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Grodstein F, Lemos B, Yang J, de Paiva Lopes K, Vialle RA, Seyfried N, Wang Y, Shireby G, Hannon E, Thomas A, Brookes K, Mill J, De Jager PL, Bennett DA. Genetic architecture of epigenetic cortical clock age in brain tissue from older individuals: alterations in CD46 and other loci. Epigenetics 2024; 19:2392050. [PMID: 39169872 PMCID: PMC11346548 DOI: 10.1080/15592294.2024.2392050] [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: 03/07/2024] [Revised: 07/18/2024] [Accepted: 08/06/2024] [Indexed: 08/23/2024] Open
Abstract
The cortical epigenetic clock was developed in brain tissue as a biomarker of brain aging. As one way to identify mechanisms underlying aging, we conducted a GWAS of cortical age. We leveraged postmortem cortex tissue and genotyping array data from 694 participants of the Rush Memory and Aging Project and Religious Orders Study (ROSMAP; 11000,000 SNPs), and meta-analysed ROSMAP with 522 participants of Brains for Dementia Research (5,000,000 overlapping SNPs). We confirmed results using eQTL (cortical bulk and single nucleus gene expression), cortical protein levels (ROSMAP), and phenome-wide association studies (clinical/neuropathologic phenotypes, ROSMAP). In the meta-analysis, the strongest association was rs4244620 (p = 1.29 × 10-7), which also exhibited FDR-significant cis-eQTL effects for CD46 in bulk and single nucleus (microglia, astrocyte, oligodendrocyte, neuron) cortical gene expression. Additionally, rs4244620 was nominally associated with lower cognition, faster slopes of cognitive decline, and greater Parkinsonian signs (n ~ 1700 ROSMAP with SNP/phenotypic data; all p ≤ 0.04). In ROSMAP alone, the top SNP was rs4721030 (p = 8.64 × 10-8) annotated to TMEM106B and THSD7A. Further, in ROSMAP (n = 849), TMEM106B and THSD7A protein levels in cortex were related to many phenotypes, including greater AD pathology and lower cognition (all p ≤ 0.0007). Overall, we identified converging evidence of CD46 and possibly TMEM106B/THSD7A for potential roles in cortical epigenetic clock age.
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Affiliation(s)
- Francine Grodstein
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Bernardo Lemos
- Coit Center for Longevity and Neurotherapeutics, Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Jingyun Yang
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Katia de Paiva Lopes
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Ricardo A. Vialle
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Nicholas Seyfried
- Department of Biochemistry, and Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA
| | - Yanling Wang
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Gemma Shireby
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Alan Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Keeley Brookes
- Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Philip L. De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, and Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
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2
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Yusipov I, Kalyakulina A, Trukhanov A, Franceschi C, Ivanchenko M. Map of epigenetic age acceleration: A worldwide analysis. Ageing Res Rev 2024; 100:102418. [PMID: 39002646 DOI: 10.1016/j.arr.2024.102418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
We present a systematic analysis of epigenetic age acceleration based on by far the largest collection of publicly available DNA methylation data for healthy samples (93 datasets, 23 K samples), focusing on the geographic (25 countries) and ethnic (31 ethnicities) aspects around the world. We employed the most popular epigenetic tools for assessing age acceleration and examined their quality metrics and ability to extrapolate to epigenetic data from different tissue types and age ranges different from the training data of these models. In most cases, the models proved to be inconsistent with each other and showed different signs of age acceleration, with the PhenoAge model tending to systematically underestimate and different versions of the GrimAge model tending to systematically overestimate the age prediction of healthy subjects. Referring to data availability and consistency, most countries and populations are still not represented in GEO, moreover, different datasets use different criteria for determining healthy controls. Because of this, it is difficult to fully isolate the contribution of "geography/environment", "ethnicity" and "healthiness" to epigenetic age acceleration. Among the explored metrics, only the DunedinPACE, which measures aging rate, appears to adequately reflect the standard of living and socioeconomic indicators in countries, although it has a limited application to blood methylation data only. Invariably, by epigenetic age acceleration, males age faster than females in most of the studied countries and populations.
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Affiliation(s)
- Igor Yusipov
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Alena Kalyakulina
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Arseniy Trukhanov
- Mriya Life Institute, National Academy of Active Longevity, Moscow 124489, Russia.
| | - Claudio Franceschi
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Mikhail Ivanchenko
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
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3
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Abdelmageed M, Palanisamy P, Vernail V, Silberman Y, Paul S, Paul A. An altered cell-specific subcellular distribution of translesion synthesis DNA polymerase kappa (POLK) in aging neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.27.559771. [PMID: 39026788 PMCID: PMC11257472 DOI: 10.1101/2023.09.27.559771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Genomic stability is critical for cellular function, however, in the central nervous system highly metabolically active differentiated neurons are challenged to maintain their genome over the organismal lifespan without replication. DNA damage in neurons increases with chronological age and accelerates in neurodegenerative disorders, resulting in cellular and systemic dysregulation. Distinct DNA damage response strategies have evolved with a host of polymerases. The Y-family translesion synthesis (TLS) polymerases are well known for bypassing and repairing damaged DNA in dividing cells. However, their expression, dynamics, and role if any, in enduring postmitotic differentiated neurons of the brain are completely unknown. We show through systematic longitudinal studies for the first time that DNA polymerase kappa (POLK), a member of the Y-family polymerases, is highly expressed in neurons. With chronological age, there is a progressive and significant reduction of nuclear POLK with a concomitant accumulation in the cytoplasm that is predictive of brain tissue age. The reduction of nuclear POLK in old brains is congruent with an increase in DNA damage markers. The nuclear POLK colocalizes with damaged sites and DNA repair proteins. The cytoplasmic POLK accumulates with stress granules and endo/lysosomal markers. Nuclear POLK expression is significantly higher in GABAergic interneurons compared to excitatory pyramidal neurons and lowest in non-neurons, possibly reflective of the inherent biological differences such as firing rates and neuronal activity. Interneurons associated with microglia have significantly higher levels of cytoplasmic POLK in old age. Finally, we show that neuronal activity itself can lead to an increase in nuclear POLK levels and a reduction of the cytoplasmic fraction. Our findings open a new avenue in understanding how different classes of postmitotic neurons deploy TLS polymerase(s) to maintain their genomic integrity over time, which will help design strategies for longevity, healthspan, and prevention of neurodegeneration.
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García-delaTorre P, Rivero-Segura NA, Sánchez-García S, Becerril-Rojas K, Sandoval-Rodriguez FE, Castro-Morales D, Cruz-Lopez M, Vazquez-Moreno M, Rincón-Heredia R, Ramirez-Garcia P, Gomez-Verjan JC. GrimAge is elevated in older adults with mild COVID-19 an exploratory analysis. GeroScience 2024; 46:3511-3524. [PMID: 38358578 PMCID: PMC11226692 DOI: 10.1007/s11357-024-01095-2] [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: 12/06/2023] [Accepted: 02/07/2024] [Indexed: 02/16/2024] Open
Abstract
COVID-19 has been contained; however, the side effects associated with its infection continue to be a challenge for public health, particularly for older adults. On the other hand, epigenetic status contributes to the inter-individual health status and is associated with COVID-19 severity. Nevertheless, current studies focus only on severe COVID-19. Considering that most of the worldwide population developed mild COVID-19 infection. In the present exploratory study, we aim to analyze the association of mild COVID-19 with epigenetic ages (HorvathAge, HannumAge, GrimAge, PhenoAge, SkinAge, and DNAmTL) and clinical variables obtained from a Mexican cohort of older adults. We found that all epigenetic ages significantly differ from the chronological age, but only GrimAge is elevated. Additionally, both the intrinsic epigenetic age acceleration (IEAA) and the extrinsic epigenetic age acceleration (EEAA) are accelerated in all patients. Moreover, we found that immunological estimators and DNA damage were associated with PhenoAge, SkinBloodHorvathAge, and HorvathAge, suggesting that the effects of mild COVID-19 on the epigenetic clocks are mainly associated with inflammation and immunology changes. In conclusion, our results show that the effects of mild COVID-19 on the epigenetic clock are mainly associated with the immune system and an increase in GrimAge, IEAA, and EEAA.
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Affiliation(s)
- Paola García-delaTorre
- Unidad de Investigación Médica en Enfermedades Neurológicas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, México
| | | | - Sergio Sánchez-García
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Área de Envejecimiento, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | | | | | - Diana Castro-Morales
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico
| | - Miguel Cruz-Lopez
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | - Miguel Vazquez-Moreno
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, 06720, Mexico City, Mexico
| | - Ruth Rincón-Heredia
- Unidad de Imagenología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Perla Ramirez-Garcia
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico
| | - Juan Carlos Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría (INGER), 10200, Mexico City, Mexico.
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de Luzy IR, Lee MK, Mobley WC, Studer L. Lessons from inducible pluripotent stem cell models on neuronal senescence in aging and neurodegeneration. NATURE AGING 2024; 4:309-318. [PMID: 38429379 DOI: 10.1038/s43587-024-00586-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024]
Abstract
Age remains the central risk factor for many neurodegenerative diseases including Parkinson's disease, Alzheimer's disease and amyotrophic lateral sclerosis. Although the mechanisms of aging are complex, the age-related accumulation of senescent cells in neurodegeneration is well documented and their clearance can alleviate disease-related features in preclinical models. Senescence-like characteristics are observed in both neuronal and glial lineages, but their relative contribution to aging and neurodegeneration remains unclear. Human pluripotent stem cell-derived neurons provide an experimental model system to induce neuronal senescence. However, the extensive heterogeneity in the profile of senescent neurons and the methods to assess senescence remain major challenges. Here, we review the evidence of cellular senescence in neuronal aging and disease, discuss human pluripotent stem cell-based model systems used to investigate neuronal senescence and propose a panel of cellular and molecular hallmarks to characterize senescent neurons. Understanding the role of neuronal senescence may yield novel therapeutic opportunities in neurodegenerative disease.
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Affiliation(s)
- Isabelle R de Luzy
- The Center for Stem Cell Biology and Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Michael K Lee
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - William C Mobley
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Neurosciences, University of California, San Diego, San Diego, CA, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, New York, NY, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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Yang T, Xiao Y, Cheng Y, Huang J, Wei Q, Li C, Shang H. Epigenetic clocks in neurodegenerative diseases: a systematic review. J Neurol Neurosurg Psychiatry 2023; 94:1064-1070. [PMID: 36963821 DOI: 10.1136/jnnp-2022-330931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/03/2023] [Indexed: 03/26/2023]
Abstract
BACKGROUND Biological ageing is one of the principal risk factors for neurodegenerative diseases. It is becoming increasingly clear that acceleration of DNA methylation age, as measured by the epigenetic clock, is closely associated with many age-related diseases. METHODS We searched the PubMed and Web of Science databases to identify eligible studies reporting epigenetic clocks in several neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD). RESULTS Twenty-three studies (12 for AD, 4 for PD, 5 for ALS, and 2 for HD) were included. We systematically summarised the clinical utility of 11 epigenetic clocks (based on blood and brain tissues) in assessing the risk factors, age of onset, diagnosis, progression, prognosis and pathology of AD, PD, ALS and HD. We also critically described our current understandings to these evidences, and further discussed key challenges, potential mechanisms and future perspectives of epigenetic ageing in neurodegenerative diseases. CONCLUSIONS Epigenetic clocks hold great potential in neurodegenerative diseases. Further research is encouraged to evaluate the clinical utility and promote the application. PROSPERO REGISTRATION NUMBER CRD42022365233.
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Affiliation(s)
- Tianmi Yang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Yi Xiao
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Yangfan Cheng
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Jingxuan Huang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Chunyu Li
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Huifang Shang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
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Statsenko Y, Kuznetsov NV, Morozova D, Liaonchyk K, Simiyu GL, Smetanina D, Kashapov A, Meribout S, Gorkom KNV, Hamoudi R, Ismail F, Ansari SA, Emerald BS, Ljubisavljevic M. Reappraisal of the Concept of Accelerated Aging in Neurodegeneration and Beyond. Cells 2023; 12:2451. [PMID: 37887295 PMCID: PMC10605227 DOI: 10.3390/cells12202451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Genetic and epigenetic changes, oxidative stress and inflammation influence the rate of aging, which diseases, lifestyle and environmental factors can further accelerate. In accelerated aging (AA), the biological age exceeds the chronological age. OBJECTIVE The objective of this study is to reappraise the AA concept critically, considering its weaknesses and limitations. METHODS We reviewed more than 300 recent articles dealing with the physiology of brain aging and neurodegeneration pathophysiology. RESULTS (1) Application of the AA concept to individual organs outside the brain is challenging as organs of different systems age at different rates. (2) There is a need to consider the deceleration of aging due to the potential use of the individual structure-functional reserves. The latter can be restored by pharmacological and/or cognitive therapy, environment, etc. (3) The AA concept lacks both standardised terminology and methodology. (4) Changes in specific molecular biomarkers (MBM) reflect aging-related processes; however, numerous MBM candidates should be validated to consolidate the AA theory. (5) The exact nature of many potential causal factors, biological outcomes and interactions between the former and the latter remain largely unclear. CONCLUSIONS Although AA is commonly recognised as a perspective theory, it still suffers from a number of gaps and limitations that assume the necessity for an updated AA concept.
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Affiliation(s)
- Yauhen Statsenko
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Big Data Analytic Center, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Nik V. Kuznetsov
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
| | - Daria Morozova
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
| | - Katsiaryna Liaonchyk
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
| | - Gillian Lylian Simiyu
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Darya Smetanina
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Aidar Kashapov
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Sarah Meribout
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Klaus Neidl-Van Gorkom
- Department of Radiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (Y.S.); (G.L.S.); (D.S.); (A.K.); (S.M.); (K.N.-V.G.)
| | - Rifat Hamoudi
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Division of Surgery and Interventional Science, University College London, London NW3 2PS, UK
| | - Fatima Ismail
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
| | - Suraiya Anjum Ansari
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Bright Starling Emerald
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Milos Ljubisavljevic
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain 27272, United Arab Emirates; (D.M.); (K.L.); (R.H.); (S.A.A.); (B.S.E.); (M.L.)
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Oveisgharan S, Bennett DA. Author Response: Estrogen Receptor Genes, Cognitive Decline, and Alzheimer Disease. Neurology 2023; 101:634. [PMID: 37783504 PMCID: PMC10573149 DOI: 10.1212/wnl.0000000000207842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
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9
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Sommerer Y, Dobricic V, Schilling M, Ohlei O, Sabet SS, Wesse T, Fuß J, Franzenburg S, Franke A, Parkkinen L, Lill CM, Bertram L. Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer's disease. Alzheimers Res Ther 2023; 15:92. [PMID: 37149695 PMCID: PMC10163801 DOI: 10.1186/s13195-023-01232-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/15/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND Studies on DNA methylation (DNAm) in Alzheimer's disease (AD) have recently highlighted several genomic loci showing association with disease onset and progression. METHODS Here, we conducted an epigenome-wide association study (EWAS) using DNAm profiles in entorhinal cortex (EC) from 149 AD patients and control brains and combined these with two previously published EC datasets by meta-analysis (total n = 337). RESULTS We identified 12 cytosine-phosphate-guanine (CpG) sites showing epigenome-wide significant association with either case-control status or Braak's tau-staging. Four of these CpGs, located in proximity to CNFN/LIPE, TENT5A, PALD1/PRF1, and DIRAS1, represent novel findings. Integrating DNAm levels with RNA sequencing-based mRNA expression data generated in the same individuals showed significant DNAm-mRNA correlations for 6 of the 12 significant CpGs. Lastly, by calculating rates of epigenetic age acceleration using two recently proposed "epigenetic clock" estimators we found a significant association with accelerated epigenetic aging in the brains of AD patients vs. controls. CONCLUSION In summary, our study represents the hitherto most comprehensive EWAS in AD using EC and highlights several novel differentially methylated loci with potential effects on gene expression.
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Affiliation(s)
- Yasmine Sommerer
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Marcel Schilling
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Sanaz Sedghpour Sabet
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tanja Wesse
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Janina Fuß
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Christina M Lill
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
- Ageing Epidemiology Unit (AGE), School of Public Health, Imperial College London, London, UK
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany.
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, Oslo, Norway.
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Simons RL, Ong ML, Lei MK, Beach SRH, Zhang Y, Philibert R, Mielke MM. Changes in Loneliness, BDNF, and Biological Aging Predict Trajectories in a Blood-Based Epigenetic Measure of Cortical Aging: A Study of Older Black Americans. Genes (Basel) 2023; 14:842. [PMID: 37107599 PMCID: PMC10138024 DOI: 10.3390/genes14040842] [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: 02/13/2023] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
A recent epigenetic measure of aging has developed based on human cortex tissue. This cortical clock (CC) dramatically outperformed extant blood-based epigenetic clocks in predicting brain age and neurological degeneration. Unfortunately, measures that require brain tissue are of limited utility to investigators striving to identify everyday risk factors for dementia. The present study investigated the utility of using the CpG sites included in the CC to formulate a peripheral blood-based cortical measure of brain age (CC-Bd). To establish the utility of CC-Bd, we used growth curves with individually varying time points and longitudinal data from a sample of 694 aging African Americans. We examined whether three risk factors that have been linked to cognitive decline-loneliness, depression, and BDNFm-predicted CC-Bd after controlling for several factors, including three new-generation epigenetic clocks. Our findings showed that two clocks-DunedinPACE and PoAm-predicted CC-BD, but that increases in loneliness and BDNFm continued to be robust predictors of accelerated CC-Bd even after taking these effects into account. This suggests that CC-Bd is assessing something more than the pan-tissue epigenetic clocks but that, at least in part, brain health is also associated with the general aging of the organism.
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Affiliation(s)
- Ronald L. Simons
- Department of Sociology, University of Georgia, Athens, GA 30602, USA
| | - Mei Ling Ong
- Center for Family Research, University of Georgia, Athens, GA 30602, USA
| | - Man-Kit Lei
- Department of Sociology, University of Georgia, Athens, GA 30602, USA
| | | | - Yue Zhang
- Department of Sociology, University of Georgia, Athens, GA 30602, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa School of Medicine, Iowa City, IA 52242, USA
| | - Michelle M. Mielke
- Department of Epidemiology and Prevention, Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
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11
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Baldelli L, Pirazzini C, Sambati L, Ravaioli F, Gentilini D, Calandra-Buonaura G, Guaraldi P, Franceschi C, Cortelli P, Garagnani P, Bacalini MG, Provini F. Epigenetic clocks suggest accelerated aging in patients with isolated REM Sleep Behavior Disorder. NPJ Parkinsons Dis 2023; 9:48. [PMID: 36997543 PMCID: PMC10063653 DOI: 10.1038/s41531-023-00492-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 03/08/2023] [Indexed: 04/03/2023] Open
Abstract
Isolated REM Sleep Behavior Disorder (iRBD) is the strongest prodromal marker for α-synucleinopathies. Overt α-synucleinopathies and aging share several mechanisms, but this relationship has been poorly investigated in prodromal phases. Using DNA methylation-based epigenetic clocks, we measured biological aging in videopolysomnography confirmed iRBD patients, videopolysomnography-negative and population-based controls. We found that iRBDs tended to be epigenetically older than controls, suggesting that accelerated aging characterizes prodromal neurodegeneration.
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Affiliation(s)
- Luca Baldelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Chiara Pirazzini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Luisa Sambati
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Francesco Ravaioli
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Giovanna Calandra-Buonaura
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Pietro Guaraldi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, Russia
| | - Pietro Cortelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | | | - Federica Provini
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Bologna, Italy.
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.
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12
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Fingelkurts AA, Fingelkurts AA. Turning Back the Clock: A Retrospective Single-Blind Study on Brain Age Change in Response to Nutraceuticals Supplementation vs. Lifestyle Modifications. Brain Sci 2023; 13:520. [PMID: 36979330 PMCID: PMC10046544 DOI: 10.3390/brainsci13030520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND There is a growing consensus that chronological age (CA) is not an accurate indicator of the aging process and that biological age (BA) instead is a better measure of an individual's risk of age-related outcomes and a more accurate predictor of mortality than actual CA. In this context, BA measures the "true" age, which is an integrated result of an individual's level of damage accumulation across all levels of biological organization, along with preserved resources. The BA is plastic and depends upon epigenetics. Brain state is an important factor contributing to health- and lifespan. METHODS AND OBJECTIVE Quantitative electroencephalography (qEEG)-derived brain BA (BBA) is a suitable and promising measure of brain aging. In the present study, we aimed to show that BBA can be decelerated or even reversed in humans (N = 89) by using customized programs of nutraceutical compounds or lifestyle changes (mean duration = 13 months). RESULTS We observed that BBA was younger than CA in both groups at the end of the intervention. Furthermore, the BBA of the participants in the nutraceuticals group was 2.83 years younger at the endpoint of the intervention compared with their BBA score at the beginning of the intervention, while the BBA of the participants in the lifestyle group was only 0.02 years younger at the end of the intervention. These results were accompanied by improvements in mental-physical health comorbidities in both groups. The pre-intervention BBA score and the sex of the participants were considered confounding factors and analyzed separately. CONCLUSIONS Overall, the obtained results support the feasibility of the goal of this study and also provide the first robust evidence that halting and reversal of brain aging are possible in humans within a reasonable (practical) timeframe of approximately one year.
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13
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O'Shea DM, Alaimo H, Davis JD, Galvin JE, Tremont G. A comparison of cognitive performances based on differing rates of DNA methylation GrimAge acceleration among older men and women. Neurobiol Aging 2023; 123:83-91. [PMID: 36641830 DOI: 10.1016/j.neurobiolaging.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/02/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022]
Abstract
Cognitive heterogeneity increases with age rendering sex differences difficult to identify. Given established sex differences in biological aging, we examined whether comparisons of men and women on neuropsychological test performances differed as a function of age rate. Data were obtained from 1921 adults enrolled in the 2016 wave of the Health and Retirement Study. The residual from regressing the DNA methylation GrimAge clock on chronological age was used as the measure of aging rate. Slow and fast age rates were predefined as 1 standard deviation below or above the sex-specific mean rates, respectively. ANCOVAs were used to test group differences in test performances. Pairwise comparisons revealed that slow aging men outperformed fast aging women (and vice versa) on measures of executive function/speed, visual memory and semantic fluency; however, when groups were matched by aging rates, no significant differences remained. In contrast, women, regardless of their aging rates, education or depressive symptoms maintained their advantage on verbal learning and memory. Implications for research on sex differences in cognitive aging are discussed.
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Affiliation(s)
- Deirdre M O'Shea
- Department of Psychiatry & Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA; Rhode Island Hospital, Providence, RI, USA; Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Boca Raton, FL, USA.
| | | | - Jennifer D Davis
- Department of Psychiatry & Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA; Rhode Island Hospital, Providence, RI, USA
| | - James E Galvin
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami Miller School of Medicine, Boca Raton, FL, USA
| | - Geoffrey Tremont
- Department of Psychiatry & Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA; Rhode Island Hospital, Providence, RI, USA
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14
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Faul JD, Kim JK, Levine ME, Thyagarajan B, Weir DR, Crimmins EM. Epigenetic-based age acceleration in a representative sample of older Americans: Associations with aging-related morbidity and mortality. Proc Natl Acad Sci U S A 2023; 120:e2215840120. [PMID: 36802439 PMCID: PMC9992763 DOI: 10.1073/pnas.2215840120] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/12/2023] [Indexed: 02/23/2023] Open
Abstract
Biomarkers developed from DNA methylation (DNAm) data are of growing interest as predictors of health outcomes and mortality in older populations. However, it is unknown how epigenetic aging fits within the context of known socioeconomic and behavioral associations with aging-related health outcomes in a large, population-based, and diverse sample. This study uses data from a representative, panel study of US older adults to examine the relationship between DNAm-based age acceleration measures in the prediction of cross-sectional and longitudinal health outcomes and mortality. We examine whether recent improvements to these scores, using principal component (PC)-based measures designed to remove some of the technical noise and unreliability in measurement, improve the predictive capability of these measures. We also examine how well DNAm-based measures perform against well-known predictors of health outcomes such as demographics, SES, and health behaviors. In our sample, age acceleration calculated using "second and third generation clocks," PhenoAge, GrimAge, and DunedinPACE, is consistently a significant predictor of health outcomes including cross-sectional cognitive dysfunction, functional limitations and chronic conditions assessed 2 y after DNAm measurement, and 4-y mortality. PC-based epigenetic age acceleration measures do not significantly change the relationship of DNAm-based age acceleration measures to health outcomes or mortality compared to earlier versions of these measures. While the usefulness of DNAm-based age acceleration as a predictor of later life health outcomes is quite clear, other factors such as demographics, SES, mental health, and health behaviors remain equally, if not more robust, predictors of later life outcomes.
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Affiliation(s)
- Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI48104
| | - Jung Ki Kim
- Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Morgan E. Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT06510
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN55455
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI48104
| | - Eileen M. Crimmins
- Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
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15
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Murthy M, Shireby G, Miki Y, Viré E, Lashley T, Warner TT, Mill J, Bettencourt C. Epigenetic age acceleration is associated with oligodendrocyte proportions in MSA and control brain tissue. Neuropathol Appl Neurobiol 2023; 49:e12872. [PMID: 36542090 PMCID: PMC10107510 DOI: 10.1111/nan.12872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/15/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
AIMS Epigenetic clocks are widely applied as surrogates for biological age in different tissues and/or diseases, including several neurodegenerative diseases. Despite white matter (WM) changes often being observed in neurodegenerative diseases, no study has investigated epigenetic ageing in white matter. METHODS We analysed the performances of two DNA methylation-based clocks, DNAmClockMulti and DNAmClockCortical , in post-mortem WM tissue from multiple subcortical regions and the cerebellum, and in oligodendrocyte-enriched nuclei. We also examined epigenetic ageing in control and multiple system atrophy (MSA) (WM and mixed WM and grey matter), as MSA is a neurodegenerative disease comprising pronounced WM changes and α-synuclein aggregates in oligodendrocytes. RESULTS Estimated DNA methylation (DNAm) ages showed strong correlations with chronological ages, even in WM (e.g., DNAmClockCortical , r = [0.80-0.97], p < 0.05). However, performances and DNAm age estimates differed between clocks and brain regions. DNAmClockMulti significantly underestimated ages in all cohorts except in the MSA prefrontal cortex mixed tissue, whereas DNAmClockCortical tended towards age overestimations. Pronounced age overestimations in the oligodendrocyte-enriched cohorts (e.g., oligodendrocyte-enriched nuclei, p = 6.1 × 10-5 ) suggested that this cell type ages faster. Indeed, significant positive correlations were observed between estimated oligodendrocyte proportions and DNAm age acceleration estimated by DNAmClockCortical (r > 0.31, p < 0.05), and similar trends were obtained with DNAmClockMulti . Although increased age acceleration was observed in MSA compared with controls, no significant differences were detected upon adjustment for possible confounders (e.g., cell-type proportions). CONCLUSIONS Our findings show that oligodendrocyte proportions positively influence epigenetic age acceleration across brain regions and highlight the need to further investigate this in ageing and neurodegeneration.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
| | - Gemma Shireby
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Yasuo Miki
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neuropathology, Institute of Brain ScienceHirosaki University Graduate School of MedicineHirosakiJapan
| | - Emmanuelle Viré
- UCL Institute of Prion Diseases, MRC Prion Unit at UCLUniversity College LondonLondonUK
| | - Tammaryn Lashley
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neurodegenerative Disease, Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of Neurology1 Wakefield StreetLondonWC1N 1PJUK
| | - Thomas T. Warner
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
- Reta Lila Weston InstituteUCL Queen Square Institute of NeurologyLondonUK
| | - Jonathan Mill
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Conceição Bettencourt
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neurodegenerative Disease, Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of Neurology1 Wakefield StreetLondonWC1N 1PJUK
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16
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Perret LC, Geoffroy MC, Barr E, Parnet F, Provencal N, Boivin M, O’Donnell KJ, Suderman M, Power C, Turecki G, Ouellet-Morin I. Associations between epigenetic aging and childhood peer victimization, depression, and suicidal ideation in adolescence and adulthood: A study of two population-based samples. Front Cell Dev Biol 2023; 10:1051556. [PMID: 36712964 PMCID: PMC9879289 DOI: 10.3389/fcell.2022.1051556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Background: Prior studies indicate that peer victimization (including bullying) is associated with higher risk for depression and suicidal ideation across the life course. However, molecular mechanisms underlying these associations remain unclear. This two-cohort study proposes to test whether epigenetic aging and pace of aging, as well as a DNA methylation marker of responsive to glucocorticoids, are associated to childhood peer victimization and later depressive symptoms, or suicidal ideation. Methods: Cohort 1: Epigenome-wide DNA methylation (EPIC array) was measured in saliva collected when participants were 10.47 years (standard deviation = 0.35) in a subsample of the Quebec Longitudinal Study of Child Development (QLSCD, n = 149 participants), with self-reported peer victimization at 6-8 years, depressive symptoms (mean symptoms, and dichotomized top 30% symptoms) and suicidal ideation at 15-17 years. Cohort 2: Epigenome-wide DNA methylation (EPIC array) was measured in blood collected from participants aged 45.13 years (standard deviation = 0.37) in a subsample of the 1958 British Birth cohort (1958BBC, n = 238 participants) with information on mother-reported peer victimization at 7-11 years, self-reported depressive symptoms at 50 years, and suicidal ideation at 45 years. Five epigenetic indices were derived: three indicators of epigenetic aging [Horvath's pan-tissue (Horvath1), Horvath's Skin-and-Blood (Horvath2), Pediatric-Buccal-Epigenetic age (PedBE)], pace of aging (DunedinPACE), and stress response reactivity (Epistress). Results: Peer victimization was not associated with the epigenetic indices in either cohort. In the QLSCD, higher PedBE epigenetic aging and a slower pace of aging as measured by DunedinPACE predicted higher depressive symptoms scores. In contrast, neither the Horvath1, or Horvath2 epigenetic age estimates, nor the Epistress score were associated with depressive symptoms in either cohort, and none of the epigenetic indices predicted suicidal ideation. Conclusion: The findings are consistent with epigenome-wide and candidate gene studies suggesting that these epigenetic indices did not relate to peer victimization, challenging the hypothesis that cumulative epigenetic aging indices could translate vulnerability to depressive symptoms and suicidal ideation following peer victimization. Since some indices of epigenetic aging and pace of aging signaled higher risk for depressive symptoms, future studies should pursue this investigation to further evaluate the robustness and generalization of these preliminary findings.
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Affiliation(s)
- L. C. Perret
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - M-C. Geoffroy
- Department of Psychiatry, McGill University, Montreal, QC, Canada,Department of Educational and Counselling Psychology, McGill University, Montreal, QC, Canada
| | - E. Barr
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - F. Parnet
- School of Criminology, Research Center of the Montreal Mental Health University Institute, Université de Montréal, Montreal, QC, Canada
| | - N. Provencal
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - M. Boivin
- School of Psychology, Université Laval, Québec City, QC, Canada
| | - K. J. O’Donnell
- Department of Psychiatry, McGill University, Montreal, QC, Canada,Yale Child Study Center, Yale School of Medicine, New Haven, CT, United States,Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, United States,Child and Brain Development Program, CIFAR, Toronto, ON, Canada
| | - M. Suderman
- MRC Integrative Epidemiology Unit, Bristol Medical School, Bristol Population Health Science Institute, Bristol, United Kingdom
| | - C. Power
- UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - G. Turecki
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - I. Ouellet-Morin
- School of Criminology, Research Center of the Montreal Mental Health University Institute, Université de Montréal, Montreal, QC, Canada,*Correspondence: I. Ouellet-Morin,
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17
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Schäfer Hackenhaar F, Josefsson M, Nordin Adolfsson A, Landfors M, Kauppi K, Porter T, Milicic L, Laws SM, Hultdin M, Adolfsson R, Degerman S, Pudas S. Sixteen-Year Longitudinal Evaluation of Blood-Based DNA Methylation Biomarkers for Early Prediction of Alzheimer's Disease. J Alzheimers Dis 2023; 94:1443-1464. [PMID: 37393498 PMCID: PMC10473121 DOI: 10.3233/jad-230039] [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] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND DNA methylation (DNAm), an epigenetic mark reflecting both inherited and environmental influences, has shown promise for Alzheimer's disease (AD) prediction. OBJECTIVE Testing long-term predictive ability (>15 years) of existing DNAm-based epigenetic age acceleration (EAA) measures and identifying novel early blood-based DNAm AD-prediction biomarkers. METHODS EAA measures calculated from Illumina EPIC data from blood were tested with linear mixed-effects models (LMMs) in a longitudinal case-control sample (50 late-onset AD cases; 51 matched controls) with prospective data up to 16 years before clinical onset, and post-onset follow-up. Novel DNAm biomarkers were generated with epigenome-wide LMMs, and Sparse Partial Least Squares Discriminant Analysis applied at pre- (10-16 years), and post-AD-onset time-points. RESULTS EAA did not differentiate cases from controls during the follow-up time (p > 0.05). Three new DNA biomarkers showed in-sample predictive ability on average 8 years pre-onset, after adjustment for age, sex, and white blood cell proportions (p-values: 0.022-<0.00001). Our longitudinally-derived panel replicated nominally (p = 0.012) in an external cohort (n = 146 cases, 324 controls). However, its effect size and discriminatory accuracy were limited compared to APOEɛ4-carriership (OR = 1.38 per 1 SD DNAm score increase versus OR = 13.58 for ɛ4-allele carriage; AUCs = 77.2% versus 87.0%). Literature review showed low overlap (n = 4) across 3275 AD-associated CpGs from 8 published studies, and no overlap with our identified CpGs.
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Affiliation(s)
- Fernanda Schäfer Hackenhaar
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
| | - Maria Josefsson
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
- Department of Statistics, USBE, Umeå University, Umeå, Sweden
- Center for Ageing and Demographic Research, Umeå University, Umeå, Sweden
| | | | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Karolina Kauppi
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Rolf Adolfsson
- Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Sara Pudas
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
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18
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The Role of Epigenetics in Neuroinflammatory-Driven Diseases. Int J Mol Sci 2022; 23:ijms232315218. [PMID: 36499544 PMCID: PMC9740629 DOI: 10.3390/ijms232315218] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative disorders are characterized by the progressive loss of central and/or peripheral nervous system neurons. Within this context, neuroinflammation comes up as one of the main factors linked to neurodegeneration progression. In fact, neuroinflammation has been recognized as an outstanding factor for Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), Parkinson's disease (PD), and multiple sclerosis (MS). Interestingly, neuroinflammatory diseases are characterized by dramatic changes in the epigenetic profile, which might provide novel prognostic and therapeutic factors towards neuroinflammatory treatment. Deep changes in DNA and histone methylation, along with histone acetylation and altered non-coding RNA expression, have been reported at the onset of inflammatory diseases. The aim of this work is to review the current knowledge on this field.
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19
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Effects of lifespan-extending interventions on cognitive healthspan. Expert Rev Mol Med 2022; 25:e2. [PMID: 36377361 DOI: 10.1017/erm.2022.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ageing is known to be the primary risk factor for most neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease and Huntington's disease. They are currently incurable and worsen over time, which has broad implications in the context of lifespan and healthspan extension. Adding years to life and even to physical health is suboptimal or even insufficient, if cognitive ageing is not adequately improved. In this review, we will examine how interventions that have the potential to extend lifespan in animals affect the brain, and if they would be able to thwart or delay the development of cognitive dysfunction and/or neurodegeneration. These interventions range from lifestyle (caloric restriction, physical exercise and environmental enrichment) through pharmacological (nicotinamide adenine dinucleotide precursors, resveratrol, rapamycin, metformin, spermidine and senolytics) to epigenetic reprogramming. We argue that while many of these interventions have clear potential to improve cognitive health and resilience, large-scale and long-term randomised controlled trials are needed, along with studies utilising washout periods to determine the effects of supplementation cessation, particularly in aged individuals.
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20
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Liang WS, Goetz LH, Schork NJ. Assessing brain and biological aging trajectories associated with Alzheimer's disease. Front Neurosci 2022; 16:1036102. [PMID: 36389222 PMCID: PMC9650396 DOI: 10.3389/fnins.2022.1036102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022] Open
Abstract
The development of effective treatments to prevent and slow Alzheimer's disease (AD) pathogenesis is needed in order to tackle the steady increase in the global prevalence of AD. This challenge is complicated by the need to identify key health shifts that precede the onset of AD and cognitive decline as these represent windows of opportunity for intervening and preventing disease. Such shifts may be captured through the measurement of biomarkers that reflect the health of the individual, in particular those that reflect brain age and biological age. Brain age biomarkers provide a composite view of the health of the brain based on neuroanatomical analyses, while biological age biomarkers, which encompass the epigenetic clock, provide a measurement of the overall health state of an individual based on DNA methylation analysis. Acceleration of brain and biological ages is associated with changes in cognitive function, as well as neuropathological markers of AD. In this mini-review, we discuss brain age and biological age research in the context of cognitive decline and AD. While more research is needed, studies show that brain and biological aging trajectories are variable across individuals and that such trajectories are non-linear at older ages. Longitudinal monitoring of these biomarkers may be valuable for enabling earlier identification of divergent pathological trajectories toward AD and providing insight into points for intervention.
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Affiliation(s)
- Winnie S. Liang
- NetBio, Inc., Los Angeles, CA, United States
- Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Laura H. Goetz
- NetBio, Inc., Los Angeles, CA, United States
- Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Nicholas J. Schork
- NetBio, Inc., Los Angeles, CA, United States
- Translational Genomics Research Institute, Phoenix, AZ, United States
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21
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Kular L, Klose D, Urdánoz-Casado A, Ewing E, Planell N, Gomez-Cabrero D, Needhamsen M, Jagodic M. Epigenetic clock indicates accelerated aging in glial cells of progressive multiple sclerosis patients. Front Aging Neurosci 2022; 14:926468. [PMID: 36092807 PMCID: PMC9454196 DOI: 10.3389/fnagi.2022.926468] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/18/2022] [Indexed: 11/28/2022] Open
Abstract
Background Multiple sclerosis (MS) is a chronic inflammatory neurodegenerative disease of the central nervous system (CNS) characterized by irreversible disability at later progressive stages. A growing body of evidence suggests that disease progression depends on age and inflammation within the CNS. We aimed to investigate epigenetic aging in bulk brain tissue and sorted nuclei from MS patients using DNA methylation-based epigenetic clocks. Methods We applied Horvath’s multi-tissue and Shireby’s brain-specific Cortical clock on bulk brain tissue (n = 46), sorted neuronal (n = 54), and glial nuclei (n = 66) from post-mortem brain tissue of progressive MS patients and controls. Results We found a significant increase in age acceleration residuals, corresponding to 3.6 years, in glial cells of MS patients compared to controls (P = 0.0024) using the Cortical clock, which held after adjustment for covariates (Padj = 0.0263). The 4.8-year age acceleration found in MS neurons (P = 0.0054) did not withstand adjustment for covariates and no significant difference in age acceleration residuals was observed in bulk brain tissue between MS patients and controls. Conclusion While the findings warrant replication in larger cohorts, our study suggests that glial cells of progressive MS patients exhibit accelerated biological aging.
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Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- Lara Kular,
| | - Dennis Klose
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Amaya Urdánoz-Casado
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- Neuroepigenetics Laboratory, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Nuria Planell
- Translational Bioinformatics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - David Gomez-Cabrero
- Translational Bioinformatics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- Mucosal and Salivary Biology Division, King’s College London Dental Institute, London, United Kingdom
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
- *Correspondence: Maja Jagodic,
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22
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Liu W, Fan M, Lu W, Zhu W, Meng L, Lu S. Emerging Roles of T Helper Cells in Non-Infectious Neuroinflammation: Savior or Sinner. Front Immunol 2022; 13:872167. [PMID: 35844577 PMCID: PMC9280647 DOI: 10.3389/fimmu.2022.872167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/30/2022] [Indexed: 12/03/2022] Open
Abstract
CD4+ T cells, also known as T helper (Th) cells, contribute to the adaptive immunity both in the periphery and in the central nervous system (CNS). At least seven subsets of Th cells along with their signature cytokines have been identified nowadays. Neuroinflammation denotes the brain’s immune response to inflammatory conditions. In recent years, various CNS disorders have been related to the dysregulation of adaptive immunity, especially the process concerning Th cells and their cytokines. However, as the functions of Th cells are being discovered, it’s also found that their roles in different neuroinflammatory conditions, or even the participation of a specific Th subset in one CNS disorder may differ, and sometimes contrast. Based on those recent and contradictory evidence, the conflicting roles of Th cells in multiple sclerosis, Alzheimer’s disease, Parkinson’s disease, epilepsy, traumatic brain injury as well as some typical mental disorders will be reviewed herein. Research progress, limitations and novel approaches concerning different neuroinflammatory conditions will also be mentioned and compared.
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Affiliation(s)
- Wenbin Liu
- Institute of Molecular and Translational Medicine, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Department of Neurosurgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Meiyang Fan
- Institute of Molecular and Translational Medicine, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Wen Lu
- Department of Psychiatry, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Wenhua Zhu
- Institute of Molecular and Translational Medicine, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
- National Joint Engineering Research Center of Biodiagnostics and Biotherapy, Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Wenhua Zhu, ; Liesu Meng,
| | - Liesu Meng
- Institute of Molecular and Translational Medicine, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
- National Joint Engineering Research Center of Biodiagnostics and Biotherapy, Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an, China
- *Correspondence: Wenhua Zhu, ; Liesu Meng,
| | - Shemin Lu
- Institute of Molecular and Translational Medicine, and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi’an Jiaotong University Health Science Center, Xi’an, China
- National Joint Engineering Research Center of Biodiagnostics and Biotherapy, Second Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an, China
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23
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Morales Berstein F, McCartney DL, Lu AT, Tsilidis KK, Bouras E, Haycock P, Burrows K, Phipps AI, Buchanan DD, Cheng I, Martin RM, Davey Smith G, Relton CL, Horvath S, Marioni RE, Richardson TG, Richmond RC. Assessing the causal role of epigenetic clocks in the development of multiple cancers: a Mendelian randomization study. eLife 2022; 11:e75374. [PMID: 35346416 PMCID: PMC9049976 DOI: 10.7554/elife.75374] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background Epigenetic clocks have been associated with cancer risk in several observational studies. Nevertheless, it is unclear whether they play a causal role in cancer risk or if they act as a non-causal biomarker. Methods We conducted a two-sample Mendelian randomization (MR) study to examine the genetically predicted effects of epigenetic age acceleration as measured by HannumAge (nine single-nucleotide polymorphisms (SNPs)), Horvath Intrinsic Age (24 SNPs), PhenoAge (11 SNPs), and GrimAge (4 SNPs) on multiple cancers (i.e. breast, prostate, colorectal, ovarian and lung cancer). We obtained genome-wide association data for biological ageing from a meta-analysis (N = 34,710), and for cancer from the UK Biobank (N cases = 2671-13,879; N controls = 173,493-372,016), FinnGen (N cases = 719-8401; N controls = 74,685-174,006) and several international cancer genetic consortia (N cases = 11,348-122,977; N controls = 15,861-105,974). Main analyses were performed using multiplicative random effects inverse variance weighted (IVW) MR. Individual study estimates were pooled using fixed effect meta-analysis. Sensitivity analyses included MR-Egger, weighted median, weighted mode and Causal Analysis using Summary Effect Estimates (CAUSE) methods, which are robust to some of the assumptions of the IVW approach. Results Meta-analysed IVW MR findings suggested that higher GrimAge acceleration increased the risk of colorectal cancer (OR = 1.12 per year increase in GrimAge acceleration, 95% CI 1.04-1.20, p = 0.002). The direction of the genetically predicted effects was consistent across main and sensitivity MR analyses. Among subtypes, the genetically predicted effect of GrimAge acceleration was greater for colon cancer (IVW OR = 1.15, 95% CI 1.09-1.21, p = 0.006), than rectal cancer (IVW OR = 1.05, 95% CI 0.97-1.13, p = 0.24). Results were less consistent for associations between other epigenetic clocks and cancers. Conclusions GrimAge acceleration may increase the risk of colorectal cancer. Findings for other clocks and cancers were inconsistent. Further work is required to investigate the potential mechanisms underlying the results. Funding FMB was supported by a Wellcome Trust PhD studentship in Molecular, Genetic and Lifecourse Epidemiology (224982/Z/22/Z which is part of grant 218495/Z/19/Z). KKT was supported by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme) and by the Hellenic Republic's Operational Programme 'Competitiveness, Entrepreneurship & Innovation' (OΠΣ 5047228). PH was supported by Cancer Research UK (C18281/A29019). RMM was supported by the NIHR Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol and by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme). RMM is a National Institute for Health Research Senior Investigator (NIHR202411). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care. GDS and CLR were supported by the Medical Research Council (MC_UU_00011/1 and MC_UU_00011/5, respectively) and by a Cancer Research UK (C18281/A29019) programme grant (the Integrative Cancer Epidemiology Programme). REM was supported by an Alzheimer's Society project grant (AS-PG-19b-010) and NIH grant (U01 AG-18-018, PI: Steve Horvath). RCR is a de Pass Vice Chancellor's Research Fellow at the University of Bristol.
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Affiliation(s)
- Fernanda Morales Berstein
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Konstantinos K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College LondonLondonUnited Kingdom
- Department of Hygiene and Epidemiology, School of Medicine, University of IoanninaIoanninaGreece
| | - Emmanouil Bouras
- Department of Hygiene and Epidemiology, School of Medicine, University of IoanninaIoanninaGreece
| | - Philip Haycock
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Amanda I Phipps
- Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Department of Epidemiology, School of Public Health, University of WashingtonSeattleUnited States
| | - Daniel D Buchanan
- Department of Clinical Pathology, Melbourne Medical School, University of MelbourneParkvilleAustralia
| | - Iona Cheng
- Cancer Prevention Institute of CaliforniaFremontUnited States
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of BristolBristolUnited Kingdom
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
- Department of Biostatistics, Fielding School of Public Health, University of California, Los AngelesLos AngelesUnited States
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
- Novo Nordisk Research CentreOxfordUnited Kingdom
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, University of BristolBristolUnited Kingdom
- Population Health Sciences, Bristol Medical SchoolBristolUnited Kingdom
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24
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Xue X, Wu JJ, Huo BB, Xing XX, Ma J, Li YL, Zheng MX, Hua XY, Xu JG. Age-related alterations of brain metabolic network based on [18F]FDG-PET of rats. Aging (Albany NY) 2022; 14:923-942. [PMID: 35077393 PMCID: PMC8833125 DOI: 10.18632/aging.203851] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 01/14/2022] [Indexed: 11/25/2022]
Abstract
Using animal models to study the underlying mechanisms of aging will create a critical foundation from which to develop new interventions for aging-related brain disorders. Aging-related reorganization of the brain network has been described for the human brain based on functional, metabolic and structural connectivity. However, alterations in the brain metabolic network of aging rats remain unknown. Here, we submitted young and aged rats to [18F]fluorodeoxyglucose with positron emission tomography (18F-FDG PET) and constructed brain metabolic networks. The topological properties were detected, and the network robustness against random failures and targeted attacks was analyzed for age-group comparison. Compared with young rats, aged rats showed reduced betweenness centrality (BC) in the superior colliculus and a decreased degree (D) in the parietal association cortex. With regard to network robustness, the brain metabolic networks of aged rats were more vulnerable to simulated damage, which showed significantly lower local efficiency and clustering coefficients than those of the young rats against targeted attacks and random failures. The findings support the idea that aged rats have similar aging-related changes in the brain metabolic network to the human brain and can therefore be used as a model for aging studies to provide targets for potential therapies that promote healthy aging.
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Affiliation(s)
- Xin Xue
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jia-Jia Wu
- Department of Rehabilitation Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Bei-Bei Huo
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xiang-Xin Xing
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.,Department of Rehabilitation Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Jie Ma
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yu-Lin Li
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mou-Xiong Zheng
- Department of Rehabilitation Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China.,Department of Traumatology and Orthopedics, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Xu-Yun Hua
- Department of Rehabilitation Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China.,Department of Traumatology and Orthopedics, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Jian-Guang Xu
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.,Department of Rehabilitation Medicine, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China.,Engineering Research Center of Traditional Chinese Medicine Intelligent Rehabilitation, Ministry of Education, Shanghai 201203, China
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25
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Jonkman TH, Dekkers KF, Slieker RC, Grant CD, Ikram MA, van Greevenbroek MMJ, Franke L, Veldink JH, Boomsma DI, Slagboom PE, Consortium BIOS, Heijmans BT. Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression. Genome Biol 2022; 23:24. [PMID: 35031073 PMCID: PMC8759260 DOI: 10.1186/s13059-021-02585-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 12/20/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Epigenetic clocks use DNA methylation (DNAm) levels of specific sets of CpG dinucleotides to accurately predict individual chronological age. A popular application of these clocks is to explore whether the deviation of predicted age from chronological age is associated with disease phenotypes, where this deviation is interpreted as a potential biomarker of biological age. This wide application, however, contrasts with the limited insight in the processes that may drive the running of epigenetic clocks. RESULTS We perform a functional genomics analysis on four epigenetic clocks, including Hannum's blood predictor and Horvath's multi-tissue predictor, using blood DNA methylome and transcriptome data from 3132 individuals. The four clocks result in similar predictions of individual chronological age, and their constituting CpGs are correlated in DNAm level and are enriched for similar histone modifications and chromatin states. Interestingly, DNAm levels of CpGs from the clocks are commonly associated with gene expression in trans. The gene sets involved are highly overlapping and enriched for T cell processes. Further analysis of the transcriptome and methylome of sorted blood cell types identifies differences in DNAm between naive and activated T and NK cells as a probable contributor to the clocks. Indeed, within the same donor, the four epigenetic clocks predict naive cells to be up to 40 years younger than activated cells. CONCLUSIONS The ability of epigenetic clocks to predict chronological age involves their ability to detect changes in proportions of naive and activated immune blood cells, an established feature of immuno-senescence. This finding may contribute to the interpretation of associations between clock-derived measures and age-related health outcomes.
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Affiliation(s)
- Thomas H Jonkman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Koen F Dekkers
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute, Amsterdam Cardiovascular Sciences Institute, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Crystal D Grant
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Marleen M J van Greevenbroek
- Department of Internal Medicine and School for Cardiovascular Diseases, Maastricht University Medical Center, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Centre Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | | | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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26
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Grodstein F, Lemos B, Yu L, Klein HU, Iatrou A, Buchman AS, Shireby GL, Mill J, Schneider JA, De Jager PL, Bennett DA. The association of epigenetic clocks in brain tissue with brain pathologies and common aging phenotypes. Neurobiol Dis 2021; 157:105428. [PMID: 34153464 PMCID: PMC8373772 DOI: 10.1016/j.nbd.2021.105428] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022] Open
Abstract
Epigenetic clocks are calculated by combining DNA methylation states across select CpG sites to estimate biologic age, and have been noted as the most successful markers of biologic aging to date. Yet, limited research has considered epigenetic clocks calculated in brain tissue. We used DNA methylation states in dorsolateral prefrontal cortex specimens from 721 older participants of the Religious Orders Study and Rush Memory and Aging Project, to calculate DNA methylation age using four established epigenetic clocks: Hannum, Horvath, PhenoAge, GrimAge, and a new Cortical clock. The four established clocks were trained in blood samples (Hannum, PhenoAge, GrimAge) or using 51 human tissue and cell types (Horvath); the recent Cortical clock is the first trained in postmortem cortical tissue. Participants were recruited beginning in 1994 (Religious Orders Study) and 1997 (Memory and Aging Project), and followed annually with questionnaires and clinical evaluations; brain specimens were obtained for 80-90% of participants. Mean age at death was 88.0 (SD 6.7) years. We used linear regression, logistic regression, and linear mixed models, to examine relations of epigenetic clock ages to neuropathologic and clinical aging phenotypes, controlling for chronologic age, sex, education, and depressive symptomatology. Hannum, Horvath, PhenoAge and Cortical clock ages were related to pathologic diagnosis of Alzheimer's disease (AD), as well as to Aβ load (a hallmark pathology of Alzheimer's disease). However, associations were substantially stronger for the Cortical than other clocks; for example, each standard deviation (SD) increase in Hannum, Horvath, and PhenoAge clock age was related to approximately 30% greater likelihood of pathologic AD (all p < 0.05), while each SD increase in Cortical age was related to 90% greater likelihood of pathologic AD (odds ratio = 1.91, 95% confidence interval 1.38, 2.62). Moreover, Cortical age was significantly related to other AD pathology (eg, mean tau tangle density, p = 0.003), and to odds of neocortical Lewy body pathology (for each SD increase in Cortical age, odds ratio = 2.00, 95% confidence 1.27, 3.17), although no clocks were related to cerebrovascular neuropathology. Cortical age was the only epigenetic clock significantly associated with the clinical phenotypes examined, from dementia to cognitive decline (5 specific cognitive systems, and a global cognitive measure averaging 17 tasks) to Parkinsonian signs. Overall, our findings provide evidence of the critical necessity for bespoke clocks of brain aging for advancing research to understand, and eventually prevent, neurodegenerative diseases of aging.
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Affiliation(s)
- Francine Grodstein
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States of America.
| | - Bernardo Lemos
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, United States of America
| | - Lei Yu
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Artemis Iatrou
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America
| | - Aron S Buchman
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
| | - Gemma L Shireby
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America; Department of Pathology, Rush University Medical Center, Chicago, IL, United States of America
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States of America
| | - David A Bennett
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
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27
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Fransquet PD, Lacaze P, Saffery R, Shah RC, Vryer R, Murray A, Woods RL, Ryan J. Accelerated Epigenetic Aging in Peripheral Blood does not Predict Dementia Risk. Curr Alzheimer Res 2021; 18:443-451. [PMID: 34429046 DOI: 10.2174/1567205018666210823100721] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 04/08/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND There is strong evidence that epigenetic age acceleration is associated with increased risk of later-life diseases and all-cause mortality. However, there is currently limited evidence that suggests accelerated epigenetic age is associated with dementia risk. OBJECTIVE This study aims to clarify whether epigenetic biomarkers of accelerated aging can predict dementia risk, which is an important consideration as aging is the greatest risk factor for the disease. METHODS DNA methylation was measured in peripheral blood samples provided by 160 participants from the ASPirin in Reducing Events in the Elderly study, including 73 pre-symptomatic dementia cases and 87 controls matched for age, sex, and smoking and education status. Epigenetic age was calculated using Horvath, Hannum, GrimAge and PhenoAge DNA methylation clocks, and age acceleration (the disparity between chronological age and epigenetic age) was determined. RESULTS There was no difference in age acceleration between dementia cases and controls. In males, only Hannum's intrinsic epigenetic age acceleration was increased in pre-symptomatic dementia cases compared to controls (Δ +1.8 years, p = 0.03). CONCLUSION These findings provide no strong evidence that accelerated epigenetic aging measured in peripheral blood can predict dementia risk.
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Affiliation(s)
- P D Fransquet
- School of Public Health and Preventive Medicine, Monash University, Melbourne, 3004, Victoria, Australia
| | - P Lacaze
- School of Public Health and Preventive Medicine, Monash University, Melbourne, 3004, Victoria, Australia
| | - R Saffery
- Murdoch Children's Research Institute, Department of Paediatrics, The University of Melbourne, Parkville, 3052 Victoria, Australia
| | - R C Shah
- Department of Family Medicine and Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, United States
| | - R Vryer
- Murdoch Children's Research Institute, Department of Paediatrics, The University of Melbourne, Parkville, 3052 Victoria, Australia
| | - A Murray
- Berman Center for Outcomes and Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare, Division of Geriatrics, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, United States
| | - R L Woods
- School of Public Health and Preventive Medicine, Monash University, Melbourne, 3004, Victoria, Australia
| | - J Ryan
- School of Public Health and Preventive Medicine, Monash University, Melbourne, 3004, Victoria, Australia
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De Jager PL. Deconstructing the epigenomic architecture of human neurodegeneration. Neurobiol Dis 2021; 153:105331. [PMID: 33711493 DOI: 10.1016/j.nbd.2021.105331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 10/21/2022] Open
Abstract
The past 10 years have seen a rapid advance in our ability to profile the epigenome from human pathologic material, opening up new study designs to investigate the role of epigenomic features in human disease. Moderate to large scale studies have now been conducted in the target tissue of neurodegenerative diseases, the brain, and, through the use of rigorous statistical methodologies, have laid a foundation of validated observations and successful study designs that inform our perspective on the role of the epigenome in these diseases, generate new hypotheses, and guide our path forward for a second generation of studies. It is clear that sampling the epigenome is not redundant with other "omic" profiling of the same tissue and that it can serve as an important vehicle for the integration of the effect of multiple environmental exposures on risk of disease. In some cases, change in the epigenome may thus have a causal impact on disease, but we now have evidence that such changes may also mediate some of the effect of tau proteinopathy and that other changes may moderate the impact of genetic risk factors. Thus, the epigenome may be involved at multiple different stages of the sequence of events that leads to human neurodegeneration, and we review the study designs that may begin to guide the development of a more comprehensive perspective on the aging brain's epigenome.
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Affiliation(s)
- Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, United States of America; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States of America; Department of Neurology, Columbia University Medical Center, New York, NY, United States of America.
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