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Signal B, Phipps AJ, Giles KA, Huskins SN, Mercer TR, Robinson MD, Woodhouse A, Taberlay PC. Ageing-Related Changes to H3K4me3, H3K27ac, and H3K27me3 in Purified Mouse Neurons. Cells 2024; 13:1393. [PMID: 39195281 DOI: 10.3390/cells13161393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/19/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024] Open
Abstract
Neurons are central to lifelong learning and memory, but ageing disrupts their morphology and function, leading to cognitive decline. Although epigenetic mechanisms are known to play crucial roles in learning and memory, neuron-specific genome-wide epigenetic maps into old age remain scarce, often being limited to whole-brain homogenates and confounded by glial cells. Here, we mapped H3K4me3, H3K27ac, and H3K27me3 in mouse neurons across their lifespan. This revealed stable H3K4me3 and global losses of H3K27ac and H3K27me3 into old age. We observed patterns of synaptic function gene deactivation, regulated through the loss of the active mark H3K27ac, but not H3K4me3. Alongside this, embryonic development loci lost repressive H3K27me3 in old age. This suggests a loss of a highly refined neuronal cellular identity linked to global chromatin reconfiguration. Collectively, these findings indicate a key role for epigenetic regulation in neurons that is inextricably linked with ageing.
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Affiliation(s)
- Brandon Signal
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Andrew J Phipps
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Katherine A Giles
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
- Children's Medical Research Institute, University of Sydney, 214 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Shannon N Huskins
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, Corner College and Cooper Roads, Brisbane, QLD 4072, Australia
| | - Mark D Robinson
- SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Adele Woodhouse
- Wicking Dementia Research and Education Centre, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
| | - Phillippa C Taberlay
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS 7000, Australia
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2
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Occean JR, Yang N, Sun Y, Dawkins MS, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price NL, Kim JS, Cui CY, Fan J, Bhattacharyya M, De S, Maragkakis M, de Cabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. Nat Commun 2024; 15:6357. [PMID: 39069555 PMCID: PMC11284234 DOI: 10.1038/s41467-024-50725-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/15/2024] [Indexed: 07/30/2024] Open
Abstract
DNA hydroxymethylation (5hmC), the most abundant oxidative derivative of DNA methylation, is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in age-related diseases, its functional role in aging remains unknown. Here, using mouse liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and restricts the magnitude of gene expression changes with age. Mechanistically, 5hmC decreases the binding of splicing associated factors and correlates with age-related alternative splicing events. We found that various age-related contexts, such as prolonged quiescence and senescence, drive the accumulation of 5hmC with age. We provide evidence that this age-related transcriptionally restrictive function is conserved in mouse and human tissues. Our findings reveal that 5hmC regulates tissue-specific function and may play a role in longevity.
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Affiliation(s)
- James R Occean
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Yan Sun
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Marshall S Dawkins
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Showkat Dar
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Lin Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Changyou Shi
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Christopher Dunn
- Flow Cytometry Unit, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Michel Bernier
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Nathan L Price
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Julie S Kim
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Chang-Yi Cui
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jinshui Fan
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | | | - Supriyo De
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA.
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3
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Mrabti C, Yang N, Desdín-Micó G, Alonso-Calleja A, Vílchez-Acosta A, Pico S, Parras A, Piao Y, Schoenfeldt L, Luo S, Haghani A, Brooke R, del Carmen Maza M, Branchina C, Maroun CY, von Meyenn F, Naveiras O, Horvath S, Sen P, Ocampo A. Loss of H3K9 trimethylation leads to premature aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604929. [PMID: 39091811 PMCID: PMC11291141 DOI: 10.1101/2024.07.24.604929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Aging is the major risk factor for most human diseases and represents a major socio-economical challenge for modern societies. Despite its importance, the process of aging remains poorly understood. Epigenetic dysregulation has been proposed as a key driver of the aging process. Modifications in transcriptional networks and chromatin structure might be central to age-related functional decline. A prevalent feature described during aging is the overall reduction in heterochromatin, specifically marked by the loss of repressive histone modification, Histone 3 lysine 9 trimethylation (H3K9me3). However, the role of H3K9me3 in aging, especially in mammals, remains unclear. Here we show using a novel mouse strain, (TKOc), carrying a triple knockout of three methyltransferases responsible for H3K9me3 deposition, that the inducible loss of H3K9me3 in adulthood results in premature aging. TKOc mice exhibit reduced lifespan, lower body weight, increased frailty index, multi-organ degeneration, transcriptional changes with significant upregulation of transposable elements, and accelerated epigenetic age. Our data strongly supports the concept that the loss of epigenetic information directly drives the aging process. These findings reveal the importance of epigenetic regulation in aging and suggest that interventions targeting epigenetic modifications could potentially slow down or reverse age-related decline. Understanding the molecular mechanisms underlying the process of aging will be crucial for developing novel therapeutic strategies that can delay the onset of age-associated diseases and preserve human health at old age specially in rapidly aging societies.
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Affiliation(s)
- Calida Mrabti
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud, Switzerland
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Gabriela Desdín-Micó
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud, Switzerland
| | - Alejandro Alonso-Calleja
- Laboratory of Regenerative Hematopoiesis, Department of Biomedical Sciences, University of Lausanne, Switzerland
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alba Vílchez-Acosta
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud, Switzerland
| | - Sara Pico
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud, Switzerland
| | | | - Yulan Piao
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Lucas Schoenfeldt
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud, Switzerland
- EPITERNA SA, Epalinges, Switzerland
| | - Siyuan Luo
- Departement of Health Sciences and Technology, ETH Zurich, Zurich
| | | | - Robert Brooke
- Epigenetic Clock Development, Foundation, Torrance, California, USA
| | - María del Carmen Maza
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud, Switzerland
| | - Clémence Branchina
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud, Switzerland
| | - Céline Yacoub Maroun
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud, Switzerland
| | | | - Olaia Naveiras
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
- Laboratory of Regenerative Hematopoiesis, Department of Biomedical Sciences, University of Lausanne, Switzerland
| | - Steve Horvath
- Altos Labs, San Diego, CA, USA
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Alejandro Ocampo
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Vaud, Switzerland
- EPITERNA SA, Epalinges, Switzerland
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4
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Pérez RF, Tezanos P, Peñarroya A, González-Ramón A, Urdinguio RG, Gancedo-Verdejo J, Tejedor JR, Santamarina-Ojeda P, Alba-Linares JJ, Sainz-Ledo L, Roberti A, López V, Mangas C, Moro M, Cintado Reyes E, Muela Martínez P, Rodríguez-Santamaría M, Ortea I, Iglesias-Rey R, Castilla-Silgado J, Tomás-Zapico C, Iglesias-Gutiérrez E, Fernández-García B, Sanchez-Mut JV, Trejo JL, Fernández AF, Fraga MF. A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment. Nat Commun 2024; 15:5829. [PMID: 39013876 PMCID: PMC11252340 DOI: 10.1038/s41467-024-49608-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
Aging involves the deterioration of organismal function, leading to the emergence of multiple pathologies. Environmental stimuli, including lifestyle, can influence the trajectory of this process and may be used as tools in the pursuit of healthy aging. To evaluate the role of epigenetic mechanisms in this context, we have generated bulk tissue and single cell multi-omic maps of the male mouse dorsal hippocampus in young and old animals exposed to environmental stimulation in the form of enriched environments. We present a molecular atlas of the aging process, highlighting two distinct axes, related to inflammation and to the dysregulation of mRNA metabolism, at the functional RNA and protein level. Additionally, we report the alteration of heterochromatin domains, including the loss of bivalent chromatin and the uncovering of a heterochromatin-switch phenomenon whereby constitutive heterochromatin loss is partially mitigated through gains in facultative heterochromatin. Notably, we observed the multi-omic reversal of a great number of aging-associated alterations in the context of environmental enrichment, which was particularly linked to glial and oligodendrocyte pathways. In conclusion, our work describes the epigenomic landscape of environmental stimulation in the context of aging and reveals how lifestyle intervention can lead to the multi-layered reversal of aging-associated decline.
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Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Patricia Tezanos
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Alfonso Peñarroya
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Alejandro González-Ramón
- Laboratory of Functional Epi-Genomics of Aging and Alzheimer's disease, Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Alicante, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Javier Gancedo-Verdejo
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Pablo Santamarina-Ojeda
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Juan José Alba-Linares
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Lidia Sainz-Ledo
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Annalisa Roberti
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Virginia López
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Cristina Mangas
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - María Moro
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
| | - Elisa Cintado Reyes
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Pablo Muela Martínez
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Mar Rodríguez-Santamaría
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Bioterio y unidad de imagen preclínica, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Ignacio Ortea
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Proteomics Unit, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), 33011, Oviedo, Spain
| | - Ramón Iglesias-Rey
- Neuroimaging and Biotechnology Laboratory (NOBEL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), 15706, Santiago de Compostela, Spain
| | - Juan Castilla-Silgado
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Cristina Tomás-Zapico
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Eduardo Iglesias-Gutiérrez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Benjamín Fernández-García
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Jose Vicente Sanchez-Mut
- Laboratory of Functional Epi-Genomics of Aging and Alzheimer's disease, Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Alicante, Spain
| | - José Luis Trejo
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
| | - Mario F Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
- Departamento de Biología de Organismos y Sistemas, Área de Fisiología Vegetal, Universidad de Oviedo, 33006, Oviedo, Spain.
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5
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Corveleyn L, Sen P, Adams P, Sidoli S. Linking Aging to Cancer: The Role of Chromatin Biology. J Gerontol A Biol Sci Med Sci 2024; 79:glae133. [PMID: 38761362 PMCID: PMC11170291 DOI: 10.1093/gerona/glae133] [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: 02/20/2024] [Indexed: 05/20/2024] Open
Abstract
Epigenetic changes have been established to be a hallmark of aging, which implies that aging science requires collaborating with the field of chromatin biology. DNA methylation patterns, changes in relative abundance of histone post-translational modifications, and chromatin remodeling are the central players in modifying chromatin structure. Aging is commonly associated with an overall increase in chromatin instability, loss of homeostasis, and decondensation. However, numerous publications have highlighted that the link between aging and chromatin changes is not nearly as linear as previously expected. This complex interplay of these epigenetic elements during the lifetime of an organism likely contributes to cellular senescence, genomic instability, and disease susceptibility. Yet, the causal links between these phenomena still need to be fully unraveled. In this perspective article, we discuss potential future directions of aging chromatin biology.
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Affiliation(s)
- Laura Corveleyn
- Laboratory of Pharmaceutical Biotechnology, Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, Maryland, USA
| | - Peter Adams
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, California, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, USA
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6
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Yang N, Sikder S, Dalal Y, Sen P. Protocol for the genomic analysis of salt-fractionated chromatin from frozen murine liver. STAR Protoc 2024; 5:103043. [PMID: 38678570 PMCID: PMC11068917 DOI: 10.1016/j.xpro.2024.103043] [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: 09/06/2023] [Revised: 12/08/2023] [Accepted: 04/12/2024] [Indexed: 05/01/2024] Open
Abstract
Salt fractionation is a classical approach for separating chromatin based on its differential salt solubility and physical properties. Here, we present a protocol to apply salt fractionation for genome-scale profiling of chromatin isolated from livers at different stages of aging in mice. We elaborate on the steps to isolate nuclei, digest with micrococcal nuclease, sequentially salt fractionate, purify DNA, and construct libraries for genome profiling. We also include information on a computational pipeline for data analysis. For complete details on the use and execution of this protocol, please refer to Yang et al.1 This protocol is an adaptation of the salt fractionation method of Teves and Henikoff.2.
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Affiliation(s)
- Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA.
| | - Sweta Sikder
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA.
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7
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Del Blanco B, Niñerola S, Martín-González AM, Paraíso-Luna J, Kim M, Muñoz-Viana R, Racovac C, Sanchez-Mut JV, Ruan Y, Barco Á. Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons. Nat Commun 2024; 15:1781. [PMID: 38453932 PMCID: PMC10920760 DOI: 10.1038/s41467-024-45773-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a's function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.
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Affiliation(s)
- Beatriz Del Blanco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
| | - Sergio Niñerola
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Ana M Martín-González
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Juan Paraíso-Luna
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Minji Kim
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rafael Muñoz-Viana
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Bioinformatics Unit, Hospital universitario Puerta de Hierro Majadahonda, 28220, Majadahonda, Spain
| | - Carina Racovac
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Jose V Sanchez-Mut
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Yijun Ruan
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
| | - Ángel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
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Bisht S, Mao Y, Easwaran H. Epigenetic dynamics of aging and cancer development: current concepts from studies mapping aging and cancer epigenomes. Curr Opin Oncol 2024; 36:82-92. [PMID: 38441107 PMCID: PMC10939788 DOI: 10.1097/cco.0000000000001020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
PURPOSE OF REVIEW This review emphasizes the role of epigenetic processes as incidental changes occurring during aging, which, in turn, promote the development of cancer. RECENT FINDINGS Aging is a complex biological process associated with the progressive deterioration of normal physiological functions, making age a significant risk factor for various disorders, including cancer. The increasing longevity of the population has made cancer a global burden, as the risk of developing most cancers increases with age due to the cumulative effect of exposure to environmental carcinogens and DNA replication errors. The classical 'somatic mutation theory' of cancer cause is being challenged by the observation that multiple normal cells harbor cancer driver mutations without resulting in cancer. In this review, we discuss the role of age-associated epigenetic alterations, including DNA methylation, which occur across all cell types and tissues with advancing age. There is an increasing body of evidence linking these changes with cancer risk and prognosis. SUMMARY A better understanding about the epigenetic changes acquired during aging is critical for comprehending the mechanisms leading to the age-associated increase in cancer and for developing novel therapeutic strategies for cancer treatment and prevention.
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Affiliation(s)
- Shilpa Bisht
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yiqing Mao
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hariharan Easwaran
- Cancer Genetics and Epigenetics, Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Dubey SK, Dubey R, Kleinman ME. Unraveling Histone Loss in Aging and Senescence. Cells 2024; 13:320. [PMID: 38391933 PMCID: PMC10886805 DOI: 10.3390/cells13040320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
As the global population experiences a notable surge in aging demographics, the need to understand the intricate molecular pathways exacerbated by age-related stresses, including epigenetic dysregulation, becomes a priority. Epigenetic mechanisms play a critical role in driving age-related diseases through altered gene expression, genomic instability, and irregular chromatin remodeling. In this review, we focus on histones, a central component of the epigenome, and consolidate the key findings of histone loss and genome-wide redistribution as fundamental processes contributing to aging and senescence. The review provides insights into novel histone expression profiles, nucleosome occupancy, disruptions in higher-order chromatin architecture, and the emergence of noncanonical histone variants in the aging cellular landscape. Furthermore, we explore the current state of our understanding of the molecular mechanisms of histone deficiency in aging cells. Specific emphasis is placed on highlighting histone degradation pathways in the cell and studies that have explored potential strategies to mitigate histone loss or restore histone levels in aging cells. Finally, in addressing future perspectives, the insights gained from this review hold profound implications for advancing strategies that actively intervene in modulating histone expression profiles in the context of cellular aging and identifying potential therapeutic targets for alleviating a multitude of age-related diseases.
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Affiliation(s)
| | | | - Mark Ellsworth Kleinman
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA; (S.K.D.); (R.D.)
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Baechle JJ, Chen N, Makhijani P, Winer S, Furman D, Winer DA. Chronic inflammation and the hallmarks of aging. Mol Metab 2023; 74:101755. [PMID: 37329949 PMCID: PMC10359950 DOI: 10.1016/j.molmet.2023.101755] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND Recently, the hallmarks of aging were updated to include dysbiosis, disabled macroautophagy, and chronic inflammation. In particular, the low-grade chronic inflammation during aging, without overt infection, is defined as "inflammaging," which is associated with increased morbidity and mortality in the aging population. Emerging evidence suggests a bidirectional and cyclical relationship between chronic inflammation and the development of age-related conditions, such as cardiovascular diseases, neurodegeneration, cancer, and frailty. How the crosstalk between chronic inflammation and other hallmarks of aging underlies biological mechanisms of aging and age-related disease is thus of particular interest to the current geroscience research. SCOPE OF REVIEW This review integrates the cellular and molecular mechanisms of age-associated chronic inflammation with the other eleven hallmarks of aging. Extra discussion is dedicated to the hallmark of "altered nutrient sensing," given the scope of Molecular Metabolism. The deregulation of hallmark processes during aging disrupts the delicate balance between pro-inflammatory and anti-inflammatory signaling, leading to a persistent inflammatory state. The resultant chronic inflammation, in turn, further aggravates the dysfunction of each hallmark, thereby driving the progression of aging and age-related diseases. MAIN CONCLUSIONS The crosstalk between chronic inflammation and other hallmarks of aging results in a vicious cycle that exacerbates the decline in cellular functions and promotes aging. Understanding this complex interplay will provide new insights into the mechanisms of aging and the development of potential anti-aging interventions. Given their interconnectedness and ability to accentuate the primary elements of aging, drivers of chronic inflammation may be an ideal target with high translational potential to address the pathological conditions associated with aging.
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Affiliation(s)
- Jordan J Baechle
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA
| | - Nan Chen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON, Canada
| | - Priya Makhijani
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Shawn Winer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - David Furman
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA; Instituto de Investigaciones en Medicina Traslacional (IIMT), Universidad Austral, CONICET, Pilar, Argentina.
| | - Daniel A Winer
- Buck Artificial Intelligence Platform, the Buck Institute for Research on Aging, Novato, CA, USA; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada; Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON, Canada; Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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Pollina EA, Greer EL. Prometheus unshackled: Liver regeneration makes you young. Mol Cell 2023; 83:1546-1548. [PMID: 37207622 DOI: 10.1016/j.molcel.2023.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/21/2023]
Abstract
In this issue of Molecular Cell, Yang and colleagues1 discover age-dependent increases in broad regions of the repressive histone modification H3K27me3. They also demonstrate partial reversion to younger H3K27me3 patterns and gene expression upon resection of older livers.
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Affiliation(s)
- Elizabeth Ann Pollina
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Eric Lieberman Greer
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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