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Tomusiak A, Floro A, Tiwari R, Riley R, Matsui H, Andrews N, Kasler HG, Verdin E. Development of an epigenetic clock resistant to changes in immune cell composition. Commun Biol 2024; 7:934. [PMID: 39095531 PMCID: PMC11297166 DOI: 10.1038/s42003-024-06609-4] [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: 09/22/2023] [Accepted: 07/14/2024] [Indexed: 08/04/2024] Open
Abstract
Epigenetic clocks are age predictors that use machine-learning models trained on DNA CpG methylation values to predict chronological or biological age. Increases in predicted epigenetic age relative to chronological age (epigenetic age acceleration) are connected to aging-associated pathologies, and changes in epigenetic age are linked to canonical aging hallmarks. However, epigenetic clocks rely on training data from bulk tissues whose cellular composition changes with age. Here, we found that human naive CD8+ T cells, which decrease in frequency during aging, exhibit an epigenetic age 15-20 years younger than effector memory CD8+ T cells from the same individual. Importantly, homogenous naive T cells isolated from individuals of different ages show a progressive increase in epigenetic age, indicating that current epigenetic clocks measure two independent variables, aging and immune cell composition. To isolate the age-associated cell intrinsic changes, we created an epigenetic clock, the IntrinClock, that did not change among 10 immune cell types tested. IntrinClock shows a robust predicted epigenetic age increase in a model of replicative senescence in vitro and age reversal during OSKM-mediated reprogramming.
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Affiliation(s)
- Alan Tomusiak
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
- Department of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, 90089, CA, USA
| | - Ariel Floro
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
- Department of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, 90089, CA, USA
| | - Ritesh Tiwari
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Rebeccah Riley
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Hiroyuki Matsui
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Nicolas Andrews
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Herbert G Kasler
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA.
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Choza JI, Virani M, Kuhn NC, Adams M, Kochmanski J, Bernstein AI. Parkinson's disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain in PD-related genes, including PARK19 (DNAJC6) and PTPRN2 (IA-2β). RESEARCH SQUARE 2024:rs.3.rs-4572401. [PMID: 39070644 PMCID: PMC11275970 DOI: 10.21203/rs.3.rs-4572401/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: 07/30/2024]
Abstract
Background The majority of Parkinson's disease (PD) cases are due to a complex interaction between aging, genetics, and environmental factors; epigenetic mechanisms are thought to act as important mediators of these risk factors. While multiple studies to date have explored the role of DNA modifications in PD, few focus on 5-hydroxymethylcytosine (5hmC). Because 5hmC occurs at its highest levels in the brain and is thought to be particularly important in the central nervous system, particularly in the response to neurotoxicants, it is important to explore the potential role of 5hmC in PD. This study expands on our previously published epigenome-wide association study (EWAS) performed on DNA isolated from neuron-enriched nuclei from human postmortem parietal cortex from the Banner Sun Health Research Institute Brain Bank. The study aimed to identify paired changes in 5hmC and 5mC in PD in enriched neuronal nuclei isolated from PD post-mortem parietal cortex and age- and sex-matched controls. We performed oxidative bisulfite (oxBS) conversion and paired it with our previously published bisulfite (BS)-based EWAS on the same samples to identify cytosines with significant shifts between these two related epigenetic marks. Interaction differentially modified cytosines (iDMCs) were identified using our recently published mixed-effects model for co-analyzing βmC and βhmC data. Results We identified 1,030 iDMCs with paired changes in 5mC and 5hmC (FDR < 0.05) that map to 695 genes, including PARK19 (DNAJC6), a familial PD gene, and PTPRN2 (IA-2), which has been previously implicated in PD in both epigenetic and mechanistic studies. The majority of iDMC-containing genes have not previously been implicated in PD and were not identified in our previous BS-based EWAS. Conclusions These data potentially link epigenetic regulation of the PARK19 and PTPRN2 loci in the pathogenesis of idiopathic PD. In addition, iDMC-containing genes have known functions in synaptic formation and function, cell cycle and senescence, neuroinflammation, and epigenetic regulation. These data suggest that there are significant shifts between 5mC and 5hmC associated with PD in genes relevant to PD pathogenesis that are not captured by analyzing BS-based data alone or by analyzing each mark as a distinct dataset.
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Murthy M, Fodder K, Miki Y, Rambarack N, De Pablo Fernandez E, Pihlstrøm L, Mill J, Warner TT, Lashley T, Bettencourt C. DNA methylation patterns in the frontal lobe white matter of multiple system atrophy, Parkinson's disease, and progressive supranuclear palsy: a cross-comparative investigation. Acta Neuropathol 2024; 148:4. [PMID: 38995454 PMCID: PMC11245434 DOI: 10.1007/s00401-024-02764-4] [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: 04/22/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
Multiple system atrophy (MSA) is a rare neurodegenerative disease characterized by neuronal loss and gliosis, with oligodendroglial cytoplasmic inclusions (GCIs) containing α-synuclein being the primary pathological hallmark. Clinical presentations of MSA overlap with other parkinsonian disorders, such as Parkinson's disease (PD), dementia with Lewy bodies (DLB), and progressive supranuclear palsy (PSP), posing challenges in early diagnosis. Numerous studies have reported alterations in DNA methylation in neurodegenerative diseases, with candidate loci being identified in various parkinsonian disorders including MSA, PD, and PSP. Although MSA and PSP present with substantial white matter pathology, alterations in white matter have also been reported in PD. However, studies comparing the DNA methylation architectures of white matter in these diseases are lacking. We therefore aimed to investigate genome-wide DNA methylation patterns in the frontal lobe white matter of individuals with MSA (n = 17), PD (n = 17), and PSP (n = 16) along with controls (n = 15) using the Illumina EPIC array, to identify shared and disease-specific DNA methylation alterations. Genome-wide DNA methylation profiling of frontal lobe white matter in the three parkinsonian disorders revealed substantial commonalities in DNA methylation alterations in MSA, PD, and PSP. We further used weighted gene correlation network analysis to identify disease-associated co-methylation signatures and identified dysregulation in processes relating to Wnt signaling, signal transduction, endoplasmic reticulum stress, mitochondrial processes, RNA interference, and endosomal transport to be shared between these parkinsonian disorders. Our overall analysis points toward more similarities in DNA methylation patterns between MSA and PD, both synucleinopathies, compared to that between MSA and PD with PSP, which is a tauopathy. Our results also highlight several shared DNA methylation changes and pathways indicative of converging molecular mechanisms in the white matter contributing toward neurodegeneration in all three parkinsonian disorders.
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Affiliation(s)
- 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
| | - 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
| | - Yasuo Miki
- Department of Neuropathology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Naiomi Rambarack
- 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
| | - Eduardo De Pablo Fernandez
- 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
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, 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
| | - Tammaryn Lashley
- 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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4
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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5
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Ås J, Bertulyte I, Norgren N, Johansson A, Eriksson N, Green H, Wadelius M, Hallberg P. Whole genome case-control study of central nervous system toxicity due to antimicrobial drugs. PLoS One 2024; 19:e0299075. [PMID: 38422004 PMCID: PMC10903854 DOI: 10.1371/journal.pone.0299075] [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: 04/04/2023] [Accepted: 02/03/2024] [Indexed: 03/02/2024] Open
Abstract
A genetic predisposition to central nervous system (CNS) toxicity induced by antimicrobial drugs (antibiotics, antivirals, antifungals, and antiparasitic drugs) has been suspected. Whole genome sequencing of 66 cases and 833 controls was performed to investigate whether antimicrobial drug-induced CNS toxicity was associated with genetic variation. The primary objective was to test whether antimicrobial-induced CNS toxicity was associated with seventeen efflux transporters at the blood-brain barrier. In this study, variants or structural elements in efflux transporters were not significantly associated with CNS toxicity. Secondary objectives were to test whether antimicrobial-induced CNS toxicity was associated with genes over the whole genome, with HLA, or with structural genetic variation. Uncommon variants in and close to three genes were significantly associated with CNS toxicity according to a sequence kernel association test combined with an optimal unified test (SKAT-O). These genes were LCP1 (q = 0.013), RETSAT (q = 0.013) and SFMBT2 (q = 0.035). Two variants were driving the LCP1 association: rs6561297 (p = 1.15x10-6, OR: 4.60 [95% CI: 2.51-8.46]) and the regulatory variant rs10492451 (p = 1.15x10-6, OR: 4.60 [95% CI: 2.51-8.46]). No common genetic variant, HLA-type or structural variation was associated with CNS toxicity. In conclusion, CNS toxicity due to antimicrobial drugs was associated with uncommon variants in LCP1, RETSAT and SFMBT2.
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Affiliation(s)
- Joel Ås
- Department of Medical Sciences, Clinical Pharmacogenomics and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ilma Bertulyte
- Department of Medical Sciences, Clinical Pharmacogenomics and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nina Norgren
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Anna Johansson
- Dept of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Niclas Eriksson
- Department of Medical Sciences, Clinical Pharmacogenomics and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala, Sweden
| | - Henrik Green
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacogenomics and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pär Hallberg
- Department of Medical Sciences, Clinical Pharmacogenomics and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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6
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Reho P, Saez-Atienzar S, Ruffo P, Solaiman S, Shah Z, Chia R, Kaivola K, Traynor BJ, Tilley BS, Gentleman SM, Hodges AK, Aarsland D, Monuki ES, Newell KL, Woltjer R, Albert MS, Dawson TM, Rosenthal LS, Troncoso JC, Pletnikova O, Serrano GE, Beach TG, Easwaran HP, Scholz SW. Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies. Commun Biol 2024; 7:35. [PMID: 38182665 PMCID: PMC10770032 DOI: 10.1038/s42003-023-05725-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: 01/13/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
Dementia with Lewy bodies (DLB) is a common form of dementia in the elderly population. We performed genome-wide DNA methylation mapping of cerebellar tissue from pathologically confirmed DLB cases and controls to study the epigenetic profile of this understudied disease. After quality control filtering, 728,197 CpG-sites in 278 cases and 172 controls were available for the analysis. We undertook an epigenome-wide association study, which found a differential methylation signature in DLB cases. Our analysis identified seven differentially methylated probes and three regions associated with DLB. The most significant CpGs were located in ARSB (cg16086807), LINC00173 (cg18800161), and MGRN1 (cg16250093). Functional enrichment evaluations found widespread epigenetic dysregulation in genes associated with neuron-to-neuron synapse, postsynaptic specialization, postsynaptic density, and CTCF-mediated synaptic plasticity. In conclusion, our study highlights the potential importance of epigenetic alterations in the pathogenesis of DLB and provides insights into the modified genes, regions and pathways that may guide therapeutic developments.
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Affiliation(s)
- Paolo Reho
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Laboratory of Precision Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sara Saez-Atienzar
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
| | - Paola Ruffo
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Sultana Solaiman
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Zalak Shah
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
| | - Karri Kaivola
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
| | - Bension S Tilley
- Neuropathology Unit, Department of Brain Sciences, Imperial College London, London, UK
| | - Steve M Gentleman
- Neuropathology Unit, Department of Brain Sciences, Imperial College London, London, UK
| | - Angela K Hodges
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Dag Aarsland
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Centre for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Edwin S Monuki
- Department of Pathology & Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Randy Woltjer
- Department of Neurology, Oregon Health & Sciences University, Portland, OR, USA
| | - Marilyn S Albert
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Ted M Dawson
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuroregeneration and Stem Cell Programs, Institute of Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liana S Rosenthal
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Hariharan P Easwaran
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA.
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Ohlei O, Sommerer Y, Dobricic V, Homann J, Deecke L, Schilling M, Bartrés-Faz D, Cattaneo G, Düzel S, Fjell AM, Lindenberger U, Pascual-Leone Á, Sedghpour Sabet S, Solé-Padullés C, Tormos JM, Vetter VM, Walhovd KB, Wesse T, Wittig M, Franke A, Demuth I, Lill CM, Bertram L. Genome-wide QTL mapping across three tissues highlights several Alzheimer's and Parkinson's disease loci potentially acting via DNA methylation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.22.23300365. [PMID: 38196633 PMCID: PMC10775408 DOI: 10.1101/2023.12.22.23300365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
DNA methylation (DNAm) is an epigenetic mark with essential roles in disease development and predisposition. Here, we created genome-wide maps of methylation quantitative trait loci (meQTL) in three peripheral tissues and used Mendelian randomization (MR) analyses to assess the potential causal relationships between DNAm and risk for two common neurodegenerative disorders, i.e. Alzheimer's disease (AD) and Parkinson's disease (PD). Genome-wide single nucleotide polymorphism (SNP; ~5.5M sites) and DNAm (~850K CpG sites) data were generated from whole blood (n=1,058), buccal (n=1,527) and saliva (n=837) specimens. We identified between 11 and 15 million genome-wide significant (p<10-14) SNP-CpG associations in each tissue. Combining these meQTL GWAS results with recent AD/PD GWAS summary statistics by MR strongly suggests that the previously described associations between PSMC3, PICALM, and TSPAN14 and AD may be founded on differential DNAm in or near these genes. In addition, there is strong, albeit less unequivocal, support for causal links between DNAm at PRDM7 in AD as well as at KANSL1/MAPT in AD and PD. Our study adds valuable insights on AD/PD pathogenesis by combining two high-resolution "omics" domains, and the meQTL data shared along with this publication will allow like-minded analyses in other diseases.
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Affiliation(s)
- Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Yasmine Sommerer
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Jan Homann
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Laura Deecke
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Marcel Schilling
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - David Bartrés-Faz
- Department of Medicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain
| | - Gabriele Cattaneo
- Institut Guttmann, Institut Universitari de Neurorehabilitació adscrit a la UAB, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Camí de les Escoles, Badalona, Barcelona, Spain
| | - Sandra Düzel
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Anders M Fjell
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | - Ulman Lindenberger
- Center for Lifespan Psychology, Max Planck Institute for Human Development, Berlin, Germany
| | - Álvaro Pascual-Leone
- Hinda and Arthur Marcus Institute for Aging Research and Deanna and Sidney Wolk Center for Memory Health, Hebrew SeniorLife, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Sanaz Sedghpour Sabet
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Cristina Solé-Padullés
- Department of Medicine, Faculty of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, Barcelona, Spain
| | - Josep M Tormos
- Institut Guttmann, Institut Universitari de Neurorehabilitació adscrit a la UAB, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Fundació Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Camí de les Escoles, Badalona, Barcelona, Spain
| | - Valentin M Vetter
- Biology of Aging Working Group, Department of Endocrinology and Metabolic Diseases, Division of Lipid Metabolism, Charité-Universitätsmedizin Berlin (corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany
| | - Kristine B Walhovd
- Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | - Tanja Wesse
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Ilja Demuth
- Biology of Aging Working Group, Department of Endocrinology and Metabolic Diseases, Division of Lipid Metabolism, Charité-Universitätsmedizin Berlin (corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christina M Lill
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
- Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London, London, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
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8
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Andersen MS, Leikfoss IS, Brorson IS, Cappelletti C, Bettencourt C, Toft M, Pihlstrøm L. Epigenome-wide association study of peripheral immune cell populations in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:149. [PMID: 37903812 PMCID: PMC10616224 DOI: 10.1038/s41531-023-00594-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Understanding the contribution of immune mechanisms to Parkinson's disease pathogenesis is an important challenge, potentially of major therapeutic implications. To further elucidate the involvement of peripheral immune cells, we studied epigenome-wide DNA methylation in isolated populations of CD14+ monocytes, CD19+ B cells, CD4+ T cells, and CD8+ T cells from Parkinson's disease patients and healthy control participants. We included 25 patients with a maximum five years of disease duration and 25 controls, and isolated four immune cell populations from each fresh blood sample. Epigenome-wide DNA methylation profiles were generated from 186 samples using the Illumina MethylationEpic array and association with disease status was tested using linear regression models. We identified six differentially methylated CpGs in CD14+ monocytes and one in CD8 + T cells. Four differentially methylated regions were identified in monocytes, including a region upstream of RAB32, a gene that has been linked to LRRK2. Methylation upstream of RAB32 correlated negatively with mRNA expression, and RAB32 expression was upregulated in Parkinson's disease both in our samples and in summary statistics from a previous study. Our epigenome-wide association study of early Parkinson's disease provides evidence for methylation changes across different peripheral immune cell types, highlighting monocytes and the RAB32 locus. The findings were predominantly cell-type-specific, demonstrating the value of isolating purified cell populations for genomic studies.
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Affiliation(s)
- Maren Stolp Andersen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | - Conceicao Bettencourt
- Department of Neurodegenerative Disease and Queen Square Brain Bank for Neurological Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
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Cappelletti C, Henriksen SP, Geut H, Rozemuller AJM, van de Berg WDJ, Pihlstrøm L, Toft M. Transcriptomic profiling of Parkinson's disease brains reveals disease stage specific gene expression changes. Acta Neuropathol 2023; 146:227-244. [PMID: 37347276 PMCID: PMC10329075 DOI: 10.1007/s00401-023-02597-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/02/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
Parkinson´s disease (PD) is a progressive neurodegenerative disorder characterized by both motor and non-motor symptoms. Aggravation of symptoms is mirrored by accumulation of protein aggregates mainly composed by alpha-synuclein in different brain regions, called Lewy bodies (LB). Previous studies have identified several molecular mechanisms as autophagy and inflammation playing a role in PD pathogenesis. Increased insights into mechanisms involved in early disease stages and driving the progression of the LB pathology are required for the development of disease-modifying strategies. Here, we aimed to elucidate disease stage-specific transcriptomic changes in brain tissue of well-characterized PD and control donors. We collected frontal cortex samples from 84 donors and sequenced both the coding and non-coding RNAs. We categorized our samples into groups based on their degree of LB pathology aiming to recapitulate a central aspect of disease progression. Using an analytical pipeline that corrected for sex, age at death, RNA quality, cell composition and unknown sources of variation, we found major disease stage-specific transcriptomic changes. Gene expression changes were most pronounced in donors at the disease stage when microscopic LB changes first occur in the sampled brain region. Additionally, we identified disease stage-specific enrichment of brain specific pathways and immune mechanisms. On the contrary, we showed that mitochondrial mechanisms are enriched throughout the disease course. Our data-driven approach also suggests a role for several poorly characterized lncRNAs in disease development and progression of PD. Finally, by combining genetic and epigenetic information, we highlighted two genes (MAP4K4 and PHYHIP) as candidate genes for future functional studies. Together our results indicate that transcriptomic dysregulation and associated functional changes are highly disease stage-specific, which has major implications for the study of neurodegenerative disorders.
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Affiliation(s)
- Chiara Cappelletti
- Department of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, OsloMet-Oslo Metropolitan University, Oslo, Norway
- Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | | | - Hanneke Geut
- Amsterdam UMC, Section Clinical Neuroanatomy and Biobanking, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
- Netherlands Brain Bank, Netherlands Institute of Neurosciences, Amsterdam, Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam UMC, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Wilma D J van de Berg
- Amsterdam UMC, Section Clinical Neuroanatomy and Biobanking, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Vrije Universiteit, Amsterdam, Netherlands
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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Adebisi B, Nour MA, Periñán MT. Implications of DNA Methylation in Lewy Body Pathology. Mov Disord 2023; 38:25. [PMID: 36444149 DOI: 10.1002/mds.29290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Benjamin Adebisi
- Department of Anatomy, College of Health Sciences, Osun State University, Osogbo, Nigeria
| | - Mohamed A Nour
- Faculty of Brain Sciences, University College London Queen Square Institute of Neurology, London, UK
| | - María T Periñán
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, Seville, Spain
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Ortiz-Rodríguez MA, Martínez-Salazar MF, Antunez-Bautista PK, Jiménez-Osorio AS. Strategies for the study of neuroepigenetics and aging with a translational approach. AGING AND HEALTH RESEARCH 2023. [DOI: 10.1016/j.ahr.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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