD.
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Affiliation(s)
- Xianwei Wang
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Lu Liu
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Xiaohua Jiang
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Jason Saredy
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Hang Xi
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Ramon Cueto
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Danni Sigler
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Mohsin Khan
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Sheng Wu
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Yong Ji
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Wenhui Hu
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Xiaofeng Yang
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Hong Wang
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA.
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Jeremic D, Jiménez-Díaz L, Navarro-López JD. Targeting epigenetics: A novel promise for Alzheimer's disease treatment. Ageing Res Rev 2023; 90:102003. [PMID: 37422087 DOI: 10.1016/j.arr.2023.102003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/30/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023]
Abstract
So far, the search for a cure for Alzheimer Disease (AD) has been unsuccessful. The only approved drugs attenuate some symptoms, but do not halt the progress of this disease, which affects 50 million people worldwide and will increase its incidence in the coming decades. Such scenario demands new therapeutic approaches to fight against this devastating dementia. In recent years, multi-omics research and the analysis of differential epigenetic marks in AD subjects have contributed to our understanding of AD; however, the impact of epigenetic research is yet to be seen. This review integrates the most recent data on pathological processes and epigenetic changes relevant for aging and AD, as well as current therapies targeting epigenetic machinery in clinical trials. Evidence shows that epigenetic modifications play a key role in gene expression, which could provide multi-target preventative and therapeutic approaches in AD. Both novel and repurposed drugs are employed in AD clinical trials due to their epigenetic effects, as well as increasing number of natural compounds. Given the reversible nature of epigenetic modifications and the complexity of gene-environment interactions, the combination of epigenetic-based therapies with environmental strategies and drugs with multiple targets might be needed to properly help AD patients.
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Affiliation(s)
- Danko Jeremic
- University of Castilla-La Mancha, NeuroPhysiology & Behavior Lab, Biomedical Research Center (CRIB), School of Medicine of Ciudad Real, Spain
| | - Lydia Jiménez-Díaz
- University of Castilla-La Mancha, NeuroPhysiology & Behavior Lab, Biomedical Research Center (CRIB), School of Medicine of Ciudad Real, Spain.
| | - Juan D Navarro-López
- University of Castilla-La Mancha, NeuroPhysiology & Behavior Lab, Biomedical Research Center (CRIB), School of Medicine of Ciudad Real, Spain.
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47
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Abdolmaleky HM, Zhou JR. Underlying Mechanisms of Brain Aging and Neurodegenerative Diseases as Potential Targets for Preventive or Therapeutic Strategies Using Phytochemicals. Nutrients 2023; 15:3456. [PMID: 37571393 PMCID: PMC10473240 DOI: 10.3390/nu15153456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
During aging, several tissues and biological systems undergo a progressive decline in function, leading to age-associated diseases such as neurodegenerative, inflammatory, metabolic, and cardiovascular diseases and cancer. In this review, we focus on the molecular underpinning of senescence and neurodegeneration related to age-associated brain diseases, in particular, Alzheimer's and Parkinson's diseases, along with introducing nutrients or phytochemicals that modulate age-associated molecular dysfunctions, potentially offering preventive or therapeutic benefits. Based on current knowledge, the dysregulation of microglia genes and neuroinflammation, telomere attrition, neuronal stem cell degradation, vascular system dysfunction, reactive oxygen species, loss of chromosome X inactivation in females, and gut microbiome dysbiosis have been seen to play pivotal roles in neurodegeneration in an interactive manner. There are several phytochemicals (e.g., curcumin, EGCG, fucoidan, galangin, astin C, apigenin, resveratrol, phytic acid, acacetin, daucosterol, silibinin, sulforaphane, withaferin A, and betulinic acid) that modulate the dysfunction of one or several key genes (e.g., TREM2, C3, C3aR1, TNFA, NF-kb, TGFB1&2, SIRT1&6, HMGB1, and STING) affected in the aged brain. Although phytochemicals have shown promise in slowing down the progression of age-related brain diseases, more studies to identify their efficacy, alone or in combinations, in preclinical systems can help to design novel nutritional strategies for the management of neurodegenerative diseases in humans.
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Affiliation(s)
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA;
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48
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Manichaikul A, Hu X, Logan J, Kwon Y, Lima J, Jacobs D, Duprez D, Brumback L, Taylor K, Durda P, Johnson C, Cornell E, Guo X, Liu Y, Tracy R, Blackwell T, Papanicolaou G, Mitchell G, Rich S, Rotter J, Van Den Berg D, Chirinos J, Hughes T, Garrett-Bakelman F. Multi-ancestry epigenome-wide analyses identify methylated sites associated with aortic augmentation index in TOPMed MESA. RESEARCH SQUARE 2023:rs.3.rs-3125948. [PMID: 37502922 PMCID: PMC10371087 DOI: 10.21203/rs.3.rs-3125948/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Despite the prognostic value of arterial stiffness (AS) and pulsatile hemodynamics (PH) for cardiovascular morbidity and mortality, epigenetic modifications that contribute to AS/PH remain unknown. To gain a better understanding of the link between epigenetics (DNA methylation) and AS/PH, we examined the relationship of eight measures of AS/PH with CpG sites and co-methylated regions using multi-ancestry participants from Trans-Omics for Precision Medicine (TOPMed) Multi-Ethnic Study of Atherosclerosis (MESA) with sample sizes ranging from 438 to 874. Epigenome-wide association analysis identified one genome-wide significant CpG (cg20711926-CYP1B1) associated with aortic augmentation index (AIx). Follow-up analyses, including gene set enrichment analysis, expression quantitative trait methylation analysis, and functional enrichment analysis on differentially methylated positions and regions, further prioritized three CpGs and their annotated genes (cg23800023-ETS1, cg08426368-TGFB3, and cg17350632-HLA-DPB1) for AIx. Among these, ETS1 and TGFB3 have been previously prioritized as candidate genes. Furthermore, both ETS1 and HLA-DPB1 have significant tissue correlations between Whole Blood and Aorta in GTEx, which suggests ETS1 and HLA-DPB1 could be potential biomarkers in understanding pathophysiology of AS/PH. Overall, our findings support the possible role of epigenetic regulation via DNA methylation of specific genes associated with AIx as well as identifying potential targets for regulation of AS/PH.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kent Taylor
- The Institute for Translational Genomics and Population Sciences
| | | | | | | | | | | | | | | | | | | | - Stephen Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia
| | - Jerome Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center
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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; 146:77-95. [PMID: 37149835 PMCID: PMC10261190 DOI: 10.1007/s00401-023-02583-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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50
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Fodder K, de Silva R, Warner TT, Bettencourt C. The contribution of DNA methylation to the (dys)function of oligodendroglia in neurodegeneration. Acta Neuropathol Commun 2023; 11:106. [PMID: 37386505 PMCID: PMC10311741 DOI: 10.1186/s40478-023-01607-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
Neurodegenerative diseases encompass a heterogeneous group of conditions characterised by the progressive degeneration of the structure and function of the central or peripheral nervous systems. The pathogenic mechanisms underlying these diseases are not fully understood. However, a central feature consists of regional aggregation of proteins in the brain, such as the accumulation of β-amyloid plaques in Alzheimer's disease (AD), inclusions of hyperphosphorylated microtubule-binding tau in AD and other tauopathies, or inclusions containing α-synuclein in Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). Various pathogenic mechanisms are thought to contribute to disease, and an increasing number of studies implicate dysfunction of oligodendrocytes (the myelin producing cells of the central nervous system) and myelin loss. Aberrant DNA methylation, the most widely studied epigenetic modification, has been associated with many neurodegenerative diseases, including AD, PD, DLB and MSA, and recent findings highlight aberrant DNA methylation in oligodendrocyte/myelin-related genes. Here we briefly review the evidence showing that changes to oligodendrocytes and myelin are key in neurodegeneration, and explore the relevance of DNA methylation in oligodendrocyte (dys)function. As DNA methylation is reversible, elucidating its involvement in pathogenic mechanisms of neurodegenerative diseases and in dysfunction of specific cell-types such as oligodendrocytes may bring opportunities for therapeutic interventions for these diseases.
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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
| | - Rohan de Silva
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Thomas T Warner
- 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
- Reta Lila Weston Institute, 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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