51
|
An Updated Overview on the Role of Small Molecules and Natural Compounds in the "Young Science" of Rejuvenation. Antioxidants (Basel) 2023; 12:antiox12020288. [PMID: 36829846 PMCID: PMC9951981 DOI: 10.3390/antiox12020288] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Aging is a gradual process that occurs over time which leads to a progressive decline of cells and tissues. Telomere shortening, genetic instability, epigenetic alteration, and the accumulation of misfolded proteins represent the main hallmarks that cause perturbed cellular functions; this occurs in conjunction with the progression of the so-called "aging clocks". Rejuvenation aims to influence the natural evolution of such aging clocks and to enhance regenerative capacity, thus overcoming the limitations of common anti-aging interventions. Current rejuvenation processes are based on heterochronic parabiosis, cell damage dilution through asymmetrical cell division, the excretion of extracellular vesicles, the modulation of genetic instability involving G-quadruplexes and DNA methylation, and cell reprogramming using Yamanaka factors and the actions of antioxidant species. In this context, we reviewed the most recent contributions that report on small molecules acting as senotherapeutics; these molecules act by promoting one or more of the abovementioned processes. Candidate drugs and natural compounds that are being studied as potential rejuvenation therapies act by interfering with CDGSH iron-sulfur domain 2 (CISD2) expression, G-quadruplex structures, DNA methylation, and mitochondrial decay. Moreover, direct and indirect antioxidants have been reported to counteract or revert aging through a combination of mixed mechanisms.
Collapse
|
52
|
López-Otín C, Blasco MA, Partridge L, Serrano M, Kroemer G. Hallmarks of aging: An expanding universe. Cell 2023; 186:243-278. [PMID: 36599349 DOI: 10.1016/j.cell.2022.11.001] [Citation(s) in RCA: 1094] [Impact Index Per Article: 1094.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/19/2022] [Accepted: 11/01/2022] [Indexed: 01/05/2023]
Abstract
Aging is driven by hallmarks fulfilling the following three premises: (1) their age-associated manifestation, (2) the acceleration of aging by experimentally accentuating them, and (3) the opportunity to decelerate, stop, or reverse aging by therapeutic interventions on them. We propose the following twelve hallmarks of aging: genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, disabled macroautophagy, deregulated nutrient-sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, chronic inflammation, and dysbiosis. These hallmarks are interconnected among each other, as well as to the recently proposed hallmarks of health, which include organizational features of spatial compartmentalization, maintenance of homeostasis, and adequate responses to stress.
Collapse
Affiliation(s)
- Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Maria A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
| | - Linda Partridge
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK; Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain; Altos Labs, Cambridge, UK
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Institut Universitaire de France, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France; Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
| |
Collapse
|
53
|
Buckley MT, Sun ED, George BM, Liu L, Schaum N, Xu L, Reyes JM, Goodell MA, Weissman IL, Wyss-Coray T, Rando TA, Brunet A. Cell-type-specific aging clocks to quantify aging and rejuvenation in neurogenic regions of the brain. NATURE AGING 2023; 3:121-137. [PMID: 37118510 PMCID: PMC10154228 DOI: 10.1038/s43587-022-00335-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022]
Abstract
The diversity of cell types is a challenge for quantifying aging and its reversal. Here we develop 'aging clocks' based on single-cell transcriptomics to characterize cell-type-specific aging and rejuvenation. We generated single-cell transcriptomes from the subventricular zone neurogenic region of 28 mice, tiling ages from young to old. We trained single-cell-based regression models to predict chronological age and biological age (neural stem cell proliferation capacity). These aging clocks are generalizable to independent cohorts of mice, other regions of the brains, and other species. To determine if these aging clocks could quantify transcriptomic rejuvenation, we generated single-cell transcriptomic datasets of neurogenic regions for two interventions-heterochronic parabiosis and exercise. Aging clocks revealed that heterochronic parabiosis and exercise reverse transcriptomic aging in neurogenic regions, but in different ways. This study represents the first development of high-resolution aging clocks from single-cell transcriptomic data and demonstrates their application to quantify transcriptomic rejuvenation.
Collapse
Affiliation(s)
- Matthew T Buckley
- Department of Genetics, Stanford University, Stanford, CA, USA
- Genetics Graduate Program, Stanford University, Stanford, CA, USA
| | - Eric D Sun
- Department of Genetics, Stanford University, Stanford, CA, USA
- Biomedical Informatics Graduate Program, Stanford University, Stanford, CA, USA
| | - Benson M George
- Stanford Medical Scientist Training Program, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Department of Neurology, UCLA, Los Angeles, CA, USA
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Lucy Xu
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jaime M Reyes
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA
- Neurology Service, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
- Department of Neurology, UCLA, Los Angeles, CA, USA
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA.
| |
Collapse
|
54
|
Aversano S, Caiazza C, Caiazzo M. Induced pluripotent stem cell-derived and directly reprogrammed neurons to study neurodegenerative diseases: The impact of aging signatures. Front Aging Neurosci 2022; 14:1069482. [PMID: 36620769 PMCID: PMC9810544 DOI: 10.3389/fnagi.2022.1069482] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Many diseases of the central nervous system are age-associated and do not directly result from genetic mutations. These include late-onset neurodegenerative diseases (NDDs), which represent a challenge for biomedical research and drug development due to the impossibility to access to viable human brain specimens. Advancements in reprogramming technologies have allowed to obtain neurons from induced pluripotent stem cells (iPSCs) or directly from somatic cells (iNs), leading to the generation of better models to understand the molecular mechanisms and design of new drugs. Nevertheless, iPSC technology faces some limitations due to reprogramming-associated cellular rejuvenation which resets the aging hallmarks of donor cells. Given the prominent role of aging for the development and manifestation of late-onset NDDs, this suggests that this approach is not the most suitable to accurately model age-related diseases. Direct neuronal reprogramming, by which a neuron is formed via direct conversion from a somatic cell without going through a pluripotent intermediate stage, allows the possibility to generate patient-derived neurons that maintain aging and epigenetic signatures of the donor. This aspect may be advantageous for investigating the role of aging in neurodegeneration and for finely dissecting underlying pathological mechanisms. Here, we will compare iPSC and iN models as regards the aging status and explore how this difference is reported to affect the phenotype of NDD in vitro models.
Collapse
Affiliation(s)
- Simona Aversano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Carmen Caiazza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Massimiliano Caiazzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy,Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, Netherlands,*Correspondence: Massimiliano Caiazzo,
| |
Collapse
|
55
|
Abstract
'Age reprogramming' refers to the process by which the molecular and cellular pathways of a cell that are subject to age-related decline are rejuvenated without passage through an embryonic stage. This process differs from the rejuvenation observed in differentiated derivatives of induced pluripotent stem cells, which involves passage through an embryonic stage and loss of cellular identity. Accordingly, the study of age reprogramming can provide an understanding of how ageing can be reversed while retaining cellular identity and the specialised function(s) of a cell, which will be of benefit to regenerative medicine. Here, we highlight recent work that has provided a more nuanced understanding of age reprogramming and point to some open questions in the field that might be explored in the future.
Collapse
Affiliation(s)
- Prim B. Singh
- Department of Medicine, Nazarbayev University School of Medicine, 5/1 Kerei Zhanibek Khandar Street, Astana 010000, Republic of Kazakhstan,Author for correspondence ()
| | - Assem Zhakupova
- Department of Medicine, Nazarbayev University School of Medicine, 5/1 Kerei Zhanibek Khandar Street, Astana 010000, Republic of Kazakhstan
| |
Collapse
|
56
|
Hess S, Kendall TJ, Pena M, Yamane K, Soong D, Adams L, Truman R, Rambukkana A. In vivo partial reprogramming by bacteria promotes adult liver organ growth without fibrosis and tumorigenesis. Cell Rep Med 2022; 3:100820. [PMID: 36384103 PMCID: PMC9729881 DOI: 10.1016/j.xcrm.2022.100820] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 05/04/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022]
Abstract
Ideal therapies for regenerative medicine or healthy aging require healthy organ growth and rejuvenation, but no organ-level approach is currently available. Using Mycobacterium leprae (ML) with natural partial cellular reprogramming capacity and its animal host nine-banded armadillos, we present an evolutionarily refined model of adult liver growth and regeneration. In infected armadillos, ML reprogram the entire liver and significantly increase total liver/body weight ratio by increasing healthy liver lobules, including hepatocyte proliferation and proportionate expansion of vasculature, and biliary systems. ML-infected livers are microarchitecturally and functionally normal without damage, fibrosis, or tumorigenesis. Bacteria-induced reprogramming reactivates liver progenitor/developmental/fetal genes and upregulates growth-, metabolism-, and anti-aging-associated markers with minimal change in senescence and tumorigenic genes, suggesting bacterial hijacking of homeostatic, regeneration pathways to promote de novo organogenesis. This may facilitate the unraveling of endogenous pathways that effectively and safely re-engage liver organ growth, with broad therapeutic implications including organ regeneration and rejuvenation.
Collapse
Affiliation(s)
- Samuel Hess
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
| | - Timothy J Kendall
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Centre for Inflammation Research, The University of Edinburgh, Edinburgh, UK; Edinburgh Pathology, The University of Edinburgh, Edinburgh, UK
| | - Maria Pena
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Keitaro Yamane
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
| | - Daniel Soong
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Medical Research Council Centre for Reproductive Health, The University of Edinburgh, Edinburgh, UK
| | - Linda Adams
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Richard Truman
- US Department of Health and Human Services, Health Resources and Services Administration, Healthcare Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA; Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Anura Rambukkana
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK; Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK; Edinburgh Infectious Diseases, The University of Edinburgh, Edinburgh, UK; Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
57
|
Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct Target Ther 2022; 7:374. [PMID: 36336680 PMCID: PMC9637765 DOI: 10.1038/s41392-022-01211-8] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Aging is accompanied by the decline of organismal functions and a series of prominent hallmarks, including genetic and epigenetic alterations. These aging-associated epigenetic changes include DNA methylation, histone modification, chromatin remodeling, non-coding RNA (ncRNA) regulation, and RNA modification, all of which participate in the regulation of the aging process, and hence contribute to aging-related diseases. Therefore, understanding the epigenetic mechanisms in aging will provide new avenues to develop strategies to delay aging. Indeed, aging interventions based on manipulating epigenetic mechanisms have led to the alleviation of aging or the extension of the lifespan in animal models. Small molecule-based therapies and reprogramming strategies that enable epigenetic rejuvenation have been developed for ameliorating or reversing aging-related conditions. In addition, adopting health-promoting activities, such as caloric restriction, exercise, and calibrating circadian rhythm, has been demonstrated to delay aging. Furthermore, various clinical trials for aging intervention are ongoing, providing more evidence of the safety and efficacy of these therapies. Here, we review recent work on the epigenetic regulation of aging and outline the advances in intervention strategies for aging and age-associated diseases. A better understanding of the critical roles of epigenetics in the aging process will lead to more clinical advances in the prevention of human aging and therapy of aging-related diseases.
Collapse
|
58
|
Alle Q, Le Borgne E, Bensadoun P, Lemey C, Béchir N, Gabanou M, Estermann F, Bertrand‐Gaday C, Pessemesse L, Toupet K, Desprat R, Vialaret J, Hirtz C, Noël D, Jorgensen C, Casas F, Milhavet O, Lemaitre J. A single short reprogramming early in life initiates and propagates an epigenetically related mechanism improving fitness and promoting an increased healthy lifespan. Aging Cell 2022; 21:e13714. [PMID: 36251933 PMCID: PMC9649606 DOI: 10.1111/acel.13714] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/11/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Recent advances in cell reprogramming showed that OSKM induction is able to improve cell physiology in vitro and in vivo. Here, we show that a single short reprogramming induction is sufficient to prevent musculoskeletal functions deterioration of mice, when applied in early life. In addition, in old age, treated mice have improved tissue structures in kidney, spleen, skin, and lung, with an increased lifespan of 15% associated with organ-specific differential age-related DNA methylation signatures rejuvenated by the treatment. Altogether, our results indicate that a single short reprogramming early in life might initiate and propagate an epigenetically related mechanism to promote a healthy lifespan.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Christelle Bertrand‐Gaday
- DMEM, Univ Montpellier, INRAEMontpellierFrance,RAM‐METAMUS, Univ Montpellier, INRAEMontpellierFrance
| | | | - Karine Toupet
- IRMB, Univ Montpellier, INSERMMontpellierFrance,ECELLFrance Montpellier Facility, Univ MontpellierMontpellierFrance
| | | | - Jérôme Vialaret
- IRMB, Univ Montpellier, INSERMMontpellierFrance,PPC Facility, CHU MontpellierMontpellierFrance
| | - Christophe Hirtz
- IRMB, Univ Montpellier, INSERMMontpellierFrance,PPC Facility, CHU MontpellierMontpellierFrance
| | - Danièle Noël
- IRMB, Univ Montpellier, INSERMMontpellierFrance,ECELLFrance Montpellier Facility, Univ MontpellierMontpellierFrance
| | - Christian Jorgensen
- IRMB, Univ Montpellier, INSERMMontpellierFrance,ECELLFrance Montpellier Facility, Univ MontpellierMontpellierFrance
| | - François Casas
- DMEM, Univ Montpellier, INRAEMontpellierFrance,RAM‐METAMUS, Univ Montpellier, INRAEMontpellierFrance
| | - Ollivier Milhavet
- SAFE‐iPSC Facility, CHU MontpellierMontpellierFrance,IRMB, Univ Montpellier, INSERM, CNRSMontpellierFrance
| | - Jean‐Marc Lemaitre
- IRMB, Univ Montpellier, INSERMMontpellierFrance,SAFE‐iPSC Facility, CHU MontpellierMontpellierFrance
| |
Collapse
|
59
|
Kaur P, Otgonbaatar A, Ramamoorthy A, Chua EHZ, Harmston N, Gruber J, Tolwinski NS. Combining stem cell rejuvenation and senescence targeting to synergistically extend lifespan. Aging (Albany NY) 2022; 14:8270-8291. [DOI: 10.18632/aging.204347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Prameet Kaur
- Division of Science, Yale-NUS College, Singapore 138527, Singapore
| | | | | | | | - Nathan Harmston
- Division of Science, Yale-NUS College, Singapore 138527, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jan Gruber
- Division of Science, Yale-NUS College, Singapore 138527, Singapore
- Department of Biochemistry, NUS, Singapore 117596, Singapore
| | - Nicholas S. Tolwinski
- Division of Science, Yale-NUS College, Singapore 138527, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| |
Collapse
|
60
|
Pérez RF, Tejedor JR, Fernández AF, Fraga MF. Aging and cancer epigenetics: Where do the paths fork? Aging Cell 2022; 21:e13709. [PMID: 36103298 PMCID: PMC9577950 DOI: 10.1111/acel.13709] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/29/2022] [Indexed: 01/25/2023] Open
Abstract
Aging and cancer are clearly associated processes, at both the epidemiological and molecular level. Epigenetic mechanisms are good candidates to explain the molecular links between the two phenomena, but recent reports have also revealed considerable differences, particularly regarding the loss of DNA methylation in the two processes. The large-scale generation and availability of genome-wide epigenetic data now permits systematic studies to be undertaken which may help clarify the similarities and differences between aging and cancer epigenetic alterations. In addition, the development of epigenetic clocks provides a new dimension in which to investigate diseases at the molecular level. Here, we examine current and future questions about the roles of DNA methylation mechanisms as causal factors in the processes of aging and cancer so that we may better understand if and how aging-associated epigenetic alterations lead to tumorigenesis. It seems certain that comprehending the molecular mechanisms underlying epigenetic clocks, especially with regard to somatic stem cell aging, combined with applying single-cell epigenetic-age profiling technologies to aging and cancer cohorts, and the integration of existing and upcoming epigenetic evidence within the genetic damage models of aging will prove to be crucial to improving understanding of these two interrelated phenomena.
Collapse
Affiliation(s)
- Raúl Fernández Pérez
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN‐CSIC)El EntregoSpain,Health Research Institute of Asturias (ISPA‐FINBA)Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain,Rare Diseases CIBER (CIBERER)Carlos III Health Institute (ISCIII)MadridSpain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN‐CSIC)El EntregoSpain,Health Research Institute of Asturias (ISPA‐FINBA)Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain,Rare Diseases CIBER (CIBERER)Carlos III Health Institute (ISCIII)MadridSpain
| | - Agustín Fernández Fernández
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN‐CSIC)El EntregoSpain,Health Research Institute of Asturias (ISPA‐FINBA)Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain,Rare Diseases CIBER (CIBERER)Carlos III Health Institute (ISCIII)MadridSpain
| | - Mario Fernández Fraga
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN‐CSIC)El EntregoSpain,Health Research Institute of Asturias (ISPA‐FINBA)Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain,Rare Diseases CIBER (CIBERER)Carlos III Health Institute (ISCIII)MadridSpain
| |
Collapse
|
61
|
Caliskan A, Crouch SAW, Giddins S, Dandekar T, Dangwal S. Progeria and Aging-Omics Based Comparative Analysis. Biomedicines 2022; 10:2440. [PMID: 36289702 PMCID: PMC9599154 DOI: 10.3390/biomedicines10102440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 10/21/2023] Open
Abstract
Since ancient times aging has also been regarded as a disease, and humankind has always strived to extend the natural lifespan. Analyzing the genes involved in aging and disease allows for finding important indicators and biological markers for pathologies and possible therapeutic targets. An example of the use of omics technologies is the research regarding aging and the rare and fatal premature aging syndrome progeria (Hutchinson-Gilford progeria syndrome, HGPS). In our study, we focused on the in silico analysis of differentially expressed genes (DEGs) in progeria and aging, using a publicly available RNA-Seq dataset (GEO dataset GSE113957) and a variety of bioinformatics tools. Despite the GSE113957 RNA-Seq dataset being well-known and frequently analyzed, the RNA-Seq data shared by Fleischer et al. is far from exhausted and reusing and repurposing the data still reveals new insights. By analyzing the literature citing the use of the dataset and subsequently conducting a comparative analysis comparing the RNA-Seq data analyses of different subsets of the dataset (healthy children, nonagenarians and progeria patients), we identified several genes involved in both natural aging and progeria (KRT8, KRT18, ACKR4, CCL2, UCP2, ADAMTS15, ACTN4P1, WNT16, IGFBP2). Further analyzing these genes and the pathways involved indicated their possible roles in aging, suggesting the need for further in vitro and in vivo research. In this paper, we (1) compare "normal aging" (nonagenarians vs. healthy children) and progeria (HGPS patients vs. healthy children), (2) enlist genes possibly involved in both the natural aging process and progeria, including the first mention of IGFBP2 in progeria, (3) predict miRNAs and interactomes for WNT16 (hsa-mir-181a-5p), UCP2 (hsa-mir-26a-5p and hsa-mir-124-3p), and IGFBP2 (hsa-mir-124-3p, hsa-mir-126-3p, and hsa-mir-27b-3p), (4) demonstrate the compatibility of well-established R packages for RNA-Seq analysis for researchers interested but not yet familiar with this kind of analysis, and (5) present comparative proteomics analyses to show an association between our RNA-Seq data analyses and corresponding changes in protein expression.
Collapse
Affiliation(s)
- Aylin Caliskan
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Samantha A. W. Crouch
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sara Giddins
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Seema Dangwal
- Stanford Cardiovascular Institute, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
62
|
Turpin M, Salbert G. 5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer. Front Mol Biosci 2022; 9:976862. [PMID: 36060265 PMCID: PMC9428128 DOI: 10.3389/fmolb.2022.976862] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation at the fifth position of cytosine (5mC) is one of the most studied epigenetic mechanisms essential for the control of gene expression and for many other biological processes including genomic imprinting, X chromosome inactivation and genome stability. Over the last years, accumulating evidence suggest that DNA methylation is a highly dynamic mechanism driven by a balance between methylation by DNMTs and TET-mediated demethylation processes. However, one of the main challenges is to understand the dynamics underlying steady state DNA methylation levels. In this review article, we give an overview of the latest advances highlighting DNA methylation as a dynamic cycling process with a continuous turnover of cytosine modifications. We describe the cooperative actions of DNMT and TET enzymes which combine with many additional parameters including chromatin environment and protein partners to govern 5mC turnover. We also discuss how mathematical models can be used to address variable methylation levels during development and explain cell-type epigenetic heterogeneity locally but also at the genome scale. Finally, we review the therapeutic implications of these discoveries with the use of both epigenetic clocks as predictors and the development of epidrugs that target the DNA methylation/demethylation machinery. Together, these discoveries unveil with unprecedented detail how dynamic is DNA methylation during development, underlying the establishment of heterogeneous DNA methylation landscapes which could be altered in aging, diseases and cancer.
Collapse
Affiliation(s)
- Marion Turpin
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
| | - Gilles Salbert
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
- *Correspondence: Gilles Salbert,
| |
Collapse
|
63
|
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] [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.
Collapse
Affiliation(s)
- Adiv A Johnson
- Longevity Sciences, Inc. (dba Tally Health), Greenwich, Connecticut, USA
| | - Bradley W English
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, Massachusetts, USA
| | - Maxim N Shokhirev
- Longevity Sciences, Inc. (dba Tally Health), Greenwich, Connecticut, USA
| | - David A Sinclair
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, Massachusetts, USA
| | - Trinna L Cuellar
- Longevity Sciences, Inc. (dba Tally Health), Greenwich, Connecticut, USA
| |
Collapse
|
64
|
Seale K, Horvath S, Teschendorff A, Eynon N, Voisin S. Making sense of the ageing methylome. Nat Rev Genet 2022; 23:585-605. [PMID: 35501397 DOI: 10.1038/s41576-022-00477-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
Over time, the human DNA methylation landscape accrues substantial damage, which has been associated with a broad range of age-related diseases, including cardiovascular disease and cancer. Various age-related DNA methylation changes have been described, including at the level of individual CpGs, such as differential and variable methylation, and at the level of the whole methylome, including entropy and correlation networks. Here, we review these changes in the ageing methylome as well as the statistical tools that can be used to quantify them. We detail the evidence linking DNA methylation to ageing phenotypes and the longevity strategies aimed at altering both DNA methylation patterns and machinery to extend healthspan and lifespan. Lastly, we discuss theories on the mechanistic causes of epigenetic ageing.
Collapse
Affiliation(s)
- Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Andrew Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.,UCL Cancer Institute, University College London, London, UK
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
| |
Collapse
|