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Martínez-Magaña JJ, Hurtado-Soriano J, Rivero-Segura NA, Montalvo-Ortiz JL, Garcia-delaTorre P, Becerril-Rojas K, Gomez-Verjan JC. Towards a Novel Frontier in the Use of Epigenetic Clocks in Epidemiology. Arch Med Res 2024; 55:103033. [PMID: 38955096 DOI: 10.1016/j.arcmed.2024.103033] [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: 01/10/2024] [Revised: 05/10/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
Health problems associated with aging are a major public health concern for the future. Aging is a complex process with wide intervariability among individuals. Therefore, there is a need for innovative public health strategies that target factors associated with aging and the development of tools to assess the effectiveness of these strategies accurately. Novel approaches to measure biological age, such as epigenetic clocks, have become relevant. These clocks use non-sequential variable information from the genome and employ mathematical algorithms to estimate biological age based on DNA methylation levels. Therefore, in the present study, we comprehensively review the current status of the epigenetic clocks and their associations across the human phenome. We emphasize the potential utility of these tools in an epidemiological context, particularly in evaluating the impact of public health interventions focused on promoting healthy aging. Our review describes associations between epigenetic clocks and multiple traits across the life and health span. Additionally, we highlighted the evolution of studies beyond mere associations to establish causal mechanisms between epigenetic age and disease. We explored the application of epigenetic clocks to measure the efficacy of interventions focusing on rejuvenation.
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Affiliation(s)
- José Jaime Martínez-Magaña
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; U.S. Department of Veterans Affairs National Center for Post-Traumatic Stress Disorder, Clinical Neuroscience Division, West Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | | | | | - Janitza L Montalvo-Ortiz
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA; U.S. Department of Veterans Affairs National Center for Post-Traumatic Stress Disorder, Clinical Neuroscience Division, West Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | - Paola Garcia-delaTorre
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Área de Envejecimiento, Centro Médico Nacional, Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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2
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Monnat RJ. James German and the Quest to Understand Human RECQ Helicase Deficiencies. Cells 2024; 13:1077. [PMID: 38994931 PMCID: PMC11240319 DOI: 10.3390/cells13131077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/10/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
James German's work to establish the natural history and cancer risk associated with Bloom syndrome (BS) has had a strong influence on the generation of scientists and clinicians working to understand other RECQ deficiencies and heritable cancer predisposition syndromes. I summarize work by us and others below, inspired by James German's precedents with BS, to understand and compare BS with the other heritable RECQ deficiency syndromes with a focus on Werner syndrome (WS). What we know, unanswered questions and new opportunities are discussed, as are potential ways to treat or modify WS-associated disease mechanisms and pathways.
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Affiliation(s)
- Raymond J Monnat
- Departments of Laboratory Medicine/Pathology and Genome Sciences, University of Washington, Seattle, WA 98195, USA
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3
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Humaira Amanullah F, Alam T, El Hajj N, Bejaoui Y. The impact of COVID-19 on "biological aging". Front Immunol 2024; 15:1399676. [PMID: 38919619 PMCID: PMC11197383 DOI: 10.3389/fimmu.2024.1399676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024] Open
Abstract
The global impact of the SARS-CoV-2 pandemic has been unprecedented, posing a significant public health challenge. Chronological age has been identified as a key determinant for severe outcomes associated with SARS-CoV-2 infection. Epigenetic age acceleration has previously been observed in various diseases including human immunodeficiency virus (HIV), Cytomegalovirus (CMV), cardiovascular diseases, and cancer. However, a comprehensive review of this topic is still missing in the field. In this review, we explore and summarize the research work focusing on biological aging markers, i.e., epigenetic age and telomere attrition in COVID-19 patients. From the reviewed articles, we identified a consistent pattern of epigenetic age dysregulation and shortened telomere length, revealing the impact of COVID-19 on epigenetic aging and telomere attrition.
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Affiliation(s)
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Yosra Bejaoui
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
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4
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Sandalova E, Maier AB. Targeting the epigenetically older individuals for geroprotective trials: the use of DNA methylation clocks. Biogerontology 2024; 25:423-431. [PMID: 37968337 DOI: 10.1007/s10522-023-10077-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/15/2023] [Indexed: 11/17/2023]
Abstract
Chronological age is the most important risk factor for the incidence of age-related diseases. The pace of ageing determines the magnitude of that risk and can be expressed as biological age. Targeting fundamental pathways of human aging with geroprotectors has the potential to lower the biological age and therewith prolong the healthspan, the period of life one spends in good health. Target populations for geroprotective interventions should be chosen based on the ageing mechanisms being addressed and the expected effect of the geroprotector on the primary outcome. Biomarkers of ageing, such as DNA methylation age, can be used to select populations for geroprotective interventions and as a surrogate outcome. Here, the use of DNA methylation clocks for selecting target populations for geroprotective intervention is explored.
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Affiliation(s)
- Elena Sandalova
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore, Singapore.
| | - Andrea B Maier
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore, Singapore.
- Department of Human Movement Sciences, @AgeAmsterdam, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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Perez K, Parras A, Picó S, Rechsteiner C, Haghani A, Brooke R, Mrabti C, Schoenfeldt L, Horvath S, Ocampo A. DNA repair-deficient premature aging models display accelerated epigenetic age. Aging Cell 2024; 23:e14058. [PMID: 38140713 PMCID: PMC10861193 DOI: 10.1111/acel.14058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Several premature aging mouse models have been developed to study aging and identify interventions that can delay age-related diseases. Yet, it is still unclear whether these models truly recapitulate natural aging. Here, we analyzed DNA methylation in multiple tissues of four previously reported mouse models of premature aging (Ercc1, LAKI, Polg, and Xpg). We estimated DNA methylation (DNAm) age of these samples using the Horvath clock. The most pronounced increase in DNAm age could be observed in Ercc1 mice, a strain which exhibits a deficit in DNA nucleotide excision repair. Similarly, we detected an increase in epigenetic age in fibroblasts isolated from patients with progeroid syndromes associated with mutations in DNA excision repair genes. These findings highlight that mouse models with deficiencies in DNA repair, unlike other premature aging models, display accelerated epigenetic age, suggesting a strong connection between DNA damage and epigenetic dysregulation during aging.
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Affiliation(s)
- Kevin Perez
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
| | - Alberto Parras
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
| | - Sara Picó
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Cheyenne Rechsteiner
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | | | - Robert Brooke
- Epigenetic Clock Development FoundationTorranceCaliforniaUSA
| | - Calida Mrabti
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Lucas Schoenfeldt
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
| | - Steve Horvath
- Altos LabsSan DiegoCaliforniaUSA
- Epigenetic Clock Development FoundationTorranceCaliforniaUSA
- Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Alejandro Ocampo
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
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Guvatova ZG, Kobelyatskaya AA, Pudova EA, Tarasova IV, Kudryavtseva AV, Tkacheva ON, Strazhesko ID, Moskalev AA. Decelerated Epigenetic Aging in Long Livers. Int J Mol Sci 2023; 24:16867. [PMID: 38069189 PMCID: PMC10707056 DOI: 10.3390/ijms242316867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Epigenetic aging is a hot topic in the field of aging research. The present study estimated epigenetic age in long-lived individuals, who are currently actively being studied worldwide as an example of successful aging due to their longevity. We used Bekaert's blood-based age prediction model to estimate the epigenetic age of 50 conditionally "healthy" and 45 frail long-livers over 90 years old. Frailty assessment in long-livers was conducted using the Frailty Index. The control group was composed of 32 healthy individuals aged 20-60 years. The DNA methylation status of 4 CpG sites (ASPA CpG1, PDE4C CpG1, ELOVL2 CpG6, and EDARADD CpG1) included in the epigenetic clock was assessed through pyrosequencing. According to the model calculations, the epigenetic age of long-livers was significantly lower than their chronological age (on average by 21 years) compared with data from the group of people aged 20 to 60 years. This suggests a slowing of epigenetic and potentially biological aging in long livers. At the same time, the obtained results showed no statistically significant differences in delta age (difference between the predicted and chronological age) between "healthy" long livers and long livers with frailty. We also failed to detect sex differences in epigenetic age either in the group of long livers or in the control group. It is possible that the predictive power of epigenetic clocks based on a small number of CpG sites is insufficient to detect such differences. Nevertheless, this study underscores the need for further research on the epigenetic status of centenarians to gain a deeper understanding of the factors contributing to delayed aging in this population.
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Affiliation(s)
- Zulfiya G. Guvatova
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, Moscow 129226, Russia; (I.V.T.); (O.N.T.); (I.D.S.)
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia (E.A.P.); (A.V.K.)
| | - Anastasiya A. Kobelyatskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia (E.A.P.); (A.V.K.)
| | - Elena A. Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia (E.A.P.); (A.V.K.)
| | - Irina V. Tarasova
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, Moscow 129226, Russia; (I.V.T.); (O.N.T.); (I.D.S.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia (E.A.P.); (A.V.K.)
| | - Olga N. Tkacheva
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, Moscow 129226, Russia; (I.V.T.); (O.N.T.); (I.D.S.)
| | - Irina D. Strazhesko
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, Moscow 129226, Russia; (I.V.T.); (O.N.T.); (I.D.S.)
| | - Alexey A. Moskalev
- Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Ministry of Healthcare of the Russian Federation, Moscow 129226, Russia; (I.V.T.); (O.N.T.); (I.D.S.)
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Crochemore C, Chica C, Garagnani P, Lattanzi G, Horvath S, Sarasin A, Franceschi C, Bacalini MG, Ricchetti M. Epigenomic signature of accelerated ageing in progeroid Cockayne syndrome. Aging Cell 2023; 22:e13959. [PMID: 37688320 PMCID: PMC10577576 DOI: 10.1111/acel.13959] [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: 05/17/2022] [Revised: 07/16/2023] [Accepted: 07/31/2023] [Indexed: 09/10/2023] Open
Abstract
Cockayne syndrome (CS) and UV-sensitive syndrome (UVSS) are rare genetic disorders caused by mutation of the DNA repair and multifunctional CSA or CSB protein, but only CS patients display a progeroid and neurodegenerative phenotype, providing a unique conceptual and experimental paradigm. As DNA methylation (DNAm) remodelling is a major ageing marker, we performed genome-wide analysis of DNAm of fibroblasts from healthy, UVSS and CS individuals. Differential analysis highlighted a CS-specific epigenomic signature (progeroid-related; not present in UVSS) enriched in three categories: developmental transcription factors, ion/neurotransmitter membrane transporters and synaptic neuro-developmental genes. A large fraction of CS-specific DNAm changes were associated with expression changes in CS samples, including in previously reported post-mortem cerebella. The progeroid phenotype of CS was further supported by epigenomic hallmarks of ageing: the prediction of DNAm of repetitive elements suggested an hypomethylation of Alu sequences in CS, and the epigenetic clock returned a marked increase in CS biological age respect to healthy and UVSS cells. The epigenomic remodelling of accelerated ageing in CS displayed both commonalities and differences with other progeroid diseases and regular ageing. CS shared DNAm changes with normal ageing more than other progeroid diseases do, and included genes functionally validated for regular ageing. Collectively, our results support the existence of an epigenomic basis of accelerated ageing in CS and unveil new genes and pathways that are potentially associated with the progeroid/degenerative phenotype.
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Affiliation(s)
- Clément Crochemore
- Institut Pasteur, Université Paris Cité, Molecular Mechanisms of Pathological and Physiological Ageing Unit, UMR3738 CNRSParisFrance
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR3738 CNRSParisFrance
- Sup'BiotechVillejuifFrance
| | - Claudia Chica
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HubParisFrance
| | - Paolo Garagnani
- IRCCS Azienda Ospedaliero‐Universitaria di BolognaBolognaItaly
- Department of Medical and Surgical Sciences (DIMEC)University of BolognaBolognaItaly
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli‐Sforza”, Unit of BolognaBolognaItaly
- IRCCS Istituto Ortopedico RizzoliBolognaItaly
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesUSA
- Department of Biostatistics Fielding School of Public HealthUniversity of CaliforniaLos AngelesUSA
| | - Alain Sarasin
- Laboratory of Genetic Stability and Oncogenesis, Institut de Cancérologie Gustave RoussyUniversity Paris‐SudVillejuifFrance
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and MechanicsLobachevsky UniversityNizhniy NovgorodRussia
| | | | - Miria Ricchetti
- Institut Pasteur, Université Paris Cité, Molecular Mechanisms of Pathological and Physiological Ageing Unit, UMR3738 CNRSParisFrance
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR3738 CNRSParisFrance
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Quintana‐Torres D, Valle‐Cao A, Bousquets‐Muñoz P, Freitas‐Rodríguez S, Rodríguez F, Lucia A, López‐Otín C, López‐Soto A, Folgueras AR. The secretome atlas of two mouse models of progeria. Aging Cell 2023; 22:e13952. [PMID: 37565451 PMCID: PMC10577534 DOI: 10.1111/acel.13952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disease caused by nuclear envelope alterations that lead to accelerated aging and premature death. Several studies have linked health and longevity to cell-extrinsic mechanisms, highlighting the relevance of circulating factors in the aging process as well as in age-related diseases. We performed a global plasma proteomic analysis in two preclinical progeroid models (LmnaG609G/G609G and Zmpste24-/- mice) using aptamer-based proteomic technology. Pathways related to the extracellular matrix, growth factor response and calcium ion binding were among the most enriched in the proteomic signature of progeroid samples compared to controls. Despite the global downregulation trend found in the plasma proteome of progeroid mice, several proteins associated with cardiovascular disease, the main cause of death in HGPS, were upregulated. We also developed a chronological age predictor using plasma proteome data from a cohort of healthy mice (aged 1-30 months), that reported an age acceleration when applied to progeroid mice, indicating that these mice exhibit an "old" plasma proteomic signature. Furthermore, when compared to naturally-aged mice, a great proportion of differentially expressed circulating proteins in progeroid mice were specific to premature aging, highlighting secretome-associated differences between physiological and accelerated aging. This is the first large-scale profiling of the plasma proteome in progeroid mice, which provides an extensive list of candidate circulating plasma proteins as potential biomarkers and/or therapeutic targets for further exploration and hypothesis generation in the context of both physiological and premature aging.
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Affiliation(s)
- Diego Quintana‐Torres
- Departamento de Bioquímica y Biología Molecular, Facultad de MedicinaInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)OviedoSpain
| | - Alejandra Valle‐Cao
- Departamento de Bioquímica y Biología Molecular, Facultad de MedicinaInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)OviedoSpain
| | - Pablo Bousquets‐Muñoz
- Departamento de Bioquímica y Biología Molecular, Facultad de MedicinaInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de OviedoOviedoSpain
| | - Sandra Freitas‐Rodríguez
- Departamento de Bioquímica y Biología Molecular, Facultad de MedicinaInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de OviedoOviedoSpain
| | - Francisco Rodríguez
- Departamento de Bioquímica y Biología Molecular, Facultad de MedicinaInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de OviedoOviedoSpain
| | - Alejandro Lucia
- CIBER of Frailty and Healthy Aging (CIBERFES) and Instituto de Investigación 12 de Octubre (i+12)MadridSpain
- Faculty of Sport SciencesUniversidad EuropeaMadridSpain
| | - Carlos López‐Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de MedicinaInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de OviedoOviedoSpain
| | - Alejandro López‐Soto
- Departamento de Bioquímica y Biología Molecular, Facultad de MedicinaInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)OviedoSpain
| | - Alicia R. Folgueras
- Departamento de Bioquímica y Biología Molecular, Facultad de MedicinaInstituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de OviedoOviedoSpain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)OviedoSpain
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Kerepesi C, Gladyshev VN. Intersection clock reveals a rejuvenation event during human embryogenesis. Aging Cell 2023; 22:e13922. [PMID: 37786333 PMCID: PMC10577537 DOI: 10.1111/acel.13922] [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: 02/23/2023] [Revised: 06/08/2023] [Accepted: 06/20/2023] [Indexed: 10/04/2023] Open
Abstract
Recent research revealed a rejuvenation event during early development of mice. Here, by examining epigenetic age dynamics of human embryogenesis, we tested whether a similar event exists in humans. For this purpose, we developed an epigenetic clock method, the intersection clock, that utilizes bisulfite sequencing in a way that maximizes the use of informative CpG sites with no missing clock CpG sites in test samples and applied it to human embryo development data. We observed no changes in the predicted epigenetic age between cleavage stage and blastocyst stage embryos; however, a significant decrease was observed between blastocysts and cells representing the epiblast. Additionally, by applying the intersection clock to datasets spanning pre and postimplantation, we found no significant change in the epigenetic age during preimplantation stages; however, the epigenetic age of postimplantation samples was lower compared to the preimplantation stages. We further investigated the epigenetic age of primed (representing early postimplantation) and naïve (representing preimplantation) pluripotent stem cells and observed that in all cases the epigenetic age of primed cells was significantly lower than that of naïve cells. Together, our data suggest that human embryos are rejuvenated during early embryogenesis. Hence, the rejuvenation event is conserved between the mouse and human, and it occurs around the gastrulation stage in both species. Beyond this advance, the intersection clock opens the way for other epigenetic age studies based on human bisulfite sequencing datasets as opposed to methylation arrays.
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Affiliation(s)
- Csaba Kerepesi
- Brigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
- Institute for Computer Science and Control (SZTAKI), Eötvös Loránd Research NetworkBudapestHungary
| | - Vadim N. Gladyshev
- Brigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
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10
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Lee J, Zhang J, Flanagan M, Martinez JA, Cunniff C, Kucine N, Lu AT, Haghani A, Gordevičius J, Horvath S, Chang VY. Bloom syndrome patients and mice display accelerated epigenetic aging. Aging Cell 2023; 22:e13964. [PMID: 37594403 PMCID: PMC10577546 DOI: 10.1111/acel.13964] [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: 03/20/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Bloom syndrome (BSyn) is an autosomal recessive disorder caused by variants in the BLM gene, which is involved in genome stability. Patients with BSyn present with poor growth, sun sensitivity, mild immunodeficiency, diabetes, and increased risk of cancer, most commonly leukemias. Interestingly, patients with BSyn do not have other signs of premature aging such as early, progressive hair loss and cataracts. We set out to determine epigenetic age in BSyn, which can be a better predictor of health and disease over chronological age. Our results show for the first time that patients with BSyn have evidence of accelerated epigenetic aging across several measures in blood lymphocytes, as compared to carriers. Additionally, homozygous Blm mice exhibit accelerated methylation age in multiple tissues, including brain, blood, kidney, heart, and skin, according to the brain methylation clock. Overall, we find that Bloom syndrome is associated with accelerated epigenetic aging effects in multiple tissues and more generally a strong effect on CpG methylation levels.
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Affiliation(s)
- Jamie Lee
- Division of Pediatric Hematology and OncologyUCLALos AngelesCaliforniaUSA
| | - Joshua Zhang
- Department of Human GeneticsUCLALos AngelesCaliforniaUSA
| | - Maeve Flanagan
- Department of PediatricsWeill Cornell Medical CollegeNew YorkNew YorkUSA
| | - Julian A. Martinez
- Department of Human GeneticsUCLALos AngelesCaliforniaUSA
- Division of Medical GeneticsUCLALos AngelesCaliforniaUSA
- Department of PsychiatryUCLALos AngelesCaliforniaUSA
| | | | - Nicole Kucine
- Department of PediatricsWeill Cornell Medical CollegeNew YorkNew YorkUSA
| | - Ake T. Lu
- Department of Human GeneticsUCLALos AngelesCaliforniaUSA
- Altos LabsSan DiegoCaliforniaUSA
| | - Amin Haghani
- Department of Human GeneticsUCLALos AngelesCaliforniaUSA
- Altos LabsSan DiegoCaliforniaUSA
| | | | - Steve Horvath
- Department of Human GeneticsUCLALos AngelesCaliforniaUSA
- Altos LabsSan DiegoCaliforniaUSA
| | - Vivian Y. Chang
- Division of Pediatric Hematology and OncologyUCLALos AngelesCaliforniaUSA
- Children's Discovery and Innovation InstituteUCLALos AngelesCaliforniaUSA
- Jonsson Comprehensive Cancer CenterUCLALos AngelesCaliforniaUSA
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11
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Rothermund K, Englert C, Gerstorf D. Explaining Variation in Individual Aging, Its Sources, and Consequences: A Comprehensive Conceptual Model of Human Aging. Gerontology 2023; 69:1437-1447. [PMID: 37769642 PMCID: PMC10711769 DOI: 10.1159/000534324] [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: 05/15/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
We define aging as a characteristic deterioration in one (or more) observable attributes of an organism that typically occurs during later life. With this narrow functional definition, we gain the freedom to separate aging from other processes of age-related change (e.g., maturation, growth, illness, terminal decline). We introduce a structural model that distinguishes between (1) the phenomenon of aging, (2) the subjective experience of aging, (3) sources of aging, and (4) consequences of aging. A core focus of the model is on the role of buffering mechanisms of biological repair and personal adaptation that regulate the relations between sources of aging, aging proper, and its consequences. The quality and level of functioning of these buffering mechanisms also varies across the life span, which directly affects the sources of aging, resulting in either resilience against or accelerated aging, and thus can be considered to be a major source of the variation in aging processes among different individuals. External factors comprising attributes of the physical environment and sociocultural characteristics are considered as contexts in which aging occurs. These contextual factors are assumed to feed into the various components of the model. Our model provides an interdisciplinary account of human aging, its sources and consequences, and also its subjective experience, by integrating biological, psychological, lifestyle, and sociocultural factors, and by specifying their interrelations and interactions. The model provides a comprehensive understanding of individual human aging, its underlying processes, and modulating factors. It allows for the derivation of empirically testable hypotheses, and it helps practitioners to identify elements that lend themselves to targeted intervention efforts aimed at increasing the resilience of individuals against aging and buffering its negative consequences.
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Affiliation(s)
- Klaus Rothermund
- Department of Psychology, Friedrich Schiller University Jena, Jena, Germany
- Zentrum für Alternsforschung Jena (ZAJ), Jena, Germany
| | - Christoph Englert
- Zentrum für Alternsforschung Jena (ZAJ), Jena, Germany
- Institute of Biochemistry and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
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12
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Simpson DJ, Zhao Q, Olova NN, Dabrowski J, Xie X, Latorre‐Crespo E, Chandra T. Region-based epigenetic clock design improves RRBS-based age prediction. Aging Cell 2023; 22:e13866. [PMID: 37170475 PMCID: PMC10410054 DOI: 10.1111/acel.13866] [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: 02/08/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
Recent studies suggest that epigenetic rejuvenation can be achieved using drugs that mimic calorie restriction and techniques such as reprogramming-induced rejuvenation. To effectively test rejuvenation in vivo, mouse models are the safest alternative. However, we have found that the recent epigenetic clocks developed for mouse reduced-representation bisulphite sequencing (RRBS) data have significantly poor performance when applied to external datasets. We show that the sites captured and the coverage of key CpGs required for age prediction vary greatly between datasets, which likely contributes to the lack of transferability in RRBS clocks. To mitigate these coverage issues in RRBS-based age prediction, we present two novel design strategies that use average methylation over large regions rather than individual CpGs, whereby regions are defined by sliding windows (e.g. 5 kb), or density-based clustering of CpGs. We observe improved correlation and error in our regional blood clocks (RegBCs) compared to published individual-CpG-based techniques when applied to external datasets. The RegBCs are also more robust when applied to low coverage data and detect a negative age acceleration in mice undergoing calorie restriction. Our RegBCs offer a proof of principle that age prediction of RRBS datasets can be improved by accounting for multiple CpGs over a region, which negates the lack of read depth currently hindering individual-CpG-based approaches.
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Affiliation(s)
- Daniel J. Simpson
- MRC Human Genetics Unit, MRC Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Qian Zhao
- MRC Human Genetics Unit, MRC Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Nelly N. Olova
- MRC Human Genetics Unit, MRC Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Jan Dabrowski
- MRC Human Genetics Unit, MRC Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Xiaoxiao Xie
- MRC Human Genetics Unit, MRC Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Eric Latorre‐Crespo
- MRC Human Genetics Unit, MRC Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Tamir Chandra
- MRC Human Genetics Unit, MRC Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
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13
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Milicic L, Porter T, Vacher M, Laws SM. Utility of DNA Methylation as a Biomarker in Aging and Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:475-503. [PMID: 37313495 PMCID: PMC10259073 DOI: 10.3233/adr-220109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/23/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation have been implicated in a number of diseases including cancer, heart disease, autoimmune disorders, and neurodegenerative diseases. While it is recognized that DNA methylation is tissue-specific, a limitation for many studies is the ability to sample the tissue of interest, which is why there is a need for a proxy tissue such as blood, that is reflective of the methylation state of the target tissue. In the last decade, DNA methylation has been utilized in the design of epigenetic clocks, which aim to predict an individual's biological age based on an algorithmically defined set of CpGs. A number of studies have found associations between disease and/or disease risk with increased biological age, adding weight to the theory of increased biological age being linked with disease processes. Hence, this review takes a closer look at the utility of DNA methylation as a biomarker in aging and disease, with a particular focus on Alzheimer's disease.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- CSIRO Health and Biosecurity, Australian e-Health Research Centre, Floreat, Western Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
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14
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Carlund O, Norberg A, Osterman P, Landfors M, Degerman S, Hultdin M. DNA methylation variations and epigenetic aging in telomere biology disorders. Sci Rep 2023; 13:7955. [PMID: 37193737 DOI: 10.1038/s41598-023-34922-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/10/2023] [Indexed: 05/18/2023] Open
Abstract
Telomere Biology Disorders (TBDs) are characterized by mutations in telomere-related genes leading to short telomeres and premature aging but with no strict correlation between telomere length and disease severity. Epigenetic alterations are also markers of aging and we aimed to evaluate whether DNA methylation (DNAm) could be part of the pathogenesis of TBDs. In blood from 35 TBD cases, genome-wide DNAm were analyzed and the cases were grouped based on relative telomere length (RTL): short (S), with RTL close to normal controls, and extremely short (ES). TBD cases had increased epigenetic age and DNAm alterations were most prominent in the ES-RTL group. Thus, the differentially methylated (DM) CpG sites could be markers of short telomeres but could also be one of the mechanisms contributing to disease phenotype since DNAm alterations were observed in symptomatic, but not asymptomatic, cases with S-RTL. Furthermore, two or more DM-CpGs were identified in four genes previously linked to TBD or telomere length (PRDM8, SMC4, VARS, and WNT6) and in three genes that were novel in telomere biology (MAS1L, NAV2, and TM4FS1). The DM-CpGs in these genes could be markers of aging in hematological cells, but they could also be of relevance for the progression of TBD.
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Affiliation(s)
- Olivia Carlund
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Anna Norberg
- Department of Medical Biosciences, Medical and Clinical Genetics, Umeå University, Umeå, Sweden
| | - Pia Osterman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden.
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15
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Carvalho GFDS, Costa TVMM, Nascimento AM, Wolff BM, Damasceno JG, Vieira LL, Almeida VT, Oliveira YGD, Mello CBD, Muszkat M, Kulikowski LD. DNA methylation epi-signature and biological age in attention deficit hyperactivity disorder patients. Clin Neurol Neurosurg 2023; 228:107714. [PMID: 37054476 DOI: 10.1016/j.clineuro.2023.107714] [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: 01/13/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
OBJECTIVE Attention Deficit/Hyperactivity Disorder (ADHD) is a common behavioral syndrome that begins in childhood and affects 3.4% of children worldwide. Due to its etiological complexity, there are no consistent biomarkers for ADHD, however the high heritability presented by the disorder indicates a genetic/epigenetic influence. The main epigenetic mechanism is DNA methylation, a process with an important role in gene expression and in many psychiatric disorders. Thus, our study sought to identify epi-signatures biomarkers in 29 children clinically diagnosed with ADHD. METHODS After DNA extraction and bisulfite conversion, we performed methylation array experiment for differential methylation, ontological and biological age analysis. RESULTS The biological response in ADHD patients was not sufficient to determine a conclusive epi-signature in our study. However, our results highlighted the interaction of energy metabolism and oxidative stress pathways in ADHD patients detected by differential methylation patterns. Furthermore, we were able to identify a marginal association between the DNAmAge and ADHD. CONCLUSION Our study present new methylation biomarkers findings associated with energy metabolism and oxidative stress pathways, in addition to DNAmAge in ADHD patients. However, we propose that further multiethnic studies, with larger cohorts and including maternal conditions, are necessary to demonstrate a definitive association between ADHD and these methylation biomarkers.
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Affiliation(s)
| | | | - Amom Mendes Nascimento
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Beatriz Martins Wolff
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Julian Gabriel Damasceno
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Lucas Liro Vieira
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Vanessa Tavares Almeida
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Yanca Gasparini de Oliveira
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Claudia Berlim de Mello
- Nucleo de Atendimento Neuropsicologico Infantil Interdisciplinar (NANI), Centro Paulista de Neuropsicologia, Departamento de Psicobiologia da Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil
| | - Mauro Muszkat
- Nucleo de Atendimento Neuropsicologico Infantil Interdisciplinar (NANI), Centro Paulista de Neuropsicologia, Departamento de Psicobiologia da Universidade Federal de São Paulo - UNIFESP, São Paulo, Brazil
| | - Leslie Domenici Kulikowski
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
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16
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Deryabin PI, Borodkina AV. Epigenetic clocks provide clues to the mystery of uterine ageing. Hum Reprod Update 2022; 29:259-271. [PMID: 36515535 DOI: 10.1093/humupd/dmac042] [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: 08/12/2022] [Revised: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Rising maternal ages and age-related fertility decline are a global challenge for modern reproductive medicine. Clinicians and researchers pay specific attention to ovarian ageing and hormonal insufficiency in this regard. However, uterine ageing is often left out of the picture, with the majority of reproductive clinicians being close to unanimous on the absence of age-related functional decline in the uterine tissues. Therefore, most existing techniques to treat an age-related decline in implantation rates are based primarily on hormonal supplementation and oocyte donation. Solving the issue of uterine ageing might lead to an adjustment to these methods. OBJECTIVE AND RATIONALE A focus on uterine ageing and the possibility of slowing it emerged with the development of the information theory of ageing, which identifies genomic instability and erosion of the epigenetic landscape as important drivers of age-related decline in the functionality of most cells and tissues. Age-related smoothing of this landscape and a decline in tissue function can be assessed by measuring the ticking of epigenetic clocks. Within this review, we explore whether the uterus experiences age-related alterations using this elegant approach. We analyse existing data on epigenetic clocks in the endometrium, highlight approaches to improve the accuracy of the clocks in this cycling tissue, speculate on the endometrial pathologies whose progression might be predicted by the altered speed of epigenetic clocks and discuss the possibilities of slowing down the ticking of these clocks. SEARCH METHODS Data for this review were identified by searches of Medline, PubMed and Google Scholar. References from relevant articles using the search terms 'ageing', 'maternal age', 'female reproduction', 'uterus', 'endometrium', 'implantation', 'decidualization', 'epigenetic clock', 'biological age', 'DNA methylation', 'fertility' and 'infertility' were selected. A total of 95 articles published in English between 1985 and 2022 were included, six of which describe the use of the epigenetic clock to evaluate uterine/endometrium ageing. OUTCOMES Application of the Horvath and DNAm PhenoAge epigenetic clocks demonstrated a poor correlation with chronological age in the endometrium. Several approaches were suggested to enhance the predictive power of epigenetic clocks for the endometrium. The first was to increase the number of samples in the training dataset, as for the Zang clock, or to use more sophisticated clock-building algorithms, as for the AltumAge clock. The second method is to adjust the clocks according to the dynamic nature of the endometrium. Using either approach revealed a strong correlation with chronological age in the endometrium, providing solid evidence for age-related functional decline in this tissue. Furthermore, age acceleration/deceleration, as estimated by epigenetic clocks, might be a promising tool to predict or to gain insights into the origin of various endometrial pathologies, including recurrent implantation failure, cancer and endometriosis. Finally, there are several strategies to slow down or even reverse epigenetic clocks that might be applied to reduce the risk of age-related uterine impairments. WIDER IMPLICATIONS The uterine factor should be considered, along with ovarian issues, to correct for the decline in female fertility with age. Epigenetic clocks can be tested to gain a deeper understanding of various endometrial disorders.
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Affiliation(s)
- Pavel I Deryabin
- Mechanisms of Cellular Senescence Group, Institute of Cytology of the Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Aleksandra V Borodkina
- Mechanisms of Cellular Senescence Group, Institute of Cytology of the Russian Academy of Sciences, Saint-Petersburg, Russia
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Abstract
Over the course of a human lifespan, genome integrity erodes, leading to an increased abundance of several types of chromatin changes. The abundance of DNA lesions (chemical perturbations to nucleotides) increases with age, as does the number of genomic mutations and transcriptional disruptions caused by replication or transcription of those lesions, respectively. At the epigenetic level, precise DNA methylation patterns degrade, likely causing increasingly stochastic variations in gene expression. Similarly, the tight regulation of histone modifications begins to unravel. The genomic instability caused by these mechanisms allows transposon element reactivation and remobilization, further mutations, gene dysregulation, and cytoplasmic chromatin fragments. This cumulative genomic instability promotes cell signaling events that drive cell fate decisions and extracellular communications known to disrupt tissue homeostasis and regeneration. In this Review, we focus on age-related epigenetic changes and their interactions with age-related genomic changes that instigate these events.
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Affiliation(s)
- Carolina Soto-Palma
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism
- Department of Biochemistry, Molecular Biology, and Biophysics
| | - Christopher D. Faulk
- Institute on the Biology of Aging and Metabolism
- Department of Animal Science, and
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
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18
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Della Valle F, Reddy P, Yamamoto M, Liu P, Saera-Vila A, Bensaddek D, Zhang H, Prieto Martinez J, Abassi L, Celii M, Ocampo A, Nuñez Delicado E, Mangiavacchi A, Aiese Cigliano R, Rodriguez Esteban C, Horvath S, Izpisua Belmonte JC, Orlando V. LINE-1 RNA causes heterochromatin erosion and is a target for amelioration of senescent phenotypes in progeroid syndromes. Sci Transl Med 2022; 14:eabl6057. [PMID: 35947677 DOI: 10.1126/scitranslmed.abl6057] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Constitutive heterochromatin is responsible for genome repression of DNA enriched in repetitive sequences, telomeres, and centromeres. During physiological and pathological premature aging, heterochromatin homeostasis is profoundly compromised. Here, we showed that LINE-1 (Long Interspersed Nuclear Element-1; L1) RNA accumulation was an early event in both typical and atypical human progeroid syndromes. L1 RNA negatively regulated the enzymatic activity of the histone-lysine N-methyltransferase SUV39H1 (suppression of variegation 3-9 homolog 1), resulting in heterochromatin loss and onset of senescent phenotypes in vitro. Depletion of L1 RNA in dermal fibroblast cells from patients with different progeroid syndromes using specific antisense oligonucleotides (ASOs) restored heterochromatin histone 3 lysine 9 and histone 3 lysine 27 trimethylation marks, reversed DNA methylation age, and counteracted the expression of senescence-associated secretory phenotype genes such as p16, p21, activating transcription factor 3 (ATF3), matrix metallopeptidase 13 (MMP13), interleukin 1a (IL1a), BTG anti-proliferation factor 2 (BTG2), and growth arrest and DNA damage inducible beta (GADD45b). Moreover, systemic delivery of ASOs rescued the histophysiology of tissues and increased the life span of a Hutchinson-Gilford progeria syndrome mouse model. Transcriptional profiling of human and mouse samples after L1 RNA depletion demonstrated that pathways associated with nuclear chromatin organization, cell proliferation, and transcription regulation were enriched. Similarly, pathways associated with aging, inflammatory response, innate immune response, and DNA damage were down-regulated. Our results highlight the role of L1 RNA in heterochromatin homeostasis in progeroid syndromes and identify a possible therapeutic approach to treat premature aging and related syndromes.
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Affiliation(s)
- Francesco Della Valle
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | - Pradeep Reddy
- Salk Institute for Biological Studies, La Jolla, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Mako Yamamoto
- Salk Institute for Biological Studies, La Jolla, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Peng Liu
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | | | - Dalila Bensaddek
- King Abdullah University of Science and Technology (KAUST), Bioscience Core Lab
| | - Huoming Zhang
- King Abdullah University of Science and Technology (KAUST), Bioscience Core Lab
| | | | - Leila Abassi
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | - Mirko Celii
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | | | | | - Arianna Mangiavacchi
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
| | | | | | | | | | - Valerio Orlando
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Sciences and Engineering Division BESE, KAUST Environmental Epigenetics Program, Thuwal, Saudi Arabia
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Johnson AA, English BW, Shokhirev MN, Sinclair DA, Cuellar TL. Human age reversal: Fact or fiction? Aging Cell 2022; 21:e13664. [PMID: 35778957 PMCID: PMC9381899 DOI: 10.1111/acel.13664] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/23/2022] [Accepted: 06/13/2022] [Indexed: 12/19/2022] Open
Abstract
Although chronological age correlates with various age-related diseases and conditions, it does not adequately reflect an individual's functional capacity, well-being, or mortality risk. In contrast, biological age provides information about overall health and indicates how rapidly or slowly a person is aging. Estimates of biological age are thought to be provided by aging clocks, which are computational models (e.g., elastic net) that use a set of inputs (e.g., DNA methylation sites) to make a prediction. In the past decade, aging clock studies have shown that several age-related diseases, social variables, and mental health conditions associate with an increase in predicted biological age relative to chronological age. This phenomenon of age acceleration is linked to a higher risk of premature mortality. More recent research has demonstrated that predicted biological age is sensitive to specific interventions. Human trials have reported that caloric restriction, a plant-based diet, lifestyle changes involving exercise, a drug regime including metformin, and vitamin D3 supplementation are all capable of slowing down or reversing an aging clock. Non-interventional studies have connected high-quality sleep, physical activity, a healthy diet, and other factors to age deceleration. Specific molecules have been associated with the reduction or reversal of predicted biological age, such as the antihypertensive drug doxazosin or the metabolite alpha-ketoglutarate. Although rigorous clinical trials are needed to validate these initial findings, existing data suggest that aging clocks are malleable in humans. Additional research is warranted to better understand these computational models and the clinical significance of lowering or reversing their outputs.
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Affiliation(s)
- Adiv A. Johnson
- Longevity Sciences, Inc. (dba Tally Health)GreenwichConnecticutUSA
| | - Bradley W. English
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging ResearchHarvard Medical SchoolBostonMassachusettsUSA
| | | | - David A. Sinclair
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging ResearchHarvard Medical SchoolBostonMassachusettsUSA
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20
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Reale A, Tagliatesta S, Zardo G, Zampieri M. Counteracting aged DNA methylation states to combat ageing and age-related diseases. Mech Ageing Dev 2022; 206:111695. [PMID: 35760211 DOI: 10.1016/j.mad.2022.111695] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/09/2022] [Accepted: 06/22/2022] [Indexed: 12/18/2022]
Abstract
DNA methylation (DNAm) overwrites information about multiple extrinsic factors on the genome. Age is one of these factors. Age causes characteristic DNAm changes that are thought to be not only major drivers of normal ageing but also precursors to diseases, cancer being one of these. Although there is still much to learn about the relationship between ageing, age-related diseases and DNAm, we now know how to interpret some of the effects caused by age in the form of changes in methylation marks at specific loci. In fact, these changes form the basis of the so called "epigenetic clocks", which translate the genomic methylation profile into an "epigenetic age". Epigenetic age does not only estimate chronological age but can also predict the risk of chronic diseases and mortality. Epigenetic age is believed to be one of the most accurate metrics of biological age. Initial evidence has recently been gathered pointing to the possibility that the rate of epigenetic ageing can be slowed down or even reversed. In this review, we discuss some of the most relevant advances in this field. Expected outcome is that this approach can provide insights into how to preserve health and reduce the impact of ageing diseases in humans.
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Affiliation(s)
- Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Stefano Tagliatesta
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00161 Rome, Italy.
| | - Giuseppe Zardo
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
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21
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Milicic L, Vacher M, Porter T, Doré V, Burnham SC, Bourgeat P, Shishegar R, Doecke J, Armstrong NJ, Tankard R, Maruff P, Masters CL, Rowe CC, Villemagne VL, Laws SM. Comprehensive analysis of epigenetic clocks reveals associations between disproportionate biological ageing and hippocampal volume. GeroScience 2022; 44:1807-1823. [PMID: 35445885 PMCID: PMC9213584 DOI: 10.1007/s11357-022-00558-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 12/21/2022] Open
Abstract
The concept of age acceleration, the difference between biological age and chronological age, is of growing interest, particularly with respect to age-related disorders, such as Alzheimer's Disease (AD). Whilst studies have reported associations with AD risk and related phenotypes, there remains a lack of consensus on these associations. Here we aimed to comprehensively investigate the relationship between five recognised measures of age acceleration, based on DNA methylation patterns (DNAm age), and cross-sectional and longitudinal cognition and AD-related neuroimaging phenotypes (volumetric MRI and Amyloid-β PET) in the Australian Imaging, Biomarkers and Lifestyle (AIBL) and the Alzheimer's Disease Neuroimaging Initiative (ADNI). Significant associations were observed between age acceleration using the Hannum epigenetic clock and cross-sectional hippocampal volume in AIBL and replicated in ADNI. In AIBL, several other findings were observed cross-sectionally, including a significant association between hippocampal volume and the Hannum and Phenoage epigenetic clocks. Further, significant associations were also observed between hippocampal volume and the Zhang and Phenoage epigenetic clocks within Amyloid-β positive individuals. However, these were not validated within the ADNI cohort. No associations between age acceleration and other Alzheimer's disease-related phenotypes, including measures of cognition or brain Amyloid-β burden, were observed, and there was no association with longitudinal change in any phenotype. This study presents a link between age acceleration, as determined using DNA methylation, and hippocampal volume that was statistically significant across two highly characterised cohorts. The results presented in this study contribute to a growing literature that supports the role of epigenetic modifications in ageing and AD-related phenotypes.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia
- CSIRO Health and Biosecurity, Australian E-Health Research Centre, Floreat, Western Australia, 6014, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, 6102, Australia
| | - Vincent Doré
- Australian E-Health Research Centre, CSIRO, Parkville, Victoria, 3052, Australia
- Department of Molecular Imaging and Therapy and Centre for PET, Austin Health, Heidelberg, Victoria, Australia
| | - Samantha C Burnham
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Australian E-Health Research Centre, CSIRO, Parkville, Victoria, 3052, Australia
| | - Pierrick Bourgeat
- Australian E-Health Research Centre, CSIRO, Herston, Queensland, 4029, Australia
| | - Rosita Shishegar
- Australian E-Health Research Centre, CSIRO, Parkville, Victoria, 3052, Australia
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC, Australia
| | - James Doecke
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Australian E-Health Research Centre, CSIRO, Herston, Queensland, 4029, Australia
| | - Nicola J Armstrong
- Department of Mathematics and Statistics, Curtin University, Bentley, Western Australia, Australia
| | - Rick Tankard
- School of Mathematics and Statistics, Murdoch University, Perth, Western Australia, Australia
| | - Paul Maruff
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
- Cogstate Ltd, Melbourne, VIC, Australia
| | - Colin L Masters
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Christopher C Rowe
- Department of Molecular Imaging and Therapy and Centre for PET, Austin Health, Heidelberg, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Victor L Villemagne
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Department of Molecular Imaging and Therapy and Centre for PET, Austin Health, Heidelberg, Victoria, Australia
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon M Laws
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia.
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia.
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, 6102, Australia.
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22
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Horvath S, Lin DTS, Kobor MS, Zoller JA, Said JW, Morgello S, Singer E, Yong WH, Jamieson BD, Levine AJ. HIV, pathology and epigenetic age acceleration in different human tissues. GeroScience 2022; 44:1609-1620. [PMID: 35411474 PMCID: PMC9213580 DOI: 10.1007/s11357-022-00560-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022] Open
Abstract
Epigenetic clocks based on patterns of DNA methylation have great importance in understanding aging and disease; however, there are basic questions to be resolved in their application. It remains unknown whether epigenetic age acceleration (EAA) within an individual shows strong correlation between different primary tissue sites, the extent to which tissue pathology and clinical illness correlate with EAA in the target organ, and if EAA variability across tissues differs according to sex. Considering the outsized role of age-related illness in Human Immunodeficiency Virus-1 (HIV), these questions were pursued in a sample enriched for tissue from HIV-infected individuals. We used a custom methylation array to generate DNA methylation data from 661 samples representing 11 human tissues (adipose, blood, bone marrow, heart, kidney, liver, lung, lymph node, muscle, spleen and pituitary gland) from 133 clinically characterized, deceased individuals, including 75 infected with HIV. We developed a multimorbidity index based on the clinical disease history. Epigenetic age was moderately correlated across tissues. Blood had the greatest number and degree of correlation, most notably with spleen and bone marrow. However, blood did not correlate with epigenetic age of liver. EAA in liver was weakly correlated with EAA in kidney, adipose, lung and bone marrow. Clinically, hypertension was associated with EAA in several tissues, consistent with the multiorgan impacts of this illness. HIV infection was associated with positive age acceleration in kidney and spleen. Male sex was associated with increased epigenetic acceleration in several tissues. Preliminary evidence indicates that amyotrophic lateral sclerosis is associated with positive EAA in muscle tissue. Finally, greater multimorbidity was associated with greater EAA across all tissues. Blood alone will often fail to detect EAA in other tissues. While hypertension is associated with increased EAA in several tissues, many pathologies are associated with organ-specific age acceleration.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA. .,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - David T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Childrens Hospital Research Institute, Vancouver, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Childrens Hospital Research Institute, Vancouver, Canada
| | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Jonathan W Said
- Department of Pathology and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, Los Angeles, USA
| | - Susan Morgello
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Neuroscience and Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elyse Singer
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - William H Yong
- Department of Pathology and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, Los Angeles, USA
| | - Beth D Jamieson
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Andrew J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
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23
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Adaptive feature selection framework for DNA methylation-based age prediction. Soft comput 2022. [DOI: 10.1007/s00500-022-06844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Malecki KMC, Andersen JK, Geller AM, Harry GJ, Jackson CL, James KA, Miller GW, Ottinger MA. Integrating Environment and Aging Research: Opportunities for Synergy and Acceleration. Front Aging Neurosci 2022; 14:824921. [PMID: 35264945 PMCID: PMC8901047 DOI: 10.3389/fnagi.2022.824921] [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: 11/29/2021] [Accepted: 01/12/2022] [Indexed: 12/25/2022] Open
Abstract
Despite significant overlaps in mission, the fields of environmental health sciences and aging biology are just beginning to intersect. It is increasingly clear that genetics alone does not predict an individual’s neurological aging and sensitivity to disease. Accordingly, aging neuroscience is a growing area of mutual interest within environmental health sciences. The impetus for this review came from a workshop hosted by the National Academies of Sciences, Engineering, and Medicine in June of 2020, which focused on integrating the science of aging and environmental health research. It is critical to bridge disciplines with multidisciplinary collaborations across toxicology, comparative biology, epidemiology to understand the impacts of environmental toxicant exposures and age-related outcomes. This scoping review aims to highlight overlaps and gaps in existing knowledge and identify essential research initiatives. It begins with an overview of aging biology and biomarkers, followed by examples of synergy with environmental health sciences. New areas for synergistic research and policy development are also discussed. Technological advances including next-generation sequencing and other-omics tools now offer new opportunities, including exposomic research, to integrate aging biomarkers into environmental health assessments and bridge disciplinary gaps. This is necessary to advance a more complete mechanistic understanding of how life-time exposures to toxicants and other physical and social stressors alter biological aging. New cumulative risk frameworks in environmental health sciences acknowledge that exposures and other external stressors can accumulate across the life course and the advancement of new biomarkers of exposure and response grounded in aging biology can support increased understanding of population vulnerability. Identifying the role of environmental stressors, broadly defined, on aging biology and neuroscience can similarly advance opportunities for intervention and translational research. Several areas of growing research interest include expanding exposomics and use of multi-omics, the microbiome as a mediator of environmental stressors, toxicant mixtures and neurobiology, and the role of structural and historical marginalization and racism in shaping persistent disparities in population aging and outcomes. Integrated foundational and translational aging biology research in environmental health sciences is needed to improve policy, reduce disparities, and enhance the quality of life for older individuals.
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Affiliation(s)
- Kristen M. C. Malecki
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Kristen M. C. Malecki,
| | | | - Andrew M. Geller
- United States Environmental Protection Agency, Office of Research and Development, Durham, NC, United States
| | - G. Jean Harry
- Division of National Toxicology Program, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Chandra L. Jackson
- Division of Intramural Research, Department of Health and Human Services, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
- Department of Health and Human Services, National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, United States
| | - Katherine A. James
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado Denver, Denver, CO, United States
| | - Gary W. Miller
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, United States
| | - Mary Ann Ottinger
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
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25
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Okazaki S, Kimura R, Otsuka I, Funabiki Y, Murai T, Hishimoto A. Epigenetic clock analysis and increased plasminogen activator inhibitor-1 in high-functioning autism spectrum disorder. PLoS One 2022; 17:e0263478. [PMID: 35113965 PMCID: PMC8812940 DOI: 10.1371/journal.pone.0263478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/19/2022] [Indexed: 12/23/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is characterized by impaired social communication and behavioral problems. An increased risk of premature mortality has been observed in individuals with ASD. Therefore, we hypothesized that biological aging is accelerated in individuals with ASD. Recently, several studies have established genome-wide DNA methylation (DNAm) profiles as ‘epigenetic clocks’ that can estimate biological aging. In addition, ASD has been associated with differential DNAm patterns. Methods We used two independent datasets from blood samples consisting of adult patients with high-functioning ASD and controls: the 1st cohort (38 ASD cases and 31 controls) and the 2nd cohort (6 ASD cases and 10 controls). We explored well-studied epigenetic clocks such as HorvathAge, HannumAge, SkinBloodAge, PhenoAge, GrimAge, and DNAm-based telomere length (DNAmTL). In addition, we investigated seven DNAm-based age-related plasma proteins, including plasminogen activator inhibitor-1 (PAI-1), and smoking status, which are the components of GrimAge. Results Compared to controls, individuals with ASD in the 1st cohort, but not in the 2nd cohort, exhibited a trend for increased GrimAge acceleration and a significant increase of PAI-1 levels. A meta-analysis showed significantly increased PAI-1 levels in individuals with ASD compared to controls. Conclusion Our findings suggest there is no epigenetic age acceleration in the blood of individuals with ASD. However, this study provides novel evidence regarding increased plasma PAI-1 levels in individuals with high-functioning ASD. These findings suggest PAI-1 may be a biomarker for high-functioning ASD, however, larger studies based on epigenetic clocks and PAI-1 will be necessary to confirm these findings.
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Affiliation(s)
- Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yasuko Funabiki
- Department of Cognitive and Behavioral Science, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiya Murai
- Department of Psychiatry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Psychiatry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- * E-mail:
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26
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Bejaoui Y, Razzaq A, Yousri NA, Oshima J, Megarbane A, Qannan A, Potabattula R, Alam T, Martin G, Horn HF, Haaf T, Horvath S, El Hajj N. DNA methylation signatures in Blood DNA of Hutchinson-Gilford Progeria syndrome. Aging Cell 2022; 21:e13555. [PMID: 35045206 PMCID: PMC8844112 DOI: 10.1111/acel.13555] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 12/30/2022] Open
Abstract
Hutchinson-Gilford Progeria Syndrome (HGPS) is an extremely rare genetic disorder caused by mutations in the LMNA gene and characterized by premature and accelerated aging beginning in childhood. In this study, we performed the first genome-wide methylation analysis on blood DNA of 15 patients with progeroid laminopathies using Infinium Methylation EPIC arrays including 8 patients with classical HGPS. We could observe DNA methylation alterations at 61 CpG sites as well as 32 significant regions following a 5 Kb tiling analysis. Differentially methylated probes were enriched for phosphatidylinositol biosynthetic process, phospholipid biosynthetic process, sarcoplasm, sarcoplasmic reticulum, phosphatase regulator activity, glycerolipid biosynthetic process, glycerophospholipid biosynthetic process, and phosphatidylinositol metabolic process. Differential methylation analysis at the level of promoters and CpG islands revealed no significant methylation changes in blood DNA of progeroid laminopathy patients. Nevertheless, we could observe significant methylation differences in classic HGPS when specifically looking at probes overlapping solo-WCGW partially methylated domains. Comparing aberrantly methylated sites in progeroid laminopathies, classic Werner syndrome, and Down syndrome revealed a common significantly hypermethylated region in close vicinity to the transcription start site of a long non-coding RNA located anti-sense to the Catenin Beta Interacting Protein 1 gene (CTNNBIP1). By characterizing epigenetically altered sites, we identify possible pathways/mechanisms that might have a role in the accelerated aging of progeroid laminopathies.
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Affiliation(s)
- Yosra Bejaoui
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
| | - Aleem Razzaq
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
| | | | - Junko Oshima
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
- Department of Clinical Cell Biology and MedicineGraduate School of MedicineChiba UniversityChibaJapan
| | - Andre Megarbane
- Department of Human GeneticsGilbert and Rose‐Marie Ghagoury School of MedicineLebanese American UniversityByblosLebanon
- Institut Jérôme LejeuneParisFrance
| | - Abeer Qannan
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
| | - Ramya Potabattula
- Institute of Human GeneticsJulius Maximilians UniversityWürzburgGermany
| | - Tanvir Alam
- College of Science and EngineeringHamad Bin Khalifa UniversityDohaQatar
| | - George M. Martin
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Henning F. Horn
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
| | - Thomas Haaf
- Institute of Human GeneticsJulius Maximilians UniversityWürzburgGermany
| | - Steve Horvath
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of California Los AngelesLos AngelesCaliforniaUSA
- Department of BiostatisticsFielding School of Public HealthUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Nady El Hajj
- College of Health and Life SciencesQatar FoundationHamad Bin Khalifa UniversityDohaQatar
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27
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Shinko Y, Okazaki S, Otsuka I, Horai T, Kim S, Tanifuji T, Hishimoto A. Accelerated epigenetic age and shortened telomere length based on DNA methylation in Nicolaides-Baraitser syndrome. Mol Genet Genomic Med 2022; 10:e1876. [PMID: 35092358 PMCID: PMC8922957 DOI: 10.1002/mgg3.1876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/06/2021] [Accepted: 01/06/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Nicolaides-Baraitser syndrome (NCBRS) is a rare disorder characterized by neurodevelopmental delays, seizures, and diverse physical characteristics. The DNA methylation (DNAm) profile in NCBRS is significantly different. DNAm is linked to the biological aging of cells and the health risks associated with biological aging. In this study, we examined changes in biological ages in NCBRS to provide insights into the prognosis and health risks of NCBRS. METHODS We used a publicly available dataset to examine biological aging in NCBRS using DNAm-based epigenetic ages, such as PhenoAge and GrimAge, as well as DNAm-based estimator of telomere length (DNAmTL). We investigated 12 cases, clinically diagnosed as NCBRS, and 27 controls. RESULTS Compared to controls, NCBRS cases exhibited significantly accelerated PhenoAge and GrimAge as well as significantly shortened DNAmTL. CONCLUSION These results suggest an acceleration of biological aging in NCBRS and provide insights into the prognosis and health risks of NCBRS.
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Affiliation(s)
- Yutaka Shinko
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tadasu Horai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Saehyeon Kim
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takaki Tanifuji
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Psychiatry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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28
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Galow AM, Peleg S. How to Slow down the Ticking Clock: Age-Associated Epigenetic Alterations and Related Interventions to Extend Life Span. Cells 2022; 11:468. [PMID: 35159278 PMCID: PMC8915189 DOI: 10.3390/cells11030468] [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: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic alterations pose one major hallmark of organismal aging. Here, we provide an overview on recent findings describing the epigenetic changes that arise during aging and in related maladies such as neurodegeneration and cancer. Specifically, we focus on alterations of histone modifications and DNA methylation and illustrate the link with metabolic pathways. Age-related epigenetic, transcriptional and metabolic deregulations are highly interconnected, which renders dissociating cause and effect complicated. However, growing amounts of evidence support the notion that aging is not only accompanied by epigenetic alterations, but also at least in part induced by those. DNA methylation clocks emerged as a tool to objectively determine biological aging and turned out as a valuable source in search of factors positively and negatively impacting human life span. Moreover, specific epigenetic signatures can be used as biomarkers for age-associated disorders or even as targets for therapeutic approaches, as will be covered in this review. Finally, we summarize recent potential intervention strategies that target epigenetic mechanisms to extend healthy life span and provide an outlook on future developments in the field of longevity research.
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Affiliation(s)
- Anne-Marie Galow
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Shahaf Peleg
- Research Group Epigenetics, Metabolism and Longevity, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
- Institute of Neuroregeneration and Neurorehabilitation of Qingdao University, Qingdao 266071, China
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29
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Kuzub N, Smialkovska V, Momot V, Moseiko V, Lushchak O, Koliada A. Evaluation of Epigenetic Age Based on DNA Methylation Analysis of Several CpG Sites in Ukrainian Population. Front Genet 2022; 12:772298. [PMID: 35069680 PMCID: PMC8770732 DOI: 10.3389/fgene.2021.772298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Epigenetic clocks are the models, which use CpG methylation levels for the age prediction of an organism. Although there were several epigenetic clocks developed there is a demand for development and evaluation of the relatively accurate and sensitive epigenetic clocks that can be used for routine research purposes. In this study, we evaluated two epigenetic clock models based on the 4 CpG sites and 2 CpG sites in the human genome using the pyrosequencing method for their methylation level estimation. The study sample included 153 people from the Ukrainian population with the age from 0 to 101. Both models showed a high correlation with the chronological age in our study sample (R2 = 0.85 for the 2 CpG model and R2 = 0.92 for the 4 CpG model). We also estimated the accuracy metrics of the age prediction in our study sample. For the age group from 18 to 80 MAD was 5.1 years for the 2 CpG model and 4.1 years for the 4 CpG model. In this regard, we can conclude, that the models evaluated in the study have good age predictive accuracy, and can be used for the epigenetic age evaluation due to the relative simplicity and time-effectiveness.
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Affiliation(s)
- N Kuzub
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - V Smialkovska
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - V Momot
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | | | - O Lushchak
- Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - A Koliada
- Diagen Laboratory, Kyiv, Ukraine.,Institute of Food Biotechnology and Genomics NAS of Ukraine, Kyiv, Ukraine
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30
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Macdonald-Dunlop E, Taba N, Klarić L, Frkatović A, Walker R, Hayward C, Esko T, Haley C, Fischer K, Wilson JF, Joshi PK. A catalogue of omics biological ageing clocks reveals substantial commonality and associations with disease risk. Aging (Albany NY) 2022; 14:623-659. [PMID: 35073279 PMCID: PMC8833109 DOI: 10.18632/aging.203847] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022]
Abstract
Biological age (BA), a measure of functional capacity and prognostic of health outcomes that discriminates between individuals of the same chronological age (chronAge), has been estimated using a variety of biomarkers. Previous comparative studies have mainly used epigenetic models (clocks), we use ~1000 participants to compare fifteen omics ageing clocks, with correlations of 0.21-0.97 with chronAge, even with substantial sub-setting of biomarkers. These clocks track common aspects of ageing with 95% of the variance in chronAge being shared among clocks. The difference between BA and chronAge - omics clock age acceleration (OCAA) - often associates with health measures. One year’s OCAA typically has the same effect on risk factors/10-year disease incidence as 0.09/0.25 years of chronAge. Epigenetic and IgG glycomics clocks appeared to track generalised ageing while others capture specific risks. We conclude BA is measurable and prognostic and that future work should prioritise health outcomes over chronAge.
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Affiliation(s)
- Erin Macdonald-Dunlop
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Nele Taba
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Lucija Klarić
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Azra Frkatović
- Genos Glycoscience Research Laboratory, Zagreb 10000, Croatia
| | - Rosie Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Chris Haley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.,Institute of Mathematics and Statistics, University of Tartu, Tartu 51009, Estonia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
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31
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Zhang B, Trapp A, Kerepesi C, Gladyshev VN. Emerging rejuvenation strategies-Reducing the biological age. Aging Cell 2022; 21:e13538. [PMID: 34972247 PMCID: PMC8761015 DOI: 10.1111/acel.13538] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/02/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
Several interventions have recently emerged that were proposed to reverse rather than just attenuate aging, but the criteria for what it takes to achieve rejuvenation remain controversial. Distinguishing potential rejuvenation therapies from other longevity interventions, such as those that slow down aging, is challenging, and these anti-aging strategies are often referred to interchangeably. We suggest that the prerequisite for a rejuvenation intervention is a robust, sustained, and systemic reduction in biological age, which can be assessed by biomarkers of aging, such as epigenetic clocks. We discuss known and putative rejuvenation interventions and comparatively analyze them to explore underlying mechanisms.
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Affiliation(s)
- Bohan Zhang
- Division of GeneticsDepartment of MedicineHarvard Medical SchoolBrigham and Women’s HospitalBostonMassachusettsUSA
| | - Alexandre Trapp
- Division of GeneticsDepartment of MedicineHarvard Medical SchoolBrigham and Women’s HospitalBostonMassachusettsUSA
| | - Csaba Kerepesi
- Division of GeneticsDepartment of MedicineHarvard Medical SchoolBrigham and Women’s HospitalBostonMassachusettsUSA
| | - Vadim N. Gladyshev
- Division of GeneticsDepartment of MedicineHarvard Medical SchoolBrigham and Women’s HospitalBostonMassachusettsUSA
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32
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Aliferi A, Sundaram S, Ballard D, Freire-Aradas A, Phillips C, Lareu MV, Court DS. Combining current knowledge on DNA methylation-based age estimation towards the development of a superior forensic DNA intelligence tool. Forensic Sci Int Genet 2021; 57:102637. [PMID: 34852982 DOI: 10.1016/j.fsigen.2021.102637] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 01/09/2023]
Abstract
The estimation of chronological age from biological fluids has been an important quest for forensic scientists worldwide, with recent approaches exploiting the variability of DNA methylation patterns with age in order to develop the next generation of forensic 'DNA intelligence' tools for this application. Drawing from the conclusions of previous work utilising massively parallel sequencing (MPS) for this analysis, this work introduces a DNA methylation-based age estimation method for blood that exhibits the best combination of prediction accuracy and sensitivity reported to date. Statistical evaluation of markers from 51 studies using microarray data from over 4000 individuals, followed by validation using in-house generated MPS data, revealed a final set of 11 markers with the greatest potential for accurate age estimation from minimal DNA material. Utilising an algorithm based on support vector machines, the proposed model achieved an average error (MAE) of 3.3 years, with this level of accuracy retained down to 5 ng of starting DNA input (~ 1 ng PCR input). The accuracy of the model was retained (MAE = 3.8 years) in a separate test set of 88 samples of Spanish origin, while predictions for donors of greater forensic interest (< 55 years of age) displayed even higher accuracy (MAE = 2.6 years). Finally, no sex-related bias was observed for this model, while there were also no signs of variation observed between control and disease-associated populations for schizophrenia, rheumatoid arthritis, frontal temporal dementia and progressive supranuclear palsy in microarray data relating to the 11 markers.
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Affiliation(s)
- Anastasia Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Sudha Sundaram
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Denise Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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33
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Finesso GE, McDevitt RA, Roy R, Brinster LR, Di Francesco A, Meade T, de Cabo R, Ferrucci L, Perdue KA. Impact of large granular lymphocyte leukemia on blood DNA methylation and epigenetic clock modeling in Fischer 344 rats. J Gerontol A Biol Sci Med Sci 2021; 77:956-963. [PMID: 34718551 DOI: 10.1093/gerona/glab328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 11/14/2022] Open
Abstract
Age-dependent differences in methylation at specific cytosine-guanosine sites (CpGs) have been used in "epigenetic clock" formulas to predict age. Deviations of epigenetic age from chronological age are informative of health status and are associated with adverse health outcomes, including mortality. In most cases, epigenetic clocks are performed on methylation from DNA extracted from circulating blood cells. However, the effect of neoplastic cells in the circulation on estimation and interpretation of epigenetic clocks is not well understood. Here, we explored this using Fischer 344 (F344) rats, a strain that often develops large granular lymphocyte leukemia (LGL). We found clear histological markers of LGL pathology in the spleens and livers of 27 out of 61 rats aged 17-27 months. We assessed DNA methylation by reduced representation bisulfite sequencing with coverage of 3 million cytosine residues. Although LGL broadly increased DNA methylation variability, it did not change epigenetic aging. Despite this, inclusion of rats with LGL in clock training sets significantly altered predictor selection probability at 83 of 121 commonly utilized CpGs. Furthermore, models trained on rat samples that included individuals with LGL had greater absolute age error than those trained exclusively on LGL-free rats (39% increase; p<0.0001). We conclude that the epigenetic signals for aging and LGL are distinct, such that LGL assessment is not necessary for valid measures of epigenetic age in F344 rats. The precision and architecture of constructed epigenetic clock formulas, however, can be influenced by the presence of neoplastic hematopoietic cells in training set populations.
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Affiliation(s)
- Giovanni E Finesso
- Comparative Medicine Section, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Ross A McDevitt
- Comparative Medicine Section, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Lauren R Brinster
- Office of Research Services, Division of Veterinary Resources, National Institutes of Health, Bethesda, MD
| | - Andrea Di Francesco
- Translational Gerontology Branch, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD.,Calico Life Sciences, South San Francisco, CA
| | - Theresa Meade
- Comparative Medicine Section, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
| | - Kathy A Perdue
- Comparative Medicine Section, National Institute on Aging - Intramural Research Program, National Institutes of Health, Baltimore, MD
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34
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Raj K, Szladovits B, Haghani A, Zoller JA, Li CZ, Black P, Maddox D, Robeck TR, Horvath S. Epigenetic clock and methylation studies in cats. GeroScience 2021; 43:2363-2378. [PMID: 34463900 PMCID: PMC8599556 DOI: 10.1007/s11357-021-00445-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/17/2021] [Indexed: 12/21/2022] Open
Abstract
Human DNA methylation profiles have been used successfully to develop highly accurate biomarkers of aging ("epigenetic clocks"). Although these human epigenetic clocks are not immediately applicable to all species of the animal kingdom, the principles underpinning them appear to be conserved even in animals that are evolutionarily far removed from humans. This is exemplified by recent development of epigenetic clocks for mice and other mammalian species. Here, we describe epigenetic clocks for the domestic cat (Felis catus), based on methylation profiles of CpGs with flanking DNA sequences that are highly conserved between multiple mammalian species. Methylation levels of these CpGs are measured using a custom-designed Infinium array (HorvathMammalMethylChip40). From these, we present 3 epigenetic clocks for cats; of which, one applies only to blood samples from cats, while the remaining two dual-species human-cat clocks apply both to cats and humans. We demonstrate that these domestic cat clocks also lead to high age correlations in cheetahs, tigers, and lions. It is expected that these epigenetic clocks for cats possess the potential to be further developed for monitoring feline health as well as being used for identifying and validating anti-aging interventions.
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Affiliation(s)
- Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Balazs Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, 695 Charles E. Young Drive South, Los Angeles, CA 90095 USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
| | | | | | - Todd R. Robeck
- Corporate Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, 695 Charles E. Young Drive South, Los Angeles, CA 90095 USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
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35
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Abstract
ABSTRACT Recent research efforts have provided compelling evidence of genome-wide DNA methylation alterations in pediatrics. It is currently well established that epigenetic clocks, composed of DNA methylation sites, can estimate the gestational and chronological age of cells and tissues from different ages. Also, extensive research is aimed at their correlation with early life exposure and pediatric diseases. This review aimed to systematically summarize the epigenetic clocks in the pediatric population. Publications were collected from PubMed and Web of Science databases up to Apr 2021. Epigenetic clocks, DNA methylation clocks, epigenetic age acceleration or deceleration, pediatric and the pediatric population were used as search criteria. Here, we first review the currently applicative pediatric epigenetic clocks. We then highlight the interpretation for epigenetic age deviations in the pediatric population and their association with external factors, developmental trajectories, and pediatric diseases. Considering the remaining unknown of pediatric clocks, research strategies into them are also discussed. In all, pediatric epigenetic clocks may act as potent tools to understand development, growth and diseases in early life.
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36
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前澤 善. [Basic science of Werner syndrome]. Nihon Ronen Igakkai Zasshi 2021; 58:402-408. [PMID: 34483166 DOI: 10.3143/geriatrics.58.402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- 善朗 前澤
- 千葉大学大学院医学研究院内分泌代謝・血液・老年内科学
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37
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Simpson DJ, Olova NN, Chandra T. Cellular reprogramming and epigenetic rejuvenation. Clin Epigenetics 2021; 13:170. [PMID: 34488874 PMCID: PMC8419998 DOI: 10.1186/s13148-021-01158-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/02/2021] [Indexed: 11/10/2022] Open
Abstract
Ageing is an inevitable condition that afflicts all humans. Recent achievements, such as the generation of induced pluripotent stem cells, have delivered preliminary evidence that slowing down and reversing the ageing process might be possible. However, these techniques usually involve complete dedifferentiation, i.e. somatic cell identity is lost as cells are converted to a pluripotent state. Separating the rejuvenative properties of reprogramming from dedifferentiation is a promising prospect, termed epigenetic rejuvenation. Reprogramming-induced rejuvenation strategies currently involve using Yamanaka factors (typically transiently expressed to prevent full dedifferentiation) and are promising candidates to safely reduce biological age. Here, we review the development and potential of reprogramming-induced rejuvenation as an anti-ageing strategy.
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Affiliation(s)
- Daniel J Simpson
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Nelly N Olova
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Tamir Chandra
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
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38
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Simpson DJ, Chandra T. Epigenetic age prediction. Aging Cell 2021; 20:e13452. [PMID: 34415665 PMCID: PMC8441394 DOI: 10.1111/acel.13452] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
Advanced age is the main common risk factor for cancer, cardiovascular disease and neurodegeneration. Yet, more is known about the molecular basis of any of these groups of diseases than the changes that accompany ageing itself. Progress in molecular ageing research was slow because the tools predicting whether someone aged slowly or fast (biological age) were unreliable. To understand ageing as a risk factor for disease and to develop interventions, the molecular ageing field needed a quantitative measure; a clock for biological age. Over the past decade, a number of age predictors utilising DNA methylation have been developed, referred to as epigenetic clocks. While they appear to estimate biological age, it remains unclear whether the methylation changes used to train the clocks are a reflection of other underlying cellular or molecular processes, or whether methylation itself is involved in the ageing process. The precise aspects of ageing that the epigenetic clocks capture remain hidden and seem to vary between predictors. Nonetheless, the use of epigenetic clocks has opened the door towards studying biological ageing quantitatively, and new clocks and applications, such as forensics, appear frequently. In this review, we will discuss the range of epigenetic clocks available, their strengths and weaknesses, and their applicability to various scientific queries.
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Affiliation(s)
- Daniel J. Simpson
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Tamir Chandra
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
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39
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Gudmundsrud R, Skjånes TH, Gilmour BC, Caponio D, Lautrup S, Fang EF. Crosstalk among DNA Damage, Mitochondrial Dysfunction, Impaired Mitophagy, Stem Cell Attrition, and Senescence in the Accelerated Ageing Disorder Werner Syndrome. Cytogenet Genome Res 2021; 161:297-304. [PMID: 34433164 DOI: 10.1159/000516386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022] Open
Abstract
Werner syndrome (WS) is an accelerated ageing disease caused by multiple mutations in the gene encoding the Werner DNA helicase (WRN). The major clinical features of WS include wrinkles, grey hair, osteoporosis, and metabolic phenomena such as atherosclerosis, diabetes, and fatty liver, and resemble those seen in normal ageing, but occur earlier, in middle age. Defective DNA repair resulting from mutations in WRN explain the majority of the clinical features of WS, but the underlying mechanisms driving the larger metabolic dysfunction remain elusive. Recent studies in animal models of WS and in WS patient cells and blood samples suggest the involvement of impaired mitophagy, NAD+ depletion, and accumulation of damaged mitochondria in metabolic dysfunction. This mini-review summarizes recent progress in the understanding of the molecular mechanisms of metabolic dysfunction in WS, with the involvement of DNA damage, mitochondrial dysfunction, mitophagy reduction, stem cell impairment, and senescence. Future studies on NAD+ and mitophagy may shed light on potential therapeutic strategies for the WS patients.
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Affiliation(s)
- Ruben Gudmundsrud
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Tarjei H Skjånes
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Brian C Gilmour
- The Norwegian Centre on Healthy Ageing (NO-Age), Oslo, Norway
| | - Domenica Caponio
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Sofie Lautrup
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Evandro F Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway.,The Norwegian Centre on Healthy Ageing (NO-Age), Oslo, Norway
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40
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Gindin Y, Gaggar A, Lok AS, Janssen HLA, Ferrari C, Subramanian GM, Jiang Z, Masur H, Emmanuel B, Poonia B, Kottilil S. DNA Methylation and Immune Cell Markers Demonstrate Evidence of Accelerated Aging in Patients with Chronic Hepatitis B Virus or Hepatitis C Virus, with or without Human Immunodeficienct Virus Co-infection. Clin Infect Dis 2021; 73:e184-e190. [PMID: 32915202 DOI: 10.1093/cid/ciaa1371] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/08/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Several chronic diseases accelerate biological aging. We investigated age acceleration and the association between peripheral blood DNA methylation (DNAm) and immune cell markers in patients chronically infected with the hepatitis B virus (HBV) or the hepatitis C virus (HCV) with and without human immunodeficiency virus (HIV) co-infection. METHODS Age acceleration was measured as the difference between epigenetic age (Horvath clock) and chronological age. The immune marker model of age acceleration was developed using Elastic Net regression to select both the immune markers and their associated weights in the final linear model. RESULTS Patients with chronic HBV (n = 51) had a significantly higher median epigenetic age compared to chronological age (age accelerated) (P < .001). In patients with chronic HCV infection (n = 63), age acceleration was associated with liver fibrosis as assessed by histology (P < .05), or presence of HIV co-infection (P < .05), but not HCV mono-infection. Age acceleration defined by immune markers was concordant with age acceleration by DNA methylation (correlation coefficient = .59 in HBV; P = .0025). One-year treatment of HBV patients with nucleoside therapy was associated with a modest reduction in age acceleration, as measured using the immune marker model (-.65 years, P = .018). CONCLUSION Our findings suggest that patients with chronic viral hepatitis have accelerated epigenetic aging, that immune markers define biological age, and have the potential to assess the effects of therapeutic intervention on age acceleration.
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Affiliation(s)
| | - Anuj Gaggar
- Gilead Sciences, Foster City, California, USA
| | - Anna S Lok
- Division of Gastroenterology and Hepatology, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - Harry L A Janssen
- Toronto Centre for Liver Disease, Toronto General Hospital, University Health Network Sandra Rotman Centre for Global Health, University of Toronto, Toronto, Ontario, Canada
| | - Carlo Ferrari
- Department of Infectious Diseases, University of Parma, Parma, Italy
| | | | | | - Henry Masur
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health , Bethesda, Maryland, USA
| | - Benjamin Emmanuel
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Bhawna Poonia
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shyam Kottilil
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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41
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Noroozi R, Ghafouri-Fard S, Pisarek A, Rudnicka J, Spólnicka M, Branicki W, Taheri M, Pośpiech E. DNA methylation-based age clocks: From age prediction to age reversion. Ageing Res Rev 2021; 68:101314. [PMID: 33684551 DOI: 10.1016/j.arr.2021.101314] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
Aging as an irretrievable occurrence throughout the entire life is characterized by a progressive decline in physiological functionality and enhanced disease vulnerability. Numerous studies have demonstrated that epigenetic modifications, particularly DNA methylation (DNAm), correlate with aging and age-related diseases. Several investigations have attempted to predict chronological age using the age-related alterations in the DNAm of certain CpG sites. Here we categorize different studies that tracked the aging process in the DNAm landscape to show how epigenetic age clocks evolved from a chronological age estimator to an indicator of lifespan and healthspan. We also describe the health and disease predictive potential of estimated epigenetic age acceleration regarding different clinical conditions and lifestyle factors. Considering the revealed age-related epigenetic changes, the recent age-reprogramming strategies are discussed which are promising methods for resetting the aging clocks.
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Affiliation(s)
- Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Joanna Rudnicka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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42
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Kerepesi C, Zhang B, Lee SG, Trapp A, Gladyshev VN. Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging. SCIENCE ADVANCES 2021; 7:eabg6082. [PMID: 34172448 PMCID: PMC8232908 DOI: 10.1126/sciadv.abg6082] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
The notion that the germ line does not age goes back to the 19th-century ideas of August Weismann. However, being metabolically active, the germ line accumulates damage and other changes over time, i.e., it ages. For new life to begin in the same young state, the germ line must be rejuvenated in the offspring. Here, we developed a multi-tissue epigenetic clock and applied it, together with other aging clocks, to track changes in biological age during mouse and human prenatal development. This analysis revealed a significant decrease in biological age, i.e., rejuvenation, during early stages of embryogenesis, followed by an increase in later stages. We further found that pluripotent stem cells do not age even after extensive passaging and that the examined epigenetic age dynamics is conserved across species. Overall, this study uncovers a natural rejuvenation event during embryogenesis and suggests that the minimal biological age (ground zero) marks the beginning of organismal aging.
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Affiliation(s)
- Csaba Kerepesi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexandre Trapp
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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43
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Kargapolova Y, Rehimi R, Kayserili H, Brühl J, Sofiadis K, Zirkel A, Palikyras S, Mizi A, Li Y, Yigit G, Hoischen A, Frank S, Russ N, Trautwein J, van Bon B, Gilissen C, Laugsch M, Gusmao EG, Josipovic N, Altmüller J, Nürnberg P, Längst G, Kaiser FJ, Watrin E, Brunner H, Rada-Iglesias A, Kurian L, Wollnik B, Bouazoune K, Papantonis A. Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology. Nat Commun 2021; 12:3014. [PMID: 34021162 PMCID: PMC8140133 DOI: 10.1038/s41467-021-23327-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/15/2021] [Indexed: 12/18/2022] Open
Abstract
Members of the chromodomain-helicase-DNA binding (CHD) protein family are chromatin remodelers implicated in human pathologies, with CHD6 being one of its least studied members. We discovered a de novo CHD6 missense mutation in a patient clinically presenting the rare Hallermann-Streiff syndrome (HSS). We used genome editing to generate isogenic iPSC lines and model HSS in relevant cell types. By combining genomics with functional in vivo and in vitro assays, we show that CHD6 binds a cohort of autophagy and stress response genes across cell types. The HSS mutation affects CHD6 protein folding and impairs its ability to recruit co-remodelers in response to DNA damage or autophagy stimulation. This leads to accumulation of DNA damage burden and senescence-like phenotypes. We therefore uncovered a molecular mechanism explaining HSS onset via chromatin control of autophagic flux and genotoxic stress surveillance.
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Affiliation(s)
- Yulia Kargapolova
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Heart Center, University Hospital Cologne, Cologne, Germany.
| | - Rizwan Rehimi
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Age-associated Disorders (CECAD), University of Cologne, Cologne, Germany
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine, Istanbul, Turkey
| | - Joanna Brühl
- Institute of Molecular Biology and Tumor Research, Philipps-University Marburg, Marburg, Germany
| | | | - Anne Zirkel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Spiros Palikyras
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stefan Frank
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Neurophysiology, University of Cologne, Cologne, Germany
- Bayer AG, Wuppertal, Germany
| | - Nicole Russ
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Neurophysiology, University of Cologne, Cologne, Germany
| | - Jonathan Trautwein
- Institute of Molecular Biology and Tumor Research, Philipps-University Marburg, Marburg, Germany
| | - Bregje van Bon
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Magdalena Laugsch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Eduardo Gade Gusmao
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Natasa Josipovic
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Gernot Längst
- Biochemistry Centre Regensburg (BRC), University of Regensburg, Regensburg, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Erwan Watrin
- Research Institute of Genetics and Development, Faculté de Médecine, Rennes, France
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Age-associated Disorders (CECAD), University of Cologne, Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Santander, Spain
| | - Leo Kurian
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Neurophysiology, University of Cologne, Cologne, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC), University of Göttingen, Göttingen, Germany
| | - Karim Bouazoune
- Institute of Molecular Biology and Tumor Research, Philipps-University Marburg, Marburg, Germany.
| | - Argyris Papantonis
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.
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44
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Poot M, Hochstenbach R. Prevalence and Phenotypic Impact of Robertsonian Translocations. Mol Syndromol 2021; 12:1-11. [PMID: 33776621 PMCID: PMC7983559 DOI: 10.1159/000512676] [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: 08/26/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Robertsonian translocations (RTs) result from fusion of 2 acrocentric chromosomes (e.g., 13, 14, 15, 21, 22) and consequential losses of segments of the p arms containing 47S rDNA clusters and transcription factor binding sites. Depending on the position of the breakpoints, the size of these losses vary considerably between types of RTs. The prevalence of RTs in the general population is estimated to be around 1 per 800 individuals, making RTs the most common chromosomal rearrangement in healthy individuals. Based on their prevalence, RTs are classified as "common," rob(13;14) and rob(14;21), or "rare" (the 8 remaining nonhomologous combinations). Carriers of RTs are at an increased risk for offspring with chromosomal imbalances or with uniparental disomy. RTs are generally regarded as phenotypically neutral, although, due to RTs formation, 2 of the 10 ribosomal rDNA gene clusters, several long noncoding RNAs, and in the case of RTs involving chromosome 21, several mRNA encoding genes are lost. Nevertheless, recent evidence indicates that RTs may have a significant phenotypic impact. In particular, rob(13;14) carriers have a significantly elevated risk for breast cancer. While RTs are easily spotted by routine karyotyping, they may go unnoticed if only array-CGH and NextGen sequencing methods are applied. This review first discusses possible molecular mechanisms underlying the particularly high rates of RT formation and their incidence in the general population, and second, likely causes for the elevated cancer risk of some RTs will be examined.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Ron Hochstenbach
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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45
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Chiavellini P, Canatelli-Mallat M, Lehmann M, Gallardo MD, Herenu CB, Cordeiro JL, Clement J, Goya RG. Aging and rejuvenation - a modular epigenome model. Aging (Albany NY) 2021; 13:4734-4746. [PMID: 33627519 PMCID: PMC7950254 DOI: 10.18632/aging.202712] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/08/2021] [Indexed: 12/21/2022]
Abstract
The view of aging has evolved in parallel with the advances in biomedical sciences. Long considered as an irreversible process where interventions were only aimed at slowing down its progression, breakthrough discoveries like animal cloning and cell reprogramming have deeply changed our understanding of postnatal development, giving rise to the emerging view that the epigenome is the driver of aging. The idea was significantly strengthened by the converging discovery that DNA methylation (DNAm) at specific CpG sites could be used as a highly accurate biomarker of age defined by an algorithm known as the Horvath clock. It was at this point where epigenetic rejuvenation came into play as a strategy to reveal to what extent biological age can be set back by making the clock tick backwards. Initial evidence suggests that when the clock is forced to tick backwards in vivo, it is only able to drag the phenotype to a partially rejuvenated condition. In order to explain the results, a bimodular epigenome is proposed, where module A represents the DNAm clock component and module B the remainder of the epigenome. Epigenetic rejuvenation seems to hold the key to arresting or even reversing organismal aging.
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Affiliation(s)
- Priscila Chiavellini
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Martina Canatelli-Mallat
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Marianne Lehmann
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Maria D. Gallardo
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Claudia B. Herenu
- Institute for Experimental Pharmacology (IFEC), School of Chemical Sciences, National University of Cordoba, Cordoba, Argentina
| | | | | | - Rodolfo G. Goya
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
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Feiner LK, Tierling S, Holländer S, Glanemann M, Rubie C. An aging and p53 related marker: HOXA5 promoter methylation negatively correlates with mRNA and protein expression in old age. Aging (Albany NY) 2021; 13:4831-4849. [PMID: 33547267 PMCID: PMC7950283 DOI: 10.18632/aging.202621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/04/2021] [Indexed: 12/02/2022]
Abstract
The process of aging has been associated with differential patterns of DNA methylation which relate to changes in gene expression. Hence, we aimed to identify genes with significant age-related methylation differences and to study their mRNA and protein expression profile. Genome-wide DNA methylation analysis was performed with the Illumina Infinium Methylation EPIC BeadChip Microarray on bisulfite-converted DNA prepared from monocytes derived from young (average age: 23.8 yrs) and old (average age: 81.5 yrs) volunteers that are separated by at least 50 years of age difference, n=4, respectively. Differentially methylated CpG sites were assigned to the associated genes and validated by deep sequencing analysis (n=20). Demonstrating an age-associated significant increase of methylation in the promoter region (p=1x10-8), Homeobox A5 (HOXA5), also known to activate p53, emerged as an interesting candidate for further expression analyses by Realtime PCR, ELISA and Western Blot Analysis (n=30, respectively). Consistent with its hypermethylation we observed significant HOXA5 mRNA downregulation (p=0.0053) correlating with significant p53 downregulation (p=0.0431) in the old cohort. Moreover, we observed a significant change in HOXA5 protein expression (p=3x10-5) negatively correlating with age and promoter methylation thus qualifying HOXA5 for an eligible p53-related aging marker.
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Affiliation(s)
- Laura-Kim Feiner
- Department of General-, Visceral-, Vascular- and Pediatric Surgery, University of Saarland Medical Center, Homburg 66421, Saar, Germany
| | - Sascha Tierling
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken 66123, Germany
| | - Sebastian Holländer
- Department of General-, Visceral-, Vascular- and Pediatric Surgery, University of Saarland Medical Center, Homburg 66421, Saar, Germany
| | - Matthias Glanemann
- Department of General-, Visceral-, Vascular- and Pediatric Surgery, University of Saarland Medical Center, Homburg 66421, Saar, Germany
| | - Claudia Rubie
- Department of General-, Visceral-, Vascular- and Pediatric Surgery, University of Saarland Medical Center, Homburg 66421, Saar, Germany
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Han Y, Nikolić M, Gobs M, Franzen J, de Haan G, Geiger H, Wagner W. Targeted methods for epigenetic age predictions in mice. Sci Rep 2020; 10:22439. [PMID: 33384442 PMCID: PMC7775437 DOI: 10.1038/s41598-020-79509-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Age-associated DNA methylation reflects aspect of biological aging—therefore epigenetic clocks for mice can elucidate how the aging process in this model organism is affected by specific treatments or genetic background. Initially, age-predictors for mice were trained for genome-wide DNA methylation profiles and we have recently described a targeted assay based on pyrosequencing of DNA methylation at only three age-associated genomic regions. Here, we established alternative approaches using droplet digital PCR (ddPCR) and barcoded bisulfite amplicon sequencing (BBA-seq). At individual CG dinucleotides (CpGs) the correlation of DNA methylation with chronological age was slightly higher for pyrosequencing and ddPCR as compared to BBA-seq. On the other hand, BBA-seq revealed that neighboring CpGs tend to be stochastically modified at murine age-associated regions. Furthermore, the binary sequel of methylated and non-methylated CpGs in individual reads can be used for single-read predictions, which may reflect heterogeneity in epigenetic aging. In comparison to C57BL/6 mice the single-read age-predictions using BBA-seq were also accelerated in the shorter-lived DBA/2 mice, and in C57BL/6 mice with a lifespan quantitative trait locus of DBA/2 mice. Taken together, we describe alternative targeted methods for epigenetic age predictions that provide new perspectives for aging-intervention studies in mice.
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Affiliation(s)
- Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Michael Gobs
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Gerald de Haan
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, the Netherlands
| | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, 89081, Ulm, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany.
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Ryan J, Wrigglesworth J, Loong J, Fransquet PD, Woods RL. A Systematic Review and Meta-analysis of Environmental, Lifestyle, and Health Factors Associated With DNA Methylation Age. J Gerontol A Biol Sci Med Sci 2020; 75:481-494. [PMID: 31001624 DOI: 10.1093/gerona/glz099] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 02/07/2023] Open
Abstract
DNA methylation (DNAm) algorithms of biological age provide a robust estimate of an individual's chronological age and can predict their risk of age-related disease and mortality. This study reviewed the evidence that environmental, lifestyle and health factors are associated with the Horvath and Hannum epigenetic clocks. A systematic search identified 61 studies. Chronological age was correlated with DNAm age in blood (median .83, range .13-.99). In a meta-analysis body mass index (BMI) was associated with increased DNAm age (Hannum β: 0.07, 95% CI 0.04 to 0.10; Horvath β: 0.06, 95% CI 0.02 to 0.10), but there was no association with smoking (Hannum β: 0.12, 95% CI -0.50 to 0.73; Horvath β:0.18, 95% CI -0.10 to 0.46). DNAm age was positively associated with frailty (three studies, n = 3,093), and education was negatively associated with the Hannum estimate of DNAm age specifically (four studies, n = 13,955). For most other exposures, findings were too inconsistent to draw conclusions. In conclusion, BMI was positively associated with biological aging measured using DNAm, with some evidence that frailty also increased aging. More research is needed to provide conclusive evidence regarding other exposures. This field of research has the potential to provide further insights into how to promote slower biological aging and ultimately prolong healthy life.
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Affiliation(s)
- Joanne Ryan
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia.,INSERM, Univ Montpellier, Neuropsychiatry, Epidemiological and Clinical Research, Montpellier, France
| | - Jo Wrigglesworth
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Jun Loong
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Peter D Fransquet
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Robyn L Woods
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
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Kling T, Wenger A, Carén H. DNA methylation-based age estimation in pediatric healthy tissues and brain tumors. Aging (Albany NY) 2020; 12:21037-21056. [PMID: 33168783 PMCID: PMC7695434 DOI: 10.18632/aging.202145] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/03/2020] [Indexed: 12/20/2022]
Abstract
Several DNA methylation clocks have been developed to reflect chronological age of human tissues, but most clocks have been trained on adult samples. The rapid methylome changes in children and the role of epigenetics in pediatric tumors calls for tools accurately estimating methylation age in children. We aimed to evaluate seven methylation clocks in multiple tissues from healthy children to inform future studies on the optimal clock for pediatric cohorts, and analyzed the methylation age in brain tumors. We found that clocks trained on pediatric samples were the best in all tested tissues, highlighting the need for dedicated clocks. For blood samples, the Skin and blood clock had the best correlation with chronological age, while PedBE was the most accurate for saliva and buccal samples, and Horvath for brain tissue. Horvath methylation age was accelerated in pediatric brain tumors and the acceleration was subtype-specific for atypical teratoid rhabdoid tumor (ATRT), ependymoma, medulloblastoma and glioma. The subtypes with the highest acceleration corresponded to the worst prognostic categories in ATRT, ependymoma and glioma, whereas the relationship was reversed in medulloblastoma. This suggests that methylation age has potential as a prognostic biomarker in pediatric brain tumors and should be further explored.
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Affiliation(s)
- Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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50
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Yan Q, Paul KC, Lu AT, Kusters C, Binder AM, Horvath S, Ritz B. Epigenetic mutation load is weakly correlated with epigenetic age acceleration. Aging (Albany NY) 2020; 12:17863-17894. [PMID: 32991324 PMCID: PMC7585066 DOI: 10.18632/aging.103950] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/08/2020] [Indexed: 01/24/2023]
Abstract
DNA methylation (DNAm) age estimators are widely used to study aging-related conditions. It is not yet known whether DNAm age is associated with the accumulation of stochastic epigenetic mutations (SEMs), which reflect dysfunctions of the epigenetic maintenance system. Here, we defined epigenetic mutation load (EML) as the total number of SEMs per individual. We assessed associations between EML and DNAm age acceleration estimators using biweight midcorrelations in four population-based studies (total n = 6,388). EML was not only positively associated with chronological age (meta r = 0.171), but also with four measures of epigenetic age acceleration: the Horvath pan tissue clock, intrinsic epigenetic age acceleration, the Hannum clock, and the GrimAge clock (meta-analysis correlation ranging from r = 0.109 to 0.179). We further conducted pathway enrichment analyses for each participant's SEMs. The enrichment result demonstrated the stochasticity of epigenetic mutations, meanwhile implicated several pathways: signaling, neurogenesis, neurotransmitter, glucocorticoid, and circadian rhythm pathways may contribute to faster DNAm age acceleration. Finally, investigating genomic-region specific EML, we found that EMLs located within regions of transcriptional repression (TSS1500, TSS200, and 1stExon) were associated with faster age acceleration. Overall, our findings suggest a role for the accumulation of epigenetic mutations in the aging process.
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Affiliation(s)
- Qi Yan
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Kimberly C. Paul
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Cynthia Kusters
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Alexandra M. Binder
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA,Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA,Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095, USA
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