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Arcos Hodar J, Jung S, Soudy M, Barvaux S, del Sol A. The cell rejuvenation atlas: leveraging network biology to identify master regulators of rejuvenation strategies. Aging (Albany NY) 2024; 16:12168-12190. [PMID: 39264584 PMCID: PMC11424581 DOI: 10.18632/aging.206105] [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: 03/15/2024] [Accepted: 07/19/2024] [Indexed: 09/13/2024]
Abstract
Current rejuvenation strategies, which range from calorie restriction to in vivo partial reprogramming, only improve a few specific cellular processes. In addition, the molecular mechanisms underlying these approaches are largely unknown, which hinders the design of more holistic cellular rejuvenation strategies. To address this issue, we developed SINGULAR (Single-cell RNA-seq Investigation of Rejuvenation Agents and Longevity), a cell rejuvenation atlas that provides a unified system biology analysis of diverse rejuvenation strategies across multiple organs at single-cell resolution. In particular, we leverage network biology approaches to characterize and compare the effects of each strategy at the level of intracellular signaling, cell-cell communication, and transcriptional regulation. As a result, we identified master regulators orchestrating the rejuvenation response and propose that targeting a combination of them leads to a more holistic improvement of age-dysregulated cellular processes. Thus, the interactive database accompanying SINGULAR is expected to facilitate the future design of synthetic rejuvenation interventions.
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Affiliation(s)
- Javier Arcos Hodar
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, Derio, Spain
| | - Sascha Jung
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, Derio, Spain
| | - Mohamed Soudy
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Sybille Barvaux
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
| | - Antonio del Sol
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, Derio, Spain
- Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg
- Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia 48012, Spain
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2
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Salnikov L. Cell autocloning as a pathway to their real rejuvenation. FRONTIERS IN AGING 2024; 5:1429156. [PMID: 39136004 PMCID: PMC11317467 DOI: 10.3389/fragi.2024.1429156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/25/2024] [Indexed: 08/15/2024]
Abstract
The article gives a brief description of geroprotection and rejuvenation methods known to date, presenting their main mechanisms and limitations. To overcome the main limitations of the process of rejuvenation, it is possible to use a process called "cell autocloning." The principle of the proposed method of rejuvenation is as follows: a periodic process of autocloning of the cell nucleus is initiated in the cellular genome with the formation of one unstable daughter copy and its subsequent self-elimination. In this case, the process of cell division stops in the phase of nuclei divergence without subsequent physical separation of the cell itself. This is especially important for postmitotic cells, where the looping of the "unidirectional" line of the ontogenesis program into a "ring" will mean their transition into renewable cells. The prototype for autocloning mechanisms could be the already known ways in which cells adapt to the increasing amount of their damage over time. These are polyploidy and asymmetric cell division, relying on which it is possible to obtain a renewable process of cell nuclei division, when only the original nucleus remains as a result of division. Although this is not a simple task, there are possible pathways to its solution using approaches that can suggest modern knowledge from the field of molecular and cell biology and genetics. The realization of such a goal will require a lot of work, but the expected result justifies it.
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Chambers TL, Dimet-Wiley A, Keeble AR, Haghani A, Lo WJ, Kang G, Brooke R, Horvath S, Fry CS, Watowich SJ, Wen Y, Murach KA. Methylome-proteome integration after late-life voluntary exercise training reveals regulation and target information for improved skeletal muscle health. J Physiol 2024. [PMID: 39058663 DOI: 10.1113/jp286681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Exercise is a potent stimulus for combatting skeletal muscle ageing. To study the effects of exercise on muscle in a preclinical setting, we developed a combined endurance-resistance training stimulus for mice called progressive weighted wheel running (PoWeR). PoWeR improves molecular, biochemical, cellular and functional characteristics of skeletal muscle and promotes aspects of partial epigenetic reprogramming when performed late in life (22-24 months of age). In this investigation, we leveraged pan-mammalian DNA methylome arrays and tandem mass-spectrometry proteomics in skeletal muscle to provide detailed information on late-life PoWeR adaptations in female mice relative to age-matched sedentary controls (n = 7-10 per group). Differential CpG methylation at conserved promoter sites was related to transcriptional regulation genes as well as Nr4a3, Hes1 and Hox genes after PoWeR. Using a holistic method of -omics integration called binding and expression target analysis (BETA), methylome changes were associated with upregulated proteins related to global and mitochondrial translation after PoWeR (P = 0.03). Specifically, BETA implicated methylation control of ribosomal, mitoribosomal, and mitochondrial complex I protein abundance after training. DNA methylation may also influence LACTB, MIB1 and UBR4 protein induction with exercise - all are mechanistically linked to muscle health. Computational cistrome analysis predicted several transcription factors including MYC as regulators of the exercise trained methylome-proteome landscape, corroborating prior late-life PoWeR transcriptome data. Correlating the proteome to muscle mass and fatigue resistance revealed positive relationships with VPS13A and NPL levels, respectively. Our findings expose differential epigenetic and proteomic adaptations associated with translational regulation after PoWeR that could influence skeletal muscle mass and function in aged mice. KEY POINTS: Late-life combined endurance-resistance exercise training from 22-24 months of age in mice is shown to improve molecular, biochemical, cellular and in vivo functional characteristics of skeletal muscle and promote aspects of partial epigenetic reprogramming and epigenetic age mitigation. Integration of DNA CpG 36k methylation arrays using conserved sites (which also contain methylation ageing clock sites) with exploratory proteomics in skeletal muscle extends our prior work and reveals coordinated and widespread regulation of ribosomal, translation initiation, mitochondrial ribosomal (mitoribosomal) and complex I proteins after combined voluntary exercise training in a sizeable cohort of female mice (n = 7-10 per group and analysis). Multi-omics integration predicted epigenetic regulation of serine β-lactamase-like protein (LACTB - linked to tumour resistance in muscle), mind bomb 1 (MIB1 - linked to satellite cell and type 2 fibre maintenance) and ubiquitin protein ligase E3 component N-recognin 4 (UBR4 - linked to muscle protein quality control) after training. Computational cistrome analysis identified MYC as a regulator of the late-life training proteome, in agreement with prior transcriptional analyses. Vacuolar protein sorting 13 homolog A (VPS13A) was positively correlated to muscle mass, and the glycoprotein/glycolipid associated sialylation enzyme N-acetylneuraminate pyruvate lyase (NPL) was associated to in vivo muscle fatigue resistance.
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Affiliation(s)
- Toby L Chambers
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
| | | | - Alexander R Keeble
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Amin Haghani
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Wen-Juo Lo
- Department of Educational Statistics and Research Methods, University of Arkansas, Fayetteville, AR, USA
| | - Gyumin Kang
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Robert Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - Christopher S Fry
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington, KY, USA
| | - Stanley J Watowich
- Ridgeline Therapeutics, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yuan Wen
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Kevin A Murach
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
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Jin P, Duan X, Li L, Zhou P, Zou C, Xie K. Cellular senescence in cancer: molecular mechanisms and therapeutic targets. MedComm (Beijing) 2024; 5:e542. [PMID: 38660685 PMCID: PMC11042538 DOI: 10.1002/mco2.542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 04/26/2024] Open
Abstract
Aging exhibits several hallmarks in common with cancer, such as cellular senescence, dysbiosis, inflammation, genomic instability, and epigenetic changes. In recent decades, research into the role of cellular senescence on tumor progression has received widespread attention. While how senescence limits the course of cancer is well established, senescence has also been found to promote certain malignant phenotypes. The tumor-promoting effect of senescence is mainly elicited by a senescence-associated secretory phenotype, which facilitates the interaction of senescent tumor cells with their surroundings. Targeting senescent cells therefore offers a promising technique for cancer therapy. Drugs that pharmacologically restore the normal function of senescent cells or eliminate them would assist in reestablishing homeostasis of cell signaling. Here, we describe cell senescence, its occurrence, phenotype, and impact on tumor biology. A "one-two-punch" therapeutic strategy in which cancer cell senescence is first induced, followed by the use of senotherapeutics for eliminating the senescent cells is introduced. The advances in the application of senotherapeutics for targeting senescent cells to assist cancer treatment are outlined, with an emphasis on drug categories, and the strategies for their screening, design, and efficient targeting. This work will foster a thorough comprehension and encourage additional research within this field.
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Affiliation(s)
- Ping Jin
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, School of Life SciencesYunnan UniversityKunmingYunnanChina
| | - Xirui Duan
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Lei Li
- Department of Anorectal SurgeryHospital of Chengdu University of Traditional Chinese Medicine and Chengdu University of Traditional Chinese MedicineChengduChina
| | - Ping Zhou
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Cheng‐Gang Zou
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in Yunnan, School of Life SciencesYunnan UniversityKunmingYunnanChina
| | - Ke Xie
- Department of OncologySchool of MedicineSichuan Academy of Medical Sciences and Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
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5
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Jones DP. Redox organization of living systems. Free Radic Biol Med 2024; 217:179-189. [PMID: 38490457 PMCID: PMC11313653 DOI: 10.1016/j.freeradbiomed.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Redox organization governs an underlying simplicity in living systems. Critically, redox reactions enable the essential characteristics of life: extraction of energy from the environment, use of energy to support metabolic and structural organization, use of dynamic redox responses to defend against environmental threats, and use of redox mechanisms to direct differentiation of cells and organ systems essential for reproduction. These processes are sustained through a redox context in which electron donor/acceptor couples are poised at substantially different steady-state redox potentials, some with relatively reducing steady states and others with relatively oxidizing steady states. Redox-sensitive thiols of the redox proteome, as well as low molecular weight redox-active molecules, are maintained individually by the kinetics of oxidation-reduction within this redox system. Recent research has revealed opposing network interactions of the metallome, redox proteome, metabolome and transcriptome, which appear to be an evolved redox response structure to maintain stability of an organism in the presence of variable oxidative environments. Considerable opportunity exists to improve human health through detailed understanding of these redox networks so that targeted interventions can be developed to support new avenues for redox medicine.
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Affiliation(s)
- Dean P Jones
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Whitehead Biomedical Research Building, 615 Michael St, RM205P, Atlanta, GA, 30322, USA.
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6
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Jones RG, von Walden F, Murach KA. Exercise-Induced MYC as an Epigenetic Reprogramming Factor That Combats Skeletal Muscle Aging. Exerc Sport Sci Rev 2024; 52:63-67. [PMID: 38391187 PMCID: PMC10963142 DOI: 10.1249/jes.0000000000000333] [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: 02/24/2024]
Abstract
Of the "Yamanaka factors" Oct3/4 , Sox2 , Klf4 , and c-Myc (OSKM), the transcription factor c-Myc ( Myc ) is the most responsive to exercise in skeletal muscle and is enriched within the muscle fiber. We hypothesize that the pulsatile induction of MYC protein after bouts of exercise can serve to epigenetically reprogram skeletal muscle toward a more resilient and functional state.
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Affiliation(s)
- Ronald G. Jones
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
| | - Ferdinand von Walden
- Neuropediatrics, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Kevin A. Murach
- Exercise Science Research Center, Molecular Muscle Mass Regulation Laboratory, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, AR, USA
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Cipriano A, Moqri M, Maybury-Lewis SY, Rogers-Hammond R, de Jong TA, Parker A, Rasouli S, Schöler HR, Sinclair DA, Sebastiano V. Mechanisms, pathways and strategies for rejuvenation through epigenetic reprogramming. NATURE AGING 2024; 4:14-26. [PMID: 38102454 PMCID: PMC11058000 DOI: 10.1038/s43587-023-00539-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023]
Abstract
Over the past decade, there has been a dramatic increase in efforts to ameliorate aging and the diseases it causes, with transient expression of nuclear reprogramming factors recently emerging as an intriguing approach. Expression of these factors, either systemically or in a tissue-specific manner, has been shown to combat age-related deterioration in mouse and human model systems at the cellular, tissue and organismal level. Here we discuss the current state of epigenetic rejuvenation strategies via partial reprogramming in both mouse and human models. For each classical reprogramming factor, we provide a brief description of its contribution to reprogramming and discuss additional factors or chemical strategies. We discuss what is known regarding chromatin remodeling and the molecular dynamics underlying rejuvenation, and, finally, we consider strategies to improve the practical uses of epigenetic reprogramming to treat aging and age-related diseases, focusing on the open questions and remaining challenges in this emerging field.
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Affiliation(s)
- Andrea Cipriano
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Mahdi Moqri
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Tineke Anna de Jong
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Alexander Parker
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Sajede Rasouli
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Hans Robert Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - David A Sinclair
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA.
| | - Vittorio Sebastiano
- Department of Obstetrics & Gynecology, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.
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8
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Ostermann PN, Evering TH. Cellular rejuvenation to combat HIV-1-related neurocognitive impairment. Trends Microbiol 2024; 32:13-16. [PMID: 37845134 PMCID: PMC10843288 DOI: 10.1016/j.tim.2023.09.011] [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: 06/22/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023]
Abstract
HIV-1-related neurocognitive impairment affects a significant proportion of people living with HIV, and accelerated brain aging has been implicated in its pathogenesis. This forum explores the application of cellular rejuvenation strategies to target molecular mechanisms of brain aging, promote neuronal health, and combat cognitive decline.
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Affiliation(s)
- Philipp N Ostermann
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 10065 New York, NY, USA.
| | - Teresa H Evering
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 10065 New York, NY, USA
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Ho KM, Lee A, Wu W, Chan MT, Ling L, Lipman J, Roberts J, Litton E, Joynt GM, Wong M. Flattening the biological age curve by improving metabolic health: to taurine or not to taurine, that' s the question. J Geriatr Cardiol 2023; 20:813-823. [PMID: 38098466 PMCID: PMC10716614 DOI: 10.26599/1671-5411.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
The aging population is an important issue around the world especially in developed countries. Although medical advances have substantially extended life span, the same cannot be said for the duration of health span. We are seeing increasing numbers of elderly people who are frail and/or have multiple chronic conditions; all of these can affect the quality of life of the elderly population as well as increase the burden on the healthcare system. Aging is mechanistically related to common medical conditions such as diabetes mellitus, ischemic heart disease, cognitive decline, and frailty. A recently accepted concept termed 'Accelerated Biological Aging' can be diagnosed when a person's biological age-as measured by biomarkers of DNA methylation-is older than their corresponding chronological age. Taurine, a conditionally essential amino acid, has received much attention in the past few years. A substantial number of animal studies have provided a strong scientific foundation suggesting that this amino acid can improve cellular and metabolic health, including blood glucose control, so much that it has been labelled one of the 'longevity amino acids'. In this review article, we propose the rationale that an adequately powered randomized-controlled-trial (RCT) is needed to confirm whether taurine can meaningfully improve metabolic and microbiome health, and biological age. This trial should incorporate certain elements in order to provide the much-needed evidence to guide doctors, and also the community at large, to determine whether this promising and inexpensive amino acid is useful in improving human metabolic health.
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Affiliation(s)
- Kwok M. Ho
- Department of Intensive Care Medicine, Fiona Stanley Hospital, Perth, Australia
- Medical School, The University of Western Australia, Perth, Australia
- School of Veterinary & Life Sciences, Murdoch University, Perth, Australia
| | - Anna Lee
- Department of Anaesthesia & Intensive Care, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - William Wu
- Department of Anaesthesia & Intensive Care, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Matthew T.V. Chan
- Department of Anaesthesia & Intensive Care, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Lowell Ling
- Department of Anaesthesia & Intensive Care, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Jeffrey Lipman
- Jamieson Trauma Institute, Royal Brisbane and Women’s Hospital, Brisbane, Queensland, Australia
- Division of Anaesthesiology Critical Care Emergency and Pain Medicine, Nîmes University Hospital, University of Montpellier, Nîmes, France
| | - Jason Roberts
- Division of Anaesthesiology Critical Care Emergency and Pain Medicine, Nîmes University Hospital, University of Montpellier, Nîmes, France
- University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Herston Infectious Diseases Institute (HeIDI), Metro North Health, Brisbane, Australia
- Departments of Pharmacy and Intensive Care Medicine, Royal Brisbane and Women’s Hospital, Brisbane, Australia
| | - Edward Litton
- Department of Intensive Care Medicine, Fiona Stanley Hospital, Perth, Australia
- Medical School, The University of Western Australia, Perth, Australia
| | - Gavin M. Joynt
- Department of Anaesthesia & Intensive Care, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Martin Wong
- JC School of Public Health and Primary Care, Centre for Health Education and Health Promotion, Chinese University of Hong Kong, Hong Kong, China
- School of Public Health, Peking University, Beijing, China
- School of Public Health, Fudan University, Shanghai, China
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Vladimir K, Perišić MM, Štorga M, Mostashari A, Khanin R. Epigenetics insights from perceived facial aging. Clin Epigenetics 2023; 15:176. [PMID: 37924108 PMCID: PMC10623707 DOI: 10.1186/s13148-023-01590-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
Facial aging is the most visible manifestation of aging. People desire to look younger than others of the same chronological age. Hence, perceived age is often used as a visible marker of aging, while biological age, often estimated by methylation markers, is used as an objective measure of age. Multiple epigenetics-based clocks have been developed for accurate estimation of general biological age and the age of specific organs, including the skin. However, it is not clear whether the epigenetic biomarkers (CpGs) used in these clocks are drivers of aging processes or consequences of aging. In this proof-of-concept study, we integrate data from GWAS on perceived facial aging and EWAS on CpGs measured in blood. By running EW Mendelian randomization, we identify hundreds of putative CpGs that are potentially causal to perceived facial aging with similar numbers of damaging markers that causally drive or accelerate facial aging and protective methylation markers that causally slow down or protect from aging. We further demonstrate that while candidate causal CpGs have little overlap with known epigenetics-based clocks, they affect genes or proteins with known functions in skin aging, such as skin pigmentation, elastin, and collagen levels. Overall, our results suggest that blood methylation markers reflect facial aging processes, and thus can be used to quantify skin aging and develop anti-aging solutions that target the root causes of aging.
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Affiliation(s)
- Klemo Vladimir
- LifeNome Inc., New York, 10018, NY, USA
- Faculty of Electrical Engineering and Computing, University of Zagreb, 10000, Zagreb, Croatia
| | - Marija Majda Perišić
- LifeNome Inc., New York, 10018, NY, USA
- Faculty of Mechanical Engineering and Naval Architecture, University of Zagreb, 10000, Zagreb, Croatia
| | - Mario Štorga
- LifeNome Inc., New York, 10018, NY, USA
- Faculty of Mechanical Engineering and Naval Architecture, University of Zagreb, 10000, Zagreb, Croatia
| | | | - Raya Khanin
- LifeNome Inc., New York, 10018, NY, USA.
- Bioinformatics Core, Memorial Sloan-Kettering Cancer Center, New York, 10065, NY, USA.
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11
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Ho KM, Morgan DJ, Johnstone M, Edibam C. Biological age is superior to chronological age in predicting hospital mortality of the critically ill. Intern Emerg Med 2023; 18:2019-2028. [PMID: 37635161 PMCID: PMC10543822 DOI: 10.1007/s11739-023-03397-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023]
Abstract
Biological age is increasingly recognized as being more accurate than chronological age in determining chronic health outcomes. This study assessed whether biological age, assessed on intensive care unit (ICU) admission, can predict hospital mortality. This retrospective cohort study, conducted in a tertiary multidisciplinary ICU in Western Australia, used the Levine PhenoAge model to estimate each patient's biological age (also called PhenoAge). Each patient's PhenoAge was calibrated to generate a regression residual which was equivalent to biological age unexplained by chronological age in the local context. PhenoAgeAccel was a dichotomized measure of the residuals, and its presence suggested that one was biologically older than the corresponding chronological age. Of the 2950 critically ill adult patients analyzed, 291 died (9.9%) before hospital discharge. Both PhenoAge and its residuals (after regressing on chronological age) had a significantly better ability to differentiate between hospital survivors and non-survivors than chronological age (area under the receiver-operating-characteristic curve 0.648 and 0.654 vs. 0.547 respectively). Being phenotypically older than one's chronological age was associated with an increased risk of mortality (PhenoAgeAccel hazard ratio [HR] 1.997, 95% confidence interval [CI] 1.568-2.542; p = 0.001) in a dose-related fashion and did not reach a plateau until at least a 20-year gap. This adverse association remained significant (adjusted HR 1.386, 95% CI 1.077-1.784; p = 0.011) after adjusted for severity of acute illness and comorbidities. PhenoAgeAccel was more prevalent among those with pre-existing chronic cardiovascular disease, end-stage renal failure, cirrhosis, immune disease, diabetes mellitus, or those treated with immunosuppressive therapy. Being phenotypically older than one's chronological age was more common among those with comorbidities, and this was associated with an increased risk of mortality in a dose-related fashion in the critically ill that was not fully explained by comorbidities and severity of acute illness.
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Affiliation(s)
- Kwok M Ho
- Department of Intensive Care Medicine, Fiona Stanley Hospital, Perth, WA, Robin Warren Drive, 6150, Australia.
- University of Western Australia, Perth, WA, 6009, Australia.
- Murdoch University, Perth, WA, 6150, Australia.
| | - David J Morgan
- Department of Intensive Care Medicine, Fiona Stanley Hospital, Perth, WA, Robin Warren Drive, 6150, Australia
| | - Mason Johnstone
- Department of Intensive Care Medicine, Fiona Stanley Hospital, Perth, WA, Robin Warren Drive, 6150, Australia
| | - Cyrus Edibam
- Department of Intensive Care Medicine, Fiona Stanley Hospital, Perth, WA, Robin Warren Drive, 6150, Australia
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12
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Ribeiro C, Farmer CK, de Magalhães JP, Freitas AA. Predicting lifespan-extending chemical compounds for C. elegans with machine learning and biologically interpretable features. Aging (Albany NY) 2023; 15:6073-6099. [PMID: 37450404 PMCID: PMC10373959 DOI: 10.18632/aging.204866] [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: 12/01/2022] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Recently, there has been a growing interest in the development of pharmacological interventions targeting ageing, as well as in the use of machine learning for analysing ageing-related data. In this work, we use machine learning methods to analyse data from DrugAge, a database of chemical compounds (including drugs) modulating lifespan in model organisms. To this end, we created four types of datasets for predicting whether or not a compound extends the lifespan of C. elegans (the most frequent model organism in DrugAge), using four different types of predictive biological features, based on: compound-protein interactions, interactions between compounds and proteins encoded by ageing-related genes, and two types of terms annotated for proteins targeted by the compounds, namely Gene Ontology (GO) terms and physiology terms from the WormBase's Phenotype Ontology. To analyse these datasets, we used a combination of feature selection methods in a data pre-processing phase and the well-established random forest algorithm for learning predictive models from the selected features. In addition, we interpreted the most important features in the two best models in light of the biology of ageing. One noteworthy feature was the GO term "Glutathione metabolic process", which plays an important role in cellular redox homeostasis and detoxification. We also predicted the most promising novel compounds for extending lifespan from a list of previously unlabelled compounds. These include nitroprusside, which is used as an antihypertensive medication. Overall, our work opens avenues for future work in employing machine learning to predict novel life-extending compounds.
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Affiliation(s)
- Caio Ribeiro
- School of Computing, University of Kent, Canterbury, Kent, UK
| | | | - João Pedro de Magalhães
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Alex A. Freitas
- School of Computing, University of Kent, Canterbury, Kent, UK
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13
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Rosen RS, Yarmush ML. Current Trends in Anti-Aging Strategies. Annu Rev Biomed Eng 2023; 25:363-385. [PMID: 37289554 DOI: 10.1146/annurev-bioeng-120122-123054] [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] [Indexed: 06/10/2023]
Abstract
The process of aging manifests from a highly interconnected network of biological cascades resulting in the degradation and breakdown of every living organism over time. This natural development increases risk for numerous diseases and can be debilitating. Academic and industrial investigators have long sought to impede, or potentially reverse, aging in the hopes of alleviating clinical burden, restoring functionality, and promoting longevity. Despite widespread investigation, identifying impactful therapeutics has been hindered by narrow experimental validation and the lack of rigorous study design. In this review, we explore the current understanding of the biological mechanisms of aging and how this understanding both informs and limits interpreting data from experimental models based on these mechanisms. We also discuss select therapeutic strategies that have yielded promising data in these model systems with potential clinical translation. Lastly, we propose a unifying approach needed to rigorously vet current and future therapeutics and guide evaluation toward efficacious therapies.
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Affiliation(s)
- Robert S Rosen
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA;
| | - Martin L Yarmush
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA;
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14
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Koptyug A, Sukhovei Y, Kostolomova E, Unger I, Kozlov V. Novel Strategy in Searching for Natural Compounds with Anti-Aging and Rejuvenating Potential. Int J Mol Sci 2023; 24:ijms24098020. [PMID: 37175723 PMCID: PMC10178965 DOI: 10.3390/ijms24098020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/18/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
We suggest a novel approach for searching natural compounds with anti-aging and rejuvenation potential using cell cultures, with a high potential for the further in vivo applications. The present paper discusses ways of defining age for cell populations with large numbers of cells and suggests a method of assessing how young or old a cell population is based on a cell age profile approach. This approach uses experimental distributions of the cells over the cell cycle stages, acquired using flow cytometry. This paper discusses how such a profile should evolve under homeostatic maintenance of cell numbers in the proliferation niches. We describe promising results from experiments on a commercial substance claiming rejuvenating and anti-aging activity acting upon the cultures of human mononuclear cells and dermal fibroblasts. The chosen substance promotes a shift towards larger proportion of cells in synthesis and proliferation stages, and increases cell culture longevity. Further, we describe promising in vivo testing results of a selected food supplement. Based on the described concept of cell age profile and available test results, a strategy to search for natural compounds with regenerative, anti-aging and rejuvenation potential is suggested and proposed for wider and thorough testing. Proposed methodology of age assessment is rather generic and can be used for quantitative assessment of the anti-aging and rejuvenation potential of different interventions. Further research aimed at the tests of the suggested strategy using more substances and different interventions, and the thorough studies of molecular mechanisms related to the action of the substance used for testing the suggested search methodology, are needed.
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Affiliation(s)
- Andrey Koptyug
- SportsTech Research Center, Department of Engineering, Mathematics and Science Education, Mid Sweden University, Akademigatan 1, 831 25 Östersund, Sweden
| | - Yurij Sukhovei
- Institute of Fundamental and Clinical Immunology, Tyumen Branch, Kotovskogo Str. 5, 625027 Tyumen, Russia
| | - Elena Kostolomova
- Department of Microbiology, Tyumen State Medical University, Kotovskogo Str. 5/2, 625023 Tyumen, Russia
| | - Irina Unger
- Institute of Fundamental and Clinical Immunology, Tyumen Branch, Kotovskogo Str. 5, 625027 Tyumen, Russia
| | - Vladimir Kozlov
- Institute of Fundamental and Clinical Immunology, Department of Clinical Immunology, Yadrintcevskaya Str. 14, 630099 Novosibirsk, Russia
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15
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Jung S, Arcos Hodar J, Del Sol A. Measuring biological age using a functionally interpretable multi-tissue RNA clock. Aging Cell 2023; 22:e13799. [PMID: 36929664 DOI: 10.1111/acel.13799] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 03/18/2023] Open
Abstract
The quantification of the biological age of cells yields great promises for accelerating the discovery of novel rejuvenation strategies. Here, we present MultiTIMER, the first multi-tissue aging clock that measures the biological, rather than chronological, age of cells from their transcriptional profiles by evaluating key cellular processes. We applied MultiTIMER to more than 70,000 transcriptional profiles and demonstrate that it accurately responds to cellular stressors and known interventions while informing about dysregulated cellular functions.
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Affiliation(s)
- Sascha Jung
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, Derio, Spain
| | - Javier Arcos Hodar
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, Derio, Spain
| | - Antonio Del Sol
- Computational Biology Group, CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, Derio, Spain.,Computational Biology Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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16
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Ji S, Xiong M, Chen H, Liu Y, Zhou L, Hong Y, Wang M, Wang C, Fu X, Sun X. Cellular rejuvenation: molecular mechanisms and potential therapeutic interventions for diseases. Signal Transduct Target Ther 2023; 8:116. [PMID: 36918530 PMCID: PMC10015098 DOI: 10.1038/s41392-023-01343-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 03/16/2023] Open
Abstract
The ageing process is a systemic decline from cellular dysfunction to organ degeneration, with more predisposition to deteriorated disorders. Rejuvenation refers to giving aged cells or organisms more youthful characteristics through various techniques, such as cellular reprogramming and epigenetic regulation. The great leaps in cellular rejuvenation prove that ageing is not a one-way street, and many rejuvenative interventions have emerged to delay and even reverse the ageing process. Defining the mechanism by which roadblocks and signaling inputs influence complex ageing programs is essential for understanding and developing rejuvenative strategies. Here, we discuss the intrinsic and extrinsic factors that counteract cell rejuvenation, and the targeted cells and core mechanisms involved in this process. Then, we critically summarize the latest advances in state-of-art strategies of cellular rejuvenation. Various rejuvenation methods also provide insights for treating specific ageing-related diseases, including cellular reprogramming, the removal of senescence cells (SCs) and suppression of senescence-associated secretory phenotype (SASP), metabolic manipulation, stem cells-associated therapy, dietary restriction, immune rejuvenation and heterochronic transplantation, etc. The potential applications of rejuvenation therapy also extend to cancer treatment. Finally, we analyze in detail the therapeutic opportunities and challenges of rejuvenation technology. Deciphering rejuvenation interventions will provide further insights into anti-ageing and ageing-related disease treatment in clinical settings.
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Affiliation(s)
- Shuaifei Ji
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mingchen Xiong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Huating Chen
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiqiong Liu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Laixian Zhou
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiyue Hong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mengyang Wang
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078, Macau SAR, China.
| | - Xiaobing Fu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
| | - Xiaoyan Sun
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
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17
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Jones RG, Dimet-Wiley A, Haghani A, da Silva FM, Brightwell CR, Lim S, Khadgi S, Wen Y, Dungan CM, Brooke RT, Greene NP, Peterson CA, McCarthy JJ, Horvath S, Watowich SJ, Fry CS, Murach KA. A molecular signature defining exercise adaptation with ageing and in vivo partial reprogramming in skeletal muscle. J Physiol 2023; 601:763-782. [PMID: 36533424 PMCID: PMC9987218 DOI: 10.1113/jp283836] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Exercise promotes functional improvements in aged tissues, but the extent to which it simulates partial molecular reprogramming is unknown. Using transcriptome profiling from (1) a skeletal muscle-specific in vivo Oct3/4, Klf4, Sox2 and Myc (OKSM) reprogramming-factor expression murine model; (2) an in vivo inducible muscle-specific Myc induction murine model; (3) a translatable high-volume hypertrophic exercise training approach in aged mice; and (4) human exercise muscle biopsies, we collectively defined exercise-induced genes that are common to partial reprogramming. Late-life exercise training lowered murine DNA methylation age according to several contemporary muscle-specific clocks. A comparison of the murine soleus transcriptome after late-life exercise training to the soleus transcriptome after OKSM induction revealed an overlapping signature that included higher JunB and Sun1. Also, within this signature, downregulation of specific mitochondrial and muscle-enriched genes was conserved in skeletal muscle of long-term exercise-trained humans; among these was muscle-specific Abra/Stars. Myc is the OKSM factor most induced by exercise in muscle and was elevated following exercise training in aged mice. A pulse of MYC rewired the global soleus muscle methylome, and the transcriptome after a MYC pulse partially recapitulated OKSM induction. A common signature also emerged in the murine MYC-controlled and exercise adaptation transcriptomes, including lower muscle-specific Melusin and reactive oxygen species-associated Romo1. With Myc, OKSM and exercise training in mice, as well habitual exercise in humans, the complex I accessory subunit Ndufb11 was lower; low Ndufb11 is linked to longevity in rodents. Collectively, exercise shares similarities with genetic in vivo partial reprogramming. KEY POINTS: Advances in the last decade related to cellular epigenetic reprogramming (e.g. DNA methylome remodelling) toward a pluripotent state via the Yamanaka transcription factors Oct3/4, Klf4, Sox2 and Myc (OKSM) provide a window into potential mechanisms for combatting the deleterious effects of cellular ageing. Using global gene expression analysis, we compared the effects of in vivo OKSM-mediated partial reprogramming in skeletal muscle fibres of mice to the effects of late-life murine exercise training in muscle. Myc is the Yamanaka factor most induced by exercise in skeletal muscle, and so we compared the MYC-controlled transcriptome in muscle to Yamanaka factor-mediated and exercise adaptation mRNA landscapes in mice and humans. A single pulse of MYC is sufficient to remodel the muscle methylome. We identify partial reprogramming-associated genes that are innately altered by exercise training and conserved in humans, and propose that MYC contributes to some of these responses.
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Affiliation(s)
- Ronald G. Jones
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | | | - Amin Haghani
- University of California Los Angeles, Department of Human Genetics, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Francielly Morena da Silva
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Camille R. Brightwell
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Seongkyun Lim
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Sabin Khadgi
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Yuan Wen
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
| | - Cory M. Dungan
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
| | | | - Nicholas P. Greene
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
| | - Charlotte A. Peterson
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
| | - John J. McCarthy
- Altos Labs, San Diego, CA, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
| | - Steve Horvath
- University of California Los Angeles, Department of Human Genetics, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Stanley J. Watowich
- Ridgeline Therapeutics, Houston, TX, USA
- University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Galveston, TX, USA
| | - Christopher S. Fry
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Kevin A. Murach
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
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18
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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.
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19
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Yang Q, Gao S, Lin J, Lyu K, Wu Z, Chen Y, Qiu Y, Zhao Y, Wang W, Lin T, Pan H, Chen M. A machine learning-based data mining in medical examination data: a biological features-based biological age prediction model. BMC Bioinformatics 2022; 23:411. [PMID: 36192681 PMCID: PMC9528174 DOI: 10.1186/s12859-022-04966-7] [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: 06/03/2022] [Accepted: 09/26/2022] [Indexed: 11/11/2022] Open
Abstract
Background Biological age (BA) has been recognized as a more accurate indicator of aging than chronological age (CA). However, the current limitations include: insufficient attention to the incompleteness of medical data for constructing BA; Lack of machine learning-based BA (ML-BA) on the Chinese population; Neglect of the influence of model overfitting degree on the stability of the association results. Methods and results Based on the medical examination data of the Chinese population (45–90 years), we first evaluated the most suitable missing interpolation method, then constructed 14 ML-BAs based on biomarkers, and finally explored the associations between ML-BAs and health statuses (healthy risk indicators and disease). We found that round-robin linear regression interpolation performed best, while AutoEncoder showed the highest interpolation stability. We further illustrated the potential overfitting problem in ML-BAs, which affected the stability of ML-Bas’ associations with health statuses. We then proposed a composite ML-BA based on the Stacking method with a simple meta-model (STK-BA), which overcame the overfitting problem, and associated more strongly with CA (r = 0.66, P < 0.001), healthy risk indicators, disease counts, and six types of disease. Conclusion We provided an improved aging measurement method for middle-aged and elderly groups in China, which can more stably capture aging characteristics other than CA, supporting the emerging application potential of machine learning in aging research. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04966-7.
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Affiliation(s)
- Qing Yang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Sunan Gao
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Junfen Lin
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Ke Lyu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zexu Wu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuhao Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yinwei Qiu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Yanrong Zhao
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Wei Wang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Tianxiang Lin
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Huiyun Pan
- The First Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. .,The First Affiliated Hospital of School of Medicine, Zhejiang University, Hangzhou, 310058, China.
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20
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Leysen H, Walter D, Clauwaert L, Hellemans L, van Gastel J, Vasudevan L, Martin B, Maudsley S. The Relaxin-3 Receptor, RXFP3, Is a Modulator of Aging-Related Disease. Int J Mol Sci 2022; 23:4387. [PMID: 35457203 PMCID: PMC9027355 DOI: 10.3390/ijms23084387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
During the aging process our body becomes less well equipped to deal with cellular stress, resulting in an increase in unrepaired damage. This causes varying degrees of impaired functionality and an increased risk of mortality. One of the most effective anti-aging strategies involves interventions that combine simultaneous glucometabolic support with augmented DNA damage protection/repair. Thus, it seems prudent to develop therapeutic strategies that target this combinatorial approach. Studies have shown that the ADP-ribosylation factor (ARF) GTPase activating protein GIT2 (GIT2) acts as a keystone protein in the aging process. GIT2 can control both DNA repair and glucose metabolism. Through in vivo co-regulation analyses it was found that GIT2 forms a close coexpression-based relationship with the relaxin-3 receptor (RXFP3). Cellular RXFP3 expression is directly affected by DNA damage and oxidative stress. Overexpression or stimulation of this receptor, by its endogenous ligand relaxin 3 (RLN3), can regulate the DNA damage response and repair processes. Interestingly, RLN3 is an insulin-like peptide and has been shown to control multiple disease processes linked to aging mechanisms, e.g., anxiety, depression, memory dysfunction, appetite, and anti-apoptotic mechanisms. Here we discuss the molecular mechanisms underlying the various roles of RXFP3/RLN3 signaling in aging and age-related disorders.
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Affiliation(s)
- Hanne Leysen
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Deborah Walter
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Lore Clauwaert
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Lieselot Hellemans
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Jaana van Gastel
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
- SGS Belgium, Intercity Business Park, Generaal De Wittelaan 19-A5, 2800 Mechelen, Belgium
| | | | - Bronwen Martin
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium;
| | - Stuart Maudsley
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
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