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Molière A, Park JYC, Goyala A, Vayndorf EM, Zhang B, Hsiung KC, Jung Y, Kwon S, Statzer C, Meyer D, Nguyen R, Chadwick J, Thompson MA, Schumacher B, Lee SJV, Essmann CL, MacArthur MR, Kaeberlein M, David D, Gems D, Ewald CY. Improved resilience and proteostasis mediate longevity upon DAF-2 degradation in old age. GeroScience 2024; 46:5015-5036. [PMID: 38900346 PMCID: PMC11335714 DOI: 10.1007/s11357-024-01232-x] [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: 12/14/2023] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Little is known about the possibility of reversing age-related biological changes when they have already occurred. To explore this, we have characterized the effects of reducing insulin/IGF-1 signaling (IIS) during old age. Reduction of IIS throughout life slows age-related decline in diverse species, most strikingly in the nematode Caenorhabditis elegans. Here we show that even at advanced ages, auxin-induced degradation of DAF-2 in single tissues, including neurons and the intestine, is still able to markedly increase C. elegans lifespan. We describe how reversibility varies among senescent changes. While senescent pathologies that develop in mid-life were not reversed, there was a rejuvenation of the proteostasis network, manifesting as a restoration of the capacity to eliminate otherwise intractable protein aggregates that accumulate with age. Moreover, resistance to several stressors was restored. These results support several new conclusions. (1) Loss of resilience is not solely a consequence of pathologies that develop in earlier life. (2) Restoration of proteostasis and resilience by inhibiting IIS is a plausible cause of the increase in lifespan. And (3), most interestingly, some aspects of the age-related transition from resilience to frailty can be reversed to a certain extent. This raises the possibility that the effect of IIS and related pathways on resilience and frailty during aging in higher animals might possess some degree of reversibility.
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Affiliation(s)
- Adrian Molière
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - Ji Young Cecilia Park
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - Anita Goyala
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - Elena M Vayndorf
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195-7470, USA
| | - Bruce Zhang
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Kuei Ching Hsiung
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Yoonji Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Sujeong Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Cyril Statzer
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - David Meyer
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Richard Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195-7470, USA
| | | | | | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Seung-Jae V Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Clara L Essmann
- Bioinformatics and Molecular Genetics, Institute of Biology III, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79108, Freiburg, Germany
| | - Michael R MacArthur
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195-7470, USA
| | | | - David Gems
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Collin Y Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland.
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Cheng Y, Wang H, Wu Y, Ding Y, Peng C, Qi C, Xu A, Liu Y. Light-powered biodegradation of Imidacloprid by Scenedesmus sp. TXH202001: Assessing complete removal, metabolic pathways, and toxicity verification. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135345. [PMID: 39084013 DOI: 10.1016/j.jhazmat.2024.135345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/09/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
Imidacloprid (IMI) is used extensively as an insecticide and poses a significant risk to both the ecological environment and human health. Biological methods are currently gaining recognition among the different strategies tested for wastewater treatment. This study focused on evaluating a recently discovered green alga, Scenedesmus sp. TXH202001, isolated from a municipal wastewater treatment plant (WWTP), exhibited notable capacity for IMI removal. After an 18-day evaluation, medium IMI concentrations (50 and 100 mg/L) facilitated the growth of microalgae whereas low (5 and 20 mg/L) and high (150 mg/L) concentrations had no discernible impact. No statistically significant disparities were detected in Fv/Fm, Malonaldehyde or Superoxide dismutase across all concentrations, suggesting Scenedesmus sp. TXH202001 exhibited notable resilience and adaptability to IMI conditions. Most notably, Scenedesmus sp. TXH202001 successfully eliminated > 99 % of IMI within 18 days subjected to IMI concentrations as high as 150 mg/L, which was contingent on the environmental factor of illumination. Molecular docking was used to identify the chemical reaction sites between IMI and typical degrading enzyme CYP450. Furthermore, the study revealed that the primary path for IMI removal was biodegradation and verified that the toxicity of the degraded product was lower than parent IMI in Caenorhabditis elegans. The efficacy of Scenedesmus sp. TXH202001 in wastewater was exceptional, thereby validating its practical utility.
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Affiliation(s)
- Yongtao Cheng
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Hongyu Wang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430072, China
| | - Yuanyuan Wu
- University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Yuting Ding
- University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Chuanyue Peng
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Cuicui Qi
- Anhui Provincial Academy of Eco-Environmental Science Research, Hefei 230061, China
| | - An Xu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; University of Science and Technology of China, Hefei, Anhui 230026, PR China.
| | - Ying Liu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China.
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3
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Ortega-Molina A, Lebrero-Fernández C, Sanz A, Calvo-Rubio M, Deleyto-Seldas N, de Prado-Rivas L, Plata-Gómez AB, Fernández-Florido E, González-García P, Vivas-García Y, Sánchez García E, Graña-Castro O, Price NL, Aroca-Crevillén A, Caleiras E, Monleón D, Borrás C, Casanova-Acebes M, de Cabo R, Efeyan A. A mild increase in nutrient signaling to mTORC1 in mice leads to parenchymal damage, myeloid inflammation and shortened lifespan. NATURE AGING 2024; 4:1102-1120. [PMID: 38849535 PMCID: PMC11333293 DOI: 10.1038/s43587-024-00635-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/25/2024] [Indexed: 06/09/2024]
Abstract
The mechanistic target of rapamycin complex 1 controls cellular anabolism in response to growth factor signaling and to nutrient sufficiency signaled through the Rag GTPases. Inhibition of mTOR reproducibly extends longevity across eukaryotes. Here we report that mice that endogenously express active mutant variants of RagC exhibit multiple features of parenchymal damage that include senescence, expression of inflammatory molecules, increased myeloid inflammation with extensive features of inflammaging and a ~30% reduction in lifespan. Through bone marrow transplantation experiments, we show that myeloid cells are abnormally activated by signals emanating from dysfunctional RagC-mutant parenchyma, causing neutrophil extravasation that inflicts additional inflammatory damage. Therapeutic suppression of myeloid inflammation in aged RagC-mutant mice attenuates parenchymal damage and extends survival. Together, our findings link mildly increased nutrient signaling to limited lifespan in mammals, and support a two-component process of parenchymal damage and myeloid inflammation that together precipitate a time-dependent organ deterioration that limits longevity.
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Affiliation(s)
- Ana Ortega-Molina
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
- Metabolism in cancer and aging Laboratory, Immune System Development And Function Department, Centro de Biología Molecular Severo Ochoa (CBM), Madrid, Spain.
| | - Cristina Lebrero-Fernández
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Metabolism in cancer and aging Laboratory, Immune System Development And Function Department, Centro de Biología Molecular Severo Ochoa (CBM), Madrid, Spain
| | - Alba Sanz
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miguel Calvo-Rubio
- Translational Gerontology Branch, National Institute on Aging (NIA), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Nerea Deleyto-Seldas
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Lucía de Prado-Rivas
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ana Belén Plata-Gómez
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Elena Fernández-Florido
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Yurena Vivas-García
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Elena Sánchez García
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Osvaldo Graña-Castro
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Institute of Applied Molecular Medicine (IMMA-Nemesio Díez), Department of Basic Medical Sciences, School of Medicine, San Pablo-CEU University, CEU Universities, Boadilla del Monte, Madrid, Spain
| | - Nathan L Price
- Translational Gerontology Branch, National Institute on Aging (NIA), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Alejandra Aroca-Crevillén
- Cardiovascular Regeneration Program, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Eduardo Caleiras
- Histopathology Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Daniel Monleón
- Department of Pathology, University of Valencia, Valencia, Spain; Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable-Instituto de Salud Carlos III (CIBERFES-ISCIII), Institute of Health Research-INCLIVA, Valencia, Spain
| | - Consuelo Borrás
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia, Centro de Investigación Biomédica en Red Fragilidad y Envejecimiento Saludable-Instituto de Salud Carlos III (CIBERFES-ISCIII), MiniAging Research Group, Institute of Health Research-INCLIVA, Valencia, Spain
| | - María Casanova-Acebes
- Cancer Immunity Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging (NIA), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Alejo Efeyan
- Metabolism and Cell Signaling Laboratory, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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Wang S, Wang R, Hu Y, Zhang Y, Yuan Q, Luo Y, Yuan C. Long noncoding RNA AI504432 upregulates FASN expression by sponging miR-1a-3p to promote lipogenesis in senescent adipocytes. Cell Signal 2024; 120:111232. [PMID: 38763183 DOI: 10.1016/j.cellsig.2024.111232] [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: 12/29/2023] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Aging affects lipid metabolism and can cause obesity as it is closely related to the disorder of many lipogenic regulatory factors. LncRNAs have been recognized as pivotal regulators across diverse biological processes, but their effects on lipogenesis in aging remain to be further studied. In this work, using RNA sequencing (RNA-Seq), we found that the expression of lncRNA AI504432 was significantly upregulated in the eWAT (epididymal white adipose tissue) of aging mice, and the knockdown of AI504432 notably reduced the expression of several adipogenic genes (e.g., Cebp/α, Srebp-1c, Fasn, Acaca, and Scd1) in senescent adipocytes. The bioinformatics investigation revealed that AI504432 possessed a binding site for miR-1a-3p, and the discovery was verified by the luciferase reporter assay. The expression of Fasn was increased upon the inhibition of miR-1a-3p but restored upon the simultaneous silencing of AI504432. Taken together, our results suggested that AI504432 controlled lipogenesis through the miR-1a-3p/Fasn signaling pathway. The findings may inspire new therapeutic approaches to target imbalanced lipid homeostasis due to aging.
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Affiliation(s)
- Shuwen Wang
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China; College of Basic Medical Science, China Three Gorges University, Yichang 443002, China
| | - Rui Wang
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China; College of Basic Medical Science, China Three Gorges University, Yichang 443002, China
| | - Yaqi Hu
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China; College of Basic Medical Science, China Three Gorges University, Yichang 443002, China
| | - Yifan Zhang
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China; College of Basic Medical Science, China Three Gorges University, Yichang 443002, China
| | - Qi Yuan
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China; College of Medicine and Health Science, China Three Gorges University, Yichang 443002, China
| | - Yiyang Luo
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China; College of Medicine and Health Science, China Three Gorges University, Yichang 443002, China
| | - Chengfu Yuan
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China; College of Basic Medical Science, China Three Gorges University, Yichang 443002, China.
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Sillau SH, Coughlan C, Ahmed MM, Nair K, Araya P, Galbraith MD, Bettcher BM, Espinosa JM, Chial HJ, Epperson N, Boyd TD, Potter H. Neuron loss in the brain starts in childhood, increases exponentially with age and is halted by GM-CSF treatment in Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.14.24310223. [PMID: 39072024 PMCID: PMC11275665 DOI: 10.1101/2024.07.14.24310223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Aging increases the risk of neurodegeneration, cognitive decline, and Alzheimer's disease (AD). Currently no means exist to measure neuronal cell death during life or to prevent it. Here we show that cross-sectional measures of human plasma proteins released from dying/damaged neurons (ubiquitin C-terminal hydrolase-L1/UCH-L1 and neurofilament light/NfL) become exponentially higher from age 2-85; UCH-L1 rises faster in females. Glial fibrillary acidic protein (GFAP) concentrations, indicating astrogliosis/inflammation, increase exponentially after age 40. Treatment with human granulocyte-macrophage colony-stimulating factor (GM-CSF/sargramostim) halted neuronal cell death, as evidenced by reduced plasma UCH-L1 concentrations, in AD participants to levels equivalent to those of five-year-old healthy controls. The ability of GM-CSF treatment to reduce neuronal apoptosis was confirmed in a rat model of AD. These findings suggest that the exponential increase in neurodegeneration with age, accelerated by neuroinflammation, may underlie the contribution of aging to cognitive decline and AD and can be halted by GM-CSF/sargramostim treatment.
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Zhuang X, Wang Q, Joost S, Ferrena A, Humphreys DT, Li Z, Blum M, Bastl K, Ding S, Landais Y, Zhan Y, Zhao Y, Chaligne R, Lee JH, Carrasco SE, Bhanot UK, Koche RP, Bott MJ, Katajisto P, Soto-Feliciano YM, Pisanic T, Thomas T, Zheng D, Wong ES, Tammela T. Aging limits stemness and tumorigenesis in the lung by reprogramming iron homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.23.600305. [PMID: 38979280 PMCID: PMC11230188 DOI: 10.1101/2024.06.23.600305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Aging is associated with a decline in the number and fitness of adult stem cells 1-4 . Aging-associated loss of stemness is posited to suppress tumorigenesis 5,6 , but this hypothesis has not been tested in vivo . Here, using physiologically aged autochthonous genetically engineered mouse models and primary cells 7,8 , we demonstrate aging suppresses lung cancer initiation and progression by degrading stemness of the alveolar cell of origin. This phenotype is underpinned by aging-associated induction of the transcription factor NUPR1 and its downstream target lipocalin-2 in the cell of origin in mice and humans, leading to a functional iron insufficiency in the aged cells. Genetic inactivation of the NUPR1-lipocalin-2 axis or iron supplementation rescue stemness and promote tumorigenic potential of aged alveolar cells. Conversely, targeting the NUPR1- lipocalin-2 axis is detrimental to young alveolar cells via induction of ferroptosis. We find that aging-associated DNA hypomethylation at specific enhancer sites associates with elevated NUPR1 expression, which is recapitulated in young alveolar cells by inhibition of DNA methylation. We uncover that aging drives a functional iron insufficiency, which leads to loss of stemness and tumorigenesis, but promotes resistance to ferroptosis. These findings have significant implications for the therapeutic modulation of cellular iron homeostasis in regenerative medicine and in cancer prevention. Furthermore, our findings are consistent with a model whereby most human cancers initiate in young individuals, revealing a critical window for such cancer prevention efforts.
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Alfatah M, Lim JJJ, Zhang Y, Naaz A, Cheng TYN, Yogasundaram S, Faidzinn NA, Lin JJ, Eisenhaber B, Eisenhaber F. Uncharacterized yeast gene YBR238C, an effector of TORC1 signaling in a mitochondrial feedback loop, accelerates cellular aging via HAP4- and RMD9-dependent mechanisms. eLife 2024; 12:RP92178. [PMID: 38713053 PMCID: PMC11076046 DOI: 10.7554/elife.92178] [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: 05/08/2024] Open
Abstract
Uncovering the regulators of cellular aging will unravel the complexity of aging biology and identify potential therapeutic interventions to delay the onset and progress of chronic, aging-related diseases. In this work, we systematically compared genesets involved in regulating the lifespan of Saccharomyces cerevisiae (a powerful model organism to study the cellular aging of humans) and those with expression changes under rapamycin treatment. Among the functionally uncharacterized genes in the overlap set, YBR238C stood out as the only one downregulated by rapamycin and with an increased chronological and replicative lifespan upon deletion. We show that YBR238C and its paralog RMD9 oppositely affect mitochondria and aging. YBR238C deletion increases the cellular lifespan by enhancing mitochondrial function. Its overexpression accelerates cellular aging via mitochondrial dysfunction. We find that the phenotypic effect of YBR238C is largely explained by HAP4- and RMD9-dependent mechanisms. Furthermore, we find that genetic- or chemical-based induction of mitochondrial dysfunction increases TORC1 (Target of Rapamycin Complex 1) activity that, subsequently, accelerates cellular aging. Notably, TORC1 inhibition by rapamycin (or deletion of YBR238C) improves the shortened lifespan under these mitochondrial dysfunction conditions in yeast and human cells. The growth of mutant cells (a proxy of TORC1 activity) with enhanced mitochondrial function is sensitive to rapamycin whereas the growth of defective mitochondrial mutants is largely resistant to rapamycin compared to wild type. Our findings demonstrate a feedback loop between TORC1 and mitochondria (the TORC1-MItochondria-TORC1 (TOMITO) signaling process) that regulates cellular aging processes. Hereby, YBR238C is an effector of TORC1 modulating mitochondrial function.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jolyn Jia Jia Lim
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Yizhong Zhang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Arshia Naaz
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Trishia Yi Ning Cheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Sonia Yogasundaram
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Nashrul Afiq Faidzinn
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jovian Jing Lin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
- School of Biological Sciences (SBS), Nanyang Technological University (NTU)SingaporeSingapore
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8
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Zhang M, Xing J, Zhao S, Lu M, Liu Y, Lin L, Gao W, Chen L, Li W, Shang J, Zhou J, Yin X, Zhu X. Exosomal YB-1 facilitates ovarian restoration by MALAT1/miR-211-5p/FOXO 3 axis. Cell Biol Toxicol 2024; 40:29. [PMID: 38700571 PMCID: PMC11068691 DOI: 10.1007/s10565-024-09871-8] [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: 11/20/2023] [Accepted: 04/24/2024] [Indexed: 05/06/2024]
Abstract
Premature ovarian failure (POF) affects many adult women less than 40 years of age and leads to infertility. Mesenchymal stem cells-derived small extracellular vesicles (MSCs-sEVs) are attractive candidates for ovarian function restoration and folliculogenesis for POF due to their safety and efficacy, however, the key mediator in MSCs-sEVs that modulates this response and underlying mechanisms remains elusive. Herein, we reported that YB-1 protein was markedly downregulated in vitro and in vivo models of POF induced with H2O2 and CTX respectively, accompanied by granulosa cells (GCs) senescence phenotype. Notably, BMSCs-sEVs transplantation upregulated YB-1, attenuated oxidative damage-induced cellular senescence in GCs, and significantly improved the ovarian function of POF rats, but that was reversed by YB-1 depletion. Moreover, YB-1 showed an obvious decline in serum and GCs in POF patients. Mechanistically, YB-1 as an RNA-binding protein (RBP) physically interacted with a long non-coding RNA, MALAT1, and increased its stability, further, MALAT1 acted as a competing endogenous RNA (ceRNA) to elevate FOXO3 levels by sequestering miR-211-5p to prevent its degradation, leading to repair of ovarian function. In summary, we demonstrated that BMSCs-sEVs improve ovarian function by releasing YB-1, which mediates MALAT1/miR-211-5p/FOXO3 axis regulation, providing a possible therapeutic target for patients with POF.
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Affiliation(s)
- Mengxue Zhang
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Center for Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Jie Xing
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Department of Obstetrics and Gynecology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Shijie Zhao
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Department of Obstetrics and Gynecology, The Fourth Hospital of Changsha, Changsha, People's Republic of China
| | - Minjun Lu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Institute of Reproductive Sciences, Jiangsu University, Zhenjiang, 212001, Jiangsu, People's Republic of China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Yueqin Liu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Institute of Reproductive Sciences, Jiangsu University, Zhenjiang, 212001, Jiangsu, People's Republic of China
| | - Li Lin
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Institute of Reproductive Sciences, Jiangsu University, Zhenjiang, 212001, Jiangsu, People's Republic of China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Wujiang Gao
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Institute of Reproductive Sciences, Jiangsu University, Zhenjiang, 212001, Jiangsu, People's Republic of China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Lu Chen
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Institute of Reproductive Sciences, Jiangsu University, Zhenjiang, 212001, Jiangsu, People's Republic of China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Wenxin Li
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Institute of Reproductive Sciences, Jiangsu University, Zhenjiang, 212001, Jiangsu, People's Republic of China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Junyu Shang
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Institute of Reproductive Sciences, Jiangsu University, Zhenjiang, 212001, Jiangsu, People's Republic of China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Jiamin Zhou
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China
- Institute of Reproductive Sciences, Jiangsu University, Zhenjiang, 212001, Jiangsu, People's Republic of China
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Xinming Yin
- Department of Central Laboratory, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Xiaolan Zhu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, 20 Zhengdong Road, Zhenjiang, Jiangsu, 212001, People's Republic of China.
- Institute of Reproductive Sciences, Jiangsu University, Zhenjiang, 212001, Jiangsu, People's Republic of China.
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9
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Hudock J, Kenney JW. Aging in zebrafish is associated with reduced locomotor activity and strain dependent changes in bottom dwelling and thigmotaxis. PLoS One 2024; 19:e0300227. [PMID: 38696419 PMCID: PMC11065237 DOI: 10.1371/journal.pone.0300227] [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: 11/09/2023] [Accepted: 02/25/2024] [Indexed: 05/04/2024] Open
Abstract
Aging is associated with a wide range of physiological and behavioral changes in many species. Zebrafish, like humans, rodents, and birds, exhibits gradual senescence, and thus may be a useful model organism for identifying evolutionarily conserved mechanisms related to aging. Here, we compared behavior in the novel tank test of young (6-month-old) and middle aged (12-month-old) zebrafish from two strains (TL and TU) and both sexes. We find that this modest age difference results in a reduction in locomotor activity in male fish. We also found that background strain modulated the effects of age on predator avoidance behaviors related to anxiety: older female TL fish increased bottom dwelling whereas older male TU fish decreased thigmotaxis. Although there were no consistent effects of age on either short-term (within session) or long-term (next day) habituation to the novel tank, strain affected the habituation response. TL fish tended to increase their distance from the bottom of the tank whereas TU fish had no changes in bottom distance but instead tended to increase thigmotaxis. Our findings support the use of zebrafish for the study of how age affects locomotion and how genetics interacts with age and sex to alter exploratory and emotional behaviors in response to novelty.
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Affiliation(s)
- Jacob Hudock
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States of America
| | - Justin W. Kenney
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States of America
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10
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Metcalf MG, Monshietehadi S, Sahay A, Durieux J, Frakes AE, Velichkovska M, Mena C, Farinas A, Sanchez M, Dillin A. Cell non-autonomous control of autophagy and metabolism by glial cells. iScience 2024; 27:109354. [PMID: 38500817 PMCID: PMC10946330 DOI: 10.1016/j.isci.2024.109354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 11/01/2023] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
Glia are the protectors of the nervous system, providing neurons with support and protection from cytotoxic insults. We previously discovered that four astrocyte-like glia can regulate organismal proteostasis and longevity in C. elegans. Expression of the UPRER transcription factor, XBP-1s, in these glia increases stress resistance, and longevity, and activates the UPRER in intestinal cells via neuropeptides. Autophagy, a key regulator of metabolism and aging, has been described as a cell autonomous process. Surprisingly, we find that glial XBP-1s enhances proteostasis and longevity by cell non-autonomously reprogramming organismal lipid metabolism and activating autophagy. Glial XBP-1s regulates the activation of another transcription factor, HLH-30/TFEB, in the intestine. HLH-30 activates intestinal autophagy, increases intestinal lipid catabolism, and upregulates a robust transcriptional program. Our study reveals a novel role for glia in regulating peripheral lipid metabolism, autophagy, and organellar health through peripheral activation of HLH-30 and autophagy.
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Affiliation(s)
- Melissa G. Metcalf
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Samira Monshietehadi
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Arushi Sahay
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jenni Durieux
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ashley E. Frakes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Martina Velichkovska
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cesar Mena
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Amelia Farinas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Melissa Sanchez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew Dillin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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11
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Levkovich G, Bendikov-Bar I, Malitsky S, Itkin M, Rusal M, Lokshtanov D, Shinder D, Sagi D. Reduction in metabolic noise reveals rejuvenation following transient severe caloric restriction. GeroScience 2024; 46:2343-2358. [PMID: 37946010 PMCID: PMC10828374 DOI: 10.1007/s11357-023-00969-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023] Open
Abstract
Among land vertebrates, the laying hen stands out due to its great reproductive efficiency: producing an egg daily all year long. This production rate makes the laying hen a special model animal to study the general process of reproduction and aging. One unique aspect of hens is their ability to undergo reproductive plasticity and to rejuvenate their reproductive tract during molting, a standard industrial feed restriction protocol for transiently pausing reproduction, followed by improved laying efficiency almost to peak production. Here we use longitudinal metabolomics, immunology, and physiological assays to show that molting promotes reproduction, compresses morbidity, and restores youthfulness when applied to old hens. We identified circulating metabolic biomarkers that quantitatively predict the reproduction and age of individuals. Lastly, we introduce metabolic noise, a robust, unitless, and quantifiable measure for heterogeneity of the complete metabolome as a general marker that can indicate the rate of aging of a population. Indeed, metabolic noise increased with age in control hens, whereas molted hens exhibited reduced noise following molting, indicating systemic rejuvenation. Our results suggest that metabolic noise can be used as a quick and universal proxy for assessing successful aging treatments, accelerating the timeline for drug development.
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Affiliation(s)
- Guy Levkovich
- Institute of Animal Science, Department of Poultry and Aquaculture, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, The Sagol Center for Healthy Human Longevity, Bar-Ilan University, Ramat Gan, Israel
| | - Inna Bendikov-Bar
- Institute of Animal Science, Department of Poultry and Aquaculture, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Mark Rusal
- Institute of Animal Science, Department of Poultry and Aquaculture, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dmitri Lokshtanov
- Institute of Animal Science, Department of Poultry and Aquaculture, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dmitry Shinder
- Institute of Animal Science, Department of Poultry and Aquaculture, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dror Sagi
- Institute of Animal Science, Department of Poultry and Aquaculture, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel.
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12
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Zhang Y, Huang S, Xie B, Zhong Y. Aging, Cellular Senescence, and Glaucoma. Aging Dis 2024; 15:546-564. [PMID: 37725658 PMCID: PMC10917531 DOI: 10.14336/ad.2023.0630-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/30/2023] [Indexed: 09/21/2023] Open
Abstract
Aging is one of the most serious risk factors for glaucoma, and according to age-standardized prevalence, glaucoma is the second leading cause of legal blindness worldwide. Cellular senescence is a hallmark of aging that is defined by a stable exit from the cell cycle in response to cellular damage and stress. The potential mechanisms underlying glaucomatous cellular senescence include oxidative stress, DNA damage, mitochondrial dysfunction, defective autophagy/mitophagy, and epigenetic modifications. These phenotypes interact and generate a sufficiently stable network to maintain the cell senescent state. Senescent trabecular meshwork (TM) cells, retinal ganglion cells (RGCs) and vascular endothelial cells reportedly accumulate with age and stress and may contribute to glaucoma pathologies. Therapies targeting the suppression or elimination of senescent cells have been found to ameliorate RGC death and improve vision in glaucoma models, suggesting the pivotal role of cellular senescence in the pathophysiology of glaucoma. In this review, we explore the biological links between aging and glaucoma, specifically delving into cellular senescence. Moreover, we summarize the current data on cellular senescence in key target cells associated with the development and clinical phenotypes of glaucoma. Finally, we discuss the therapeutic potential of targeting cellular senescence for the management of glaucoma.
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Affiliation(s)
- Yumeng Zhang
- Department of Ophthalmology, Ruijin Hospital Affiliated Medical School, Shanghai Jiaotong University, Shanghai 200025, China
| | - Shouyue Huang
- Department of Ophthalmology, Ruijin Hospital Affiliated Medical School, Shanghai Jiaotong University, Shanghai 200025, China
| | - Bing Xie
- Correspondence should be addressed to: Dr. Yisheng Zhong () and Bing Xie (), Department of Ophthalmology, Ruijin Hospital Affiliated Medical School, Shanghai Jiaotong University, Shanghai 200025, China
| | - Yisheng Zhong
- Correspondence should be addressed to: Dr. Yisheng Zhong () and Bing Xie (), Department of Ophthalmology, Ruijin Hospital Affiliated Medical School, Shanghai Jiaotong University, Shanghai 200025, China
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13
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Advani J, Mehta PA, Hamel AR, Mehrotra S, Kiel C, Strunz T, Corso-Díaz X, Kwicklis M, van Asten F, Ratnapriya R, Chew EY, Hernandez DG, Montezuma SR, Ferrington DA, Weber BHF, Segrè AV, Swaroop A. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration. Nat Commun 2024; 15:1972. [PMID: 38438351 PMCID: PMC10912779 DOI: 10.1038/s41467-024-46063-8] [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: 06/08/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
DNA methylation provides a crucial epigenetic mark linking genetic variations to environmental influence. We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. Methylation and expression quantitative trait loci show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration. Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of macular degeneration pathology by genotype-environment interaction in retina.
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Affiliation(s)
- Jayshree Advani
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Puja A Mehta
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew R Hamel
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sudeep Mehrotra
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christina Kiel
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Tobias Strunz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Ximena Corso-Díaz
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Madeline Kwicklis
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Freekje van Asten
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rinki Ratnapriya
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Y Chew
- Division of Epidemiology and Clinical Applications, Clinical Trials Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sandra R Montezuma
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
| | - Deborah A Ferrington
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, USA
- Doheny Eye Institute, Pasadena, CA, USA
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Ayellet V Segrè
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA, USA.
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA.
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14
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Boos F, Chen J, Brunet A. The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes. Cold Spring Harb Protoc 2024; 2024:107737. [PMID: 37100468 PMCID: PMC10890783 DOI: 10.1101/pdb.over107737] [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] [Indexed: 04/28/2023]
Abstract
The African turquoise killifish Nothobranchius furzeri is currently the shortest-lived vertebrate that can be bred in captivity. Because of its short life span of only 4-6 months, rapid generation time, high fecundity, and low cost of maintenance, the African turquoise killifish has emerged as an attractive model organism that combines the scalability of invertebrate models with the unique features of vertebrate organisms. A growing community of researchers is using the African turquoise killifish for studies in diverse fields, including aging, organ regeneration, development, "suspended animation," evolution, neuroscience, and disease. A wide range of techniques is now available for killifish research, from genetic manipulations and genomic tools to specialized assays for studying life span, organ biology, response to injury, etc. This protocol collection provides detailed descriptions of the methods that are generally applicable to all killifish laboratories and those that are limited to specific disciplines. Here, we give an overview of the features that render the African turquoise killifish a unique fast-track vertebrate model organism.
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Affiliation(s)
- Felix Boos
- Department of Genetics, Stanford, California 94305, USA
| | - Jingxun Chen
- Department of Genetics, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford, California 94305, USA
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, California 94305, USA
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15
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Schöfer S, Laffer S, Kirchberger S, Kothmayer M, Löhnert R, Ebner EE, Weipoltshammer K, Distel M, Pusch O, Schöfer C. Senescence-associated ß-galactosidase staining over the lifespan differs in a short- and a long-lived fish species. Eur J Histochem 2024; 68:3977. [PMID: 38568207 PMCID: PMC11017726 DOI: 10.4081/ejh.2024.3977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/21/2024] [Indexed: 04/05/2024] Open
Abstract
During the aging process, cells can enter cellular senescence, a state in which cells leave the cell cycle but remain viable. This mechanism is thought to protect tissues from propagation of damaged cells and the number of senescent cells has been shown to increase with age. The speed of aging determines the lifespan of a species and it varies significantly in different species. To assess the progress of cellular senescence during lifetime, we performed a comparative longitudinal study using histochemical detection of the senescence-associated beta-galactosidase as senescence marker to map the staining patterns in organs of the long-lived zebrafish and the short-lived turquoise killifish using light- and electron microscopy. We compared age stages corresponding to human stages of newborn, childhood, adolescence, adult and old age. We found tissue-specific but conserved signal patterns with respect to organ distribution. However, we found dramatic differences in the onset of tissue staining. The stained zebrafish organs show little to no signal at newborn age followed by a gradual increase in signal intensity, whereas the organs of the short-lived killifish show an early onset of staining already at newborn stage, which remains conspicuous at all age stages. The most prominent signal was found in liver, intestine, kidney and heart, with the latter showing the most prominent interspecies divergence in onset of staining and in staining intensity. In addition, we found staining predominantly in epithelial cells, some of which are post-mitotic, such as the intestinal epithelial lining. We hypothesize that the association of the strong and early-onset signal pattern in the short-lived killifish is consistent with a protective mechanism in a fast growing species. Furthermore, we believe that staining in post-mitotic cells may play a role in maintaining tissue integrity, suggesting different roles for cellular senescence during life.
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Affiliation(s)
- Simon Schöfer
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna.
| | - Sylvia Laffer
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna.
| | | | - Michael Kothmayer
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna.
| | - Renate Löhnert
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna.
| | - Elmar E Ebner
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna.
| | - Klara Weipoltshammer
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna.
| | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna.
| | - Oliver Pusch
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna.
| | - Christian Schöfer
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna.
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16
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Cheng JH, Okada D. Data-driven detection of age-related arbitrary monotonic changes in single-cell gene expression distributions. PeerJ 2024; 12:e16851. [PMID: 38344300 PMCID: PMC10859082 DOI: 10.7717/peerj.16851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Identification of genes whose expression increases or decreases with age is central to understanding the mechanisms behind aging. Recent scRNA-seq studies have shown that changes in single-cell expression profiles with aging are complex and diverse. In this study, we introduce a novel workflow to detect changes in the distribution of arbitrary monotonic age-related changes in single-cell expression profiles. Since single-cell gene expression profiles can be analyzed as probability distributions, our approach uses information theory to quantify the differences between distributions and employs distance matrices for association analysis. We tested this technique on simulated data and confirmed that potential parameter changes could be detected in a set of probability distributions. Application of the technique to a public scRNA-seq dataset demonstrated its potential utility as a straightforward screening method for identifying aging-related cellular features.
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Affiliation(s)
- Jian Hao Cheng
- Center for Genomics Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Daigo Okada
- Center for Genomics Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
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17
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Cohen NM, Lifshitz A, Jaschek R, Rinott E, Balicer R, Shlush LI, Barbash GI, Tanay A. Longitudinal machine learning uncouples healthy aging factors from chronic disease risks. NATURE AGING 2024; 4:129-144. [PMID: 38062254 DOI: 10.1038/s43587-023-00536-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/02/2023] [Indexed: 01/21/2024]
Abstract
To understand human longevity, inherent aging processes must be distinguished from known etiologies leading to age-related chronic diseases. Such deconvolution is difficult to achieve because it requires tracking patients throughout their entire lives. Here, we used machine learning to infer health trajectories over the entire adulthood age range using extrapolation from electronic medical records with partial longitudinal coverage. Using this approach, our model tracked the state of patients who were healthy and free from known chronic disease risk and distinguished individuals with higher or lower longevity potential using a multivariate score. We showed that the model and the markers it uses performed consistently on data from Israeli, British and US populations. For example, mildly low neutrophil counts and alkaline phosphatase levels serve as early indicators of healthy aging that are independent of risk for major chronic diseases. We characterize the heritability and genetic associations of our longevity score and demonstrate at least 1 year of extended lifespan for parents of high-scoring patients compared to matched controls. Longitudinal modeling of healthy individuals is thereby established as a tool for understanding healthy aging and longevity.
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Affiliation(s)
- Netta Mendelson Cohen
- Department of Computer Science and Applied Math, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Aviezer Lifshitz
- Department of Computer Science and Applied Math, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rami Jaschek
- Department of Computer Science and Applied Math, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ehud Rinott
- Department of Computer Science and Applied Math, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ran Balicer
- Clalit Research Institute, Ramat Gan, Israel
| | - Liran I Shlush
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gabriel I Barbash
- Department of Computer Science and Applied Math, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Amos Tanay
- Department of Computer Science and Applied Math, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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18
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Telpoukhovskaia MA, Murdy TJ, Marola OJ, Charland K, MacLean M, Luquez T, Lish AM, Neuner S, Dunn A, Onos KD, Wiley J, Archer D, Huentelman MJ, Arnold M, Menon V, Goate A, Van Eldik LJ, Territo PR, Howell GR, Carter GW, O'Connell KMS, Kaczorowski CC. New directions for Alzheimer's disease research from the Jackson Laboratory Center for Alzheimer's and Dementia Research 2022 workshop. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2024; 10:e12458. [PMID: 38469553 PMCID: PMC10925728 DOI: 10.1002/trc2.12458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/13/2024]
Abstract
INTRODUCTION In September 2022, The Jackson Laboratory Center for Alzheimer's and Dementia Research (JAX CADR) hosted a workshop with leading researchers in the Alzheimer's disease and related dementias (ADRD) field. METHODS During the workshop, the participants brainstormed new directions to overcome current barriers to providing patients with effective ADRD therapeutics. The participants outlined specific areas of focus. Following the workshop, each group used standard literature search methods to provide background for each topic. RESULTS The team of invited experts identified four key areas that can be collectively addressed to make a significant impact in the field: (1) Prioritize the diversification of disease targets, (2) enhance factors promoting resilience, (3) de-risk clinical pipeline, and (4) centralize data management. DISCUSSION In this report, we review these four objectives and propose innovations to expedite ADRD therapeutic pipelines.
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Affiliation(s)
| | - Thomas J. Murdy
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | | | - Kevin Charland
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | - Michael MacLean
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | - Tain Luquez
- Center for Translational and Computational NeuroimmunologyDepartment of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Alexandra M. Lish
- Ann Romney Center for Neurologic DiseasesDepartment of NeurologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Sarah Neuner
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Amy Dunn
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | - Kristen D. Onos
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | | | - Derek Archer
- Vanderbilt Memory and Alzheimer's CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of NeurologyVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Genetics InstituteVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Matthew J. Huentelman
- Neurogenomics DivisionTranslational Genomics Research Institute (TGen)PhoenixArizonaUSA
| | - Matthias Arnold
- Institute of Computational BiologyHelmholtz Zentrum München, German Research Center for Environmental HealthNeuherbergGermany
- Department of Psychiatry and Behavioral SciencesDuke UniversityDurhamNorth CarolinaUSA
| | - Vilas Menon
- Center for Translational and Computational NeuroimmunologyDepartment of NeurologyColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Alison Goate
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | | | - Paul R. Territo
- Department of MedicineDivision of Clinical PharmacologyIndiana University School of MedicineIndianapolisIndianaUSA
- Stark Neuroscience Research InstituteIndiana University School of MedicineIndianapolisIndianaUSA
| | - Gareth R. Howell
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
- Graduate School of Biomedical Science and EngineeringUniversity of MaineOronoMaineUSA
- Neuroscience Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
- Genetics Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
| | - Gregory W. Carter
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
- Graduate School of Biomedical Science and EngineeringUniversity of MaineOronoMaineUSA
- Neuroscience Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
- Genetics Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
| | - Kristen M. S. O'Connell
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
- Graduate School of Biomedical Science and EngineeringUniversity of MaineOronoMaineUSA
- Neuroscience Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
- Genetics Program, Graduate School of Biomedical ScienceTufts University School of MedicineBostonMassachusettsUSA
| | - Catherine C. Kaczorowski
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
- Department of NeurologyUniversity of MichiganAnn ArborMichiganUSA
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19
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Schwartz RE, Conboy IM. Non-Intrinsic, Systemic Mechanisms of Cellular Senescence. Cells 2023; 12:2769. [PMID: 38132089 PMCID: PMC10741531 DOI: 10.3390/cells12242769] [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: 10/28/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Cellular senescence is believed to contribute to aging and disease through the activity of secreted factors that promote inflammation, remodel the extracellular matrix, and adversely modify the behavior of non-senescent cells. While the markers and properties of senescent cells are still under investigation, it is postulated that cellular senescence manifests in vivo as the consequence of cellular damage that accumulates and becomes exacerbated with time. Yet, the notions that senescence has a solely intrinsic and time-dependent nature are questioned by the rapid induction of senescence in young mice and young cells in vitro by exposure to blood from aged animals. Here, we review some of the research on the systemically present factors that increase with age and may contribute to extrinsically induced senescence or "bystander senescence". These include proteins, reactive oxygen species, lipids, and nucleic acids, which may be present in individual soluble form, in vesicles, and in non-membranous multi-component macromolecules.
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Affiliation(s)
| | - Irina M. Conboy
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA;
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20
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Silva N, Rajado AT, Esteves F, Brito D, Apolónio J, Roberto VP, Binnie A, Araújo I, Nóbrega C, Bragança J, Castelo-Branco P. Measuring healthy ageing: current and future tools. Biogerontology 2023; 24:845-866. [PMID: 37439885 PMCID: PMC10615962 DOI: 10.1007/s10522-023-10041-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 07/14/2023]
Abstract
Human ageing is a complex, multifactorial process characterised by physiological damage, increased risk of age-related diseases and inevitable functional deterioration. As the population of the world grows older, placing significant strain on social and healthcare resources, there is a growing need to identify reliable and easy-to-employ markers of healthy ageing for early detection of ageing trajectories and disease risk. Such markers would allow for the targeted implementation of strategies or treatments that can lessen suffering, disability, and dependence in old age. In this review, we summarise the healthy ageing scores reported in the literature, with a focus on the past 5 years, and compare and contrast the variables employed. The use of approaches to determine biological age, molecular biomarkers, ageing trajectories, and multi-omics ageing scores are reviewed. We conclude that the ideal healthy ageing score is multisystemic and able to encompass all of the potential alterations associated with ageing. It should also be longitudinal and able to accurately predict ageing complications at an early stage in order to maximize the chances of successful early intervention.
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Affiliation(s)
- Nádia Silva
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Ana Teresa Rajado
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Filipa Esteves
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - David Brito
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Joana Apolónio
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
| | - Vânia Palma Roberto
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
| | - Alexandra Binnie
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Department of Critical Care, William Osler Health System, Etobicoke, ON, Canada
| | - Inês Araújo
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Clévio Nóbrega
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - José Bragança
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Pedro Castelo-Branco
- Algarve Biomedical Center Research Institute (ABC-RI), Campus Gambelas, Bld.2, 8005-139, Faro, Portugal.
- ABC Collaborative Laboratory, Association for Integrated Aging and Rejuvenation Solutions (ABC CoLAB), 8100-735, Loulé, Portugal.
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Gambelas Campus, Bld. 2, 8005-139, Faro, Portugal.
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal.
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21
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Melkikh AV. Aging and group selection: New arguments in favor of partially directed evolution. Biosystems 2023; 234:105061. [PMID: 37858738 DOI: 10.1016/j.biosystems.2023.105061] [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: 09/07/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023]
Abstract
In this study, theories of aging and its mechanisms under various environmental conditions were analyzed. The analysis of published data suggested that aging is a controlled process. It is known that many mathematical algorithms utilize an analogy of aging. However, this is possible only when a "target set" is known in advance. Various forms of selection in relation to aging were analyzed both collectively and separately. The general conclusion is that aging is one of the mechanisms of directed evolution. A model was constructed, which shows how aging is integrated into partially directed evolution.
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Affiliation(s)
- A V Melkikh
- Ural Federal University, Yekaterinburg, Russia.
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22
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Li S, Vazquez JM, Sudmant PH. The evolution of aging and lifespan. Trends Genet 2023; 39:830-843. [PMID: 37714733 PMCID: PMC11147682 DOI: 10.1016/j.tig.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Aging is a nearly inescapable trait among organisms yet lifespan varies tremendously across different species and spans several orders of magnitude in vertebrates alone. This vast phenotypic diversity is driven by distinct evolutionary trajectories and tradeoffs that are reflected in patterns of diversification and constraint in organismal genomes. Age-specific impacts of selection also shape allele frequencies in populations, thus impacting disease susceptibility and environment-specific mortality risk. Further, the mutational processes that spawn this genetic diversity in both germline and somatic cells are strongly influenced by age and life history. We discuss recent advances in our understanding of the evolution of aging and lifespan at organismal, population, and cellular scales, and highlight outstanding questions that remain unanswered.
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Affiliation(s)
- Stacy Li
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA
| | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA.
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23
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Li B, Li J, Li B, Ouchi T, Li L, Li Y, Zhao Z. A single-cell transcriptomic atlas characterizes age-related changes of murine cranial stem cell niches. Aging Cell 2023; 22:e13980. [PMID: 37681346 PMCID: PMC10652347 DOI: 10.1111/acel.13980] [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: 06/16/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023] Open
Abstract
The craniofacial bones provide structural support for the skull and accommodate the vulnerable brain tissue with a protective cavity. The bone tissue undergoes constant turnover, which relies on skeletal stem cells (SSCs) and/or mesenchymal stem cells (MSCs) and their niches. SSCs/MSCs and their perivascular niche within the bone marrow are well characterized in long bones. As for cranial bones, besides bone marrow, the suture mesenchyme has been identified as a unique niche for SSCs/MSCs of craniofacial bones. However, a comprehensive study of the two different cranial stem cell niches at single-cell resolution is still lacking. In addition, during the progression of aging, age-associated changes in cranial stem cell niches and resident cells remain uncovered. In this study, we investigated age-related changes in cranial stem cell niches via single-cell RNA sequencing (scRNA-seq). The transcriptomic profiles and cellular compositions have been delineated, indicating alterations of the cranial bone marrow microenvironment influenced by inflammaging. Moreover, we identified a senescent mesenchymal cell subcluster and several age-related immune cell subclusters by reclustering and pseudotime trajectory analysis, which might be closely linked to inflammaging. Finally, differentially expressed genes (DEGs) and cell-cell communications were analyzed during aging, revealing potential regulatory factors. Overall, this work highlights the age-related changes in cranial stem cell niches, which deepens the current understanding of cranial bone and suture biology and may provide therapeutic targets for antiaging and regenerative medicine.
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Affiliation(s)
- Bo Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of StomatologySichuan UniversitySichuanChengduChina
| | - Jingya Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of StomatologySichuan UniversitySichuanChengduChina
| | - Bingzhi Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of StomatologySichuan UniversitySichuanChengduChina
| | | | - Longjiang Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of StomatologySichuan UniversitySichuanChengduChina
| | - Yu Li
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of StomatologySichuan UniversitySichuanChengduChina
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of StomatologySichuan UniversitySichuanChengduChina
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24
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Perry AS, Zhao S, Gajjar P, Murthy VL, Lehallier B, Miller P, Nair S, Neill C, Carr JJ, Fearon W, Kapadia S, Kumbhani D, Gillam L, Lindenfeld J, Farrell L, Marron MM, Tian Q, Newman AB, Murabito J, Gerszten RE, Nayor M, Elmariah S, Lindman BR, Shah R. Proteomic architecture of frailty across the spectrum of cardiovascular disease. Aging Cell 2023; 22:e13978. [PMID: 37731195 PMCID: PMC10652351 DOI: 10.1111/acel.13978] [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: 06/05/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023] Open
Abstract
While frailty is a prominent risk factor in an aging population, the underlying biology of frailty is incompletely described. Here, we integrate 979 circulating proteins across a wide range of physiologies with 12 measures of frailty in a prospective discovery cohort of 809 individuals with severe aortic stenosis (AS) undergoing transcatheter aortic valve implantation. Our aim was to characterize the proteomic architecture of frailty in a highly susceptible population and study its relation to clinical outcome and systems-wide phenotypes to define potential novel, clinically relevant frailty biology. Proteomic signatures (specifically of physical function) were related to post-intervention outcome in AS, specifying pathways of innate immunity, cell growth/senescence, fibrosis/metabolism, and a host of proteins not widely described in human aging. In published cohorts, the "frailty proteome" displayed heterogeneous trajectories across age (20-100 years, age only explaining a small fraction of variance) and were associated with cardiac and non-cardiac phenotypes and outcomes across two broad validation cohorts (N > 35,000) over ≈2-3 decades. These findings suggest the importance of precision biomarkers of underlying multi-organ health status in age-related morbidity and frailty.
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Affiliation(s)
- Andrew S. Perry
- Vanderbilt Translational and Clinical Cardiovascular Research CenterVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Shilin Zhao
- Vanderbilt Translational and Clinical Cardiovascular Research CenterVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Priya Gajjar
- Cardiovascular Medicine Section, Department of MedicineBoston University School of MedicineBostonMassachusettsUSA
| | | | | | - Patricia Miller
- Department of Medicine, and Department of BiostatisticsBoston University School of MedicineBostonMassachusettsUSA
| | - Sangeeta Nair
- Vanderbilt Translational and Clinical Cardiovascular Research CenterVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Colin Neill
- Department of Medicine, Division of Cardiovascular MedicineUniversity of Wisconsin Hospital and ClinicsMadisonWisconsinUSA
| | - J. Jeffrey Carr
- Vanderbilt Translational and Clinical Cardiovascular Research CenterVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - William Fearon
- Department of Medicine, Division of CardiologyStanford Medical CenterPalo AltoCaliforniaUSA
| | - Samir Kapadia
- Department of Medicine, Division of CardiologyCleveland Clinic FoundationClevelandOhioUSA
| | - Dharam Kumbhani
- Department of Medicine, Division of CardiologyUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Linda Gillam
- Department of Cardiovascular MedicineMorristown Medical CenterMorristownNew JerseyUSA
| | - JoAnn Lindenfeld
- Vanderbilt Translational and Clinical Cardiovascular Research CenterVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Laurie Farrell
- Broad Institute of Harvard and MITCambridgeMassachusettsUSA
| | - Megan M. Marron
- Department of Epidemiology, Graduate School of Public HealthUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Qu Tian
- National Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Anne B. Newman
- Department of Epidemiology, Graduate School of Public HealthUniversity of PittsburghPittsburghPennsylvaniaUSA
- Departments of Medicine and Clinical and Translational ScienceUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Joanne Murabito
- Sections of Cardiovascular Medicine and Preventive Medicine and Epidemiology, Department of MedicineBoston University School of MedicineBostonMassachusettsUSA
| | - Robert E. Gerszten
- Broad Institute of Harvard and MITCambridgeMassachusettsUSA
- Cardiovascular Institute, Beth Israel Deaconess Medical Center, Harvard Medical SchoolBostonMassachusettsUSA
| | - Matthew Nayor
- Sections of Cardiovascular Medicine and Preventive Medicine and Epidemiology, Department of MedicineBoston University School of MedicineBostonMassachusettsUSA
| | - Sammy Elmariah
- Department of Medicine, Division of CardiologyThe University of CaliforniaSan FranciscoCaliforniaUSA
| | - Brian R. Lindman
- Vanderbilt Translational and Clinical Cardiovascular Research CenterVanderbilt University School of MedicineNashvilleTennesseeUSA
| | - Ravi Shah
- Vanderbilt Translational and Clinical Cardiovascular Research CenterVanderbilt University School of MedicineNashvilleTennesseeUSA
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25
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Karimi N. Approaches in line with human physiology to prevent skin aging. Front Physiol 2023; 14:1279371. [PMID: 37954446 PMCID: PMC10634238 DOI: 10.3389/fphys.2023.1279371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
Skin aging is a complex process that is influenced by intrinsic and extrinsic factors that impact the skin's protective functions and overall health. As the body's outermost layer, the skin plays a critical role in defending it against external threats, regulating body temperature, providing tactile sensation, and synthesizing vitamin D for bone health, immune function, and body homeostasis. However, as individuals age, the skin undergoes structural and functional changes, leading to impairments in these essential functions. In contemporary society, there is an increasing recognition of skin health as a significant indicator of overall wellbeing, resulting in a growing demand for anti-aging products and treatments. However, these products often have limitations in terms of safety, effective skin penetration, and potential systemic complications. To address these concerns, researchers are now focusing on approaches that are safer and better aligned with physiology of the skin. These approaches include adopting a proper diet and maintaining healthy lifestyle habits, the development of topical treatments that synchronize with the skin's circadian rhythm, utilizing endogenous antioxidant molecules, such as melatonin and natural products like polyphenols. Moreover, exploring alternative compounds for sun protection, such as natural ultraviolet (UV)-absorbing compounds, can offer safer options for shielding the skin from harmful radiation. Researchers are currently exploring the potential of adipose-derived stem cells, cell-free blood cell secretome (BCS) and other endogenous compounds for maintaining skin health. These approaches are more secure and more effective alternatives which are in line with human physiology to tackle skin aging. By emphasizing these innovative strategies, it is possible to develop effective treatments that not only slow down the skin aging process but also align better with the natural physiology of the skin. This review will focus on recent research in this field, highlighting the potential of these treatments as being safer and more in line with the skin's physiology in order to combat the signs of aging.
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Affiliation(s)
- Nazli Karimi
- Department of Physiology, Faculty of Medicine, Hacettepe University, Ankara, Türkiye
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26
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Wu M, Li Y, Miao Y, Qiao H, Wang Y. Exploring the efficient natural products for Alzheimer's disease therapy via Drosophila melanogaster (fruit fly) models. J Drug Target 2023; 31:817-831. [PMID: 37545435 DOI: 10.1080/1061186x.2023.2245582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/11/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Alzheimer's disease (AD) is a grievous neurodegenerative disorder and a major form of senile dementia, which is partially caused by abnormal amyloid-beta peptide deposition and Tau protein phosphorylation. But until now, the exact pathogenesis of AD and its treatment strategy still need to investigate. Fortunately, natural products have shown potential as therapeutic agents for treating symptoms of AD due to their neuroprotective activity. To identify the excellent lead compounds for AD control from natural products of herbal medicines, as well as, detect their modes of action, suitable animal models are required. Drosophila melanogaster (fruit fly) is an important model for studying genetic and cellular biological pathways in complex biological processes. Various Drosophila AD models were broadly used for AD research, especially for the discovery of neuroprotective natural products. This review focused on the research progress of natural products in AD disease based on the fruit fly AD model, which provides a reference for using the invertebrate model in developing novel anti-AD drugs.
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Affiliation(s)
- Mengdi Wu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Ying Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yaodong Miao
- Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Huanhuan Qiao
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Yiwen Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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27
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Cavigliasso F, Savary L, Spangenberg JE, Gallart-Ayala H, Ivanisevic J, Kawecki TJ. Experimental evolution of metabolism under nutrient restriction: enhanced amino acid catabolism and a key role of branched-chain amino acids. Evol Lett 2023; 7:273-284. [PMID: 37475747 PMCID: PMC10355184 DOI: 10.1093/evlett/qrad018] [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: 02/06/2023] [Revised: 04/04/2023] [Accepted: 04/24/2023] [Indexed: 07/22/2023] Open
Abstract
Periodic food shortage is a common ecological stressor for animals, likely to drive physiological and metabolic adaptations to alleviate its consequences, particularly for juveniles that have no option but to continue to grow and develop despite undernutrition. Here we study changes in metabolism associated with adaptation to nutrient shortage, evolved by replicate Drosophila melanogaster populations maintained on a nutrient-poor larval diet for over 240 generations. In a factorial metabolomics experiment we showed that both phenotypic plasticity and genetically-based adaptation to the poor diet involved wide-ranging changes in metabolite abundance; however, the plastic response did not predict the evolutionary change. Compared to nonadapted larvae exposed to the poor diet for the first time, the adapted larvae showed lower levels of multiple free amino acids in their tissues-and yet they grew faster. By quantifying accumulation of the nitrogen stable isotope 15N we show that adaptation to the poor diet led to an increased use of amino acids for energy generation. This apparent "waste" of scarce amino acids likely results from the trade-off between acquisition of dietary amino acids and carbohydrates observed in these populations. The three branched-chain amino acids (leucine, isoleucine, and valine) showed a unique pattern of depletion in adapted larvae raised on the poor diet. A diet supplementation experiment demonstrated that these amino acids are limiting for growth on the poor diet, suggesting that their low levels resulted from their expeditious use for protein synthesis. These results demonstrate that selection driven by nutrient shortage not only promotes improved acquisition of limiting nutrients, but also has wide-ranging effects on how the nutrients are used. They also show that the abundance of free amino acids in the tissues does not, in general, reflect the nutritional condition and growth potential of an animal.
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Affiliation(s)
- Fanny Cavigliasso
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Loriane Savary
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jorge E Spangenberg
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Hector Gallart-Ayala
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Julijana Ivanisevic
- Metabolomics Unit, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tadeusz J Kawecki
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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28
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Watanabe K, Wilmanski T, Baloni P, Robinson M, Garcia GG, Hoopmann MR, Midha MK, Baxter DH, Maes M, Morrone SR, Crebs KM, Kapil C, Kusebauch U, Wiedrick J, Lapidus J, Pflieger L, Lausted C, Roach JC, Glusman G, Cummings SR, Schork NJ, Price ND, Hood L, Miller RA, Moritz RL, Rappaport N. Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers. Commun Biol 2023; 6:768. [PMID: 37481675 PMCID: PMC10363145 DOI: 10.1038/s42003-023-05128-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/10/2023] [Indexed: 07/24/2023] Open
Abstract
Aging manifests as progressive deteriorations in homeostasis, requiring systems-level perspectives to investigate the gradual molecular dysregulation of underlying biological processes. Here, we report systemic changes in the molecular regulation of biological processes under multiple lifespan-extending interventions. Differential Rank Conservation (DIRAC) analyses of mouse liver proteomics and transcriptomics data show that mechanistically distinct lifespan-extending interventions (acarbose, 17α-estradiol, rapamycin, and calorie restriction) generally tighten the regulation of biological modules. These tightening patterns are similar across the interventions, particularly in processes such as fatty acid oxidation, immune response, and stress response. Differences in DIRAC patterns between proteins and transcripts highlight specific modules which may be tightened via augmented cap-independent translation. Moreover, the systemic shifts in fatty acid metabolism are supported through integrated analysis of liver transcriptomics data with a mouse genome-scale metabolic model. Our findings highlight the power of systems-level approaches for identifying and characterizing the biological processes involved in aging and longevity.
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Affiliation(s)
| | | | - Priyanka Baloni
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Gonzalo G Garcia
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | | | | | - Michal Maes
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Charu Kapil
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Jack Wiedrick
- Oregon Health and Science University, Portland, OR, USA
| | - Jodi Lapidus
- Oregon Health and Science University, Portland, OR, USA
| | - Lance Pflieger
- Institute for Systems Biology, Seattle, WA, USA
- Phenome Health, Seattle, WA, USA
| | | | | | | | - Steven R Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Nicholas J Schork
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
- Department of Population Sciences and Molecular and Cell Biology, The City of Hope National Medical Center, Duarte, CA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA.
- Phenome Health, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
| | - Richard A Miller
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- University of Michigan Geriatrics Center, Ann Arbor, MI, USA
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29
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Silva N, Rajado AT, Esteves F, Brito D, Apolónio J, Roberto VP, Binnie A, Araújo I, Nóbrega C, Bragança J, Castelo-Branco P, Andrade RP, Calado S, Faleiro ML, Matos C, Marques N, Marreiros A, Nzwalo H, Pais S, Palmeirim I, Simão S, Joaquim N, Miranda R, Pêgas A, Sardo A. Measuring healthy ageing: current and future tools. Biogerontology 2023. [DOI: https:/doi.org/10.1007/s10522-023-10041-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 09/01/2023]
Abstract
AbstractHuman ageing is a complex, multifactorial process characterised by physiological damage, increased risk of age-related diseases and inevitable functional deterioration. As the population of the world grows older, placing significant strain on social and healthcare resources, there is a growing need to identify reliable and easy-to-employ markers of healthy ageing for early detection of ageing trajectories and disease risk. Such markers would allow for the targeted implementation of strategies or treatments that can lessen suffering, disability, and dependence in old age. In this review, we summarise the healthy ageing scores reported in the literature, with a focus on the past 5 years, and compare and contrast the variables employed. The use of approaches to determine biological age, molecular biomarkers, ageing trajectories, and multi-omics ageing scores are reviewed. We conclude that the ideal healthy ageing score is multisystemic and able to encompass all of the potential alterations associated with ageing. It should also be longitudinal and able to accurately predict ageing complications at an early stage in order to maximize the chances of successful early intervention.
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30
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Kastury N, Hidalgo V, Pandi B, Li L, Lam MPY, Lau E. Senescence in human AC16 cardiac cells is associated with thymidine kinase induction and histone loss. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000865. [PMID: 37456137 PMCID: PMC10346100 DOI: 10.17912/micropub.biology.000865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
AC16 cells are a transformed human cardiac cell line commonly used to study cardiomyocyte biology. We show that reduced proliferation and senescence markers can be robustly induced in AC16 cells cultured in low serum condition and treated with (i) low-dose doxorubicin, (ii) UV 254 nm, or (iii) H 2 O 2 exposure for up to 48 hours. Increased p21 (CDKN1A) and H2A.X variant histone (H2AX) levels serve as reliable molecular markers upon all three treatment conditions, but the up-regulation of another common senescence marker, p16 (CDKN2A) was not observed. A proteomics screen further shows that the loss of histones and the increased expression of thymidine kinases (TK1) are prominent features of AC16 cells under doxorubicin induced senescence.
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Affiliation(s)
- Nikhitha Kastury
- Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Veronica Hidalgo
- Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Boomathi Pandi
- Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Lauren Li
- Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Maggie P. Y. Lam
- Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Edward Lau
- Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
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31
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Kahraman C, Kaya Bilecenoglu D, Sabuncuoglu S, Cankaya IT. Toxicology of pharmaceutical and nutritional longevity compounds. Expert Rev Mol Med 2023; 25:e28. [PMID: 37345424 PMCID: PMC10752229 DOI: 10.1017/erm.2023.18] [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: 07/30/2022] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/23/2023]
Abstract
Aging is the most prominent risk factor for many diseases, which is considered to be a complicated biological process. The rate of aging depends on the effectiveness of important mechanisms such as the protection of DNA from free radicals, which protects the structural and functional integrity of cells and tissues. In any organism, not all organs may age at the same rate. Slowing down primary aging and reaching maximum lifespan is the most basic necessity. In this process, it may be possible to slow down or stabilise some diseases by using the compounds for both dietary and pharmacological purposes. Natural compounds with antioxidant and anti-inflammatory effects, mostly plant-based nutraceuticals, are preferred in the treatment of age-related chronic diseases and can also be used for other diseases. An increasing number of long-term studies on synthetic and natural compounds aim to elucidate preclinically and clinically the mechanisms underlying being healthy and prolongation of life. To delay age-related diseases and prolong the lifespan, it is necessary to take these compounds with diet or pharmaceuticals, along with detailed toxicological results. In this review, the most promising and utilised compounds will be highlighted and it will be discussed whether they have toxic effects in short/long-term use, although they are thought to be used safely.
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Affiliation(s)
- Cigdem Kahraman
- Department of Pharmacognosy, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
| | | | - Suna Sabuncuoglu
- Department of Pharmaceutical Toxicology, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
| | - Irem Tatli Cankaya
- Department of Pharmaceutical Botany, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
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32
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Advani J, Corso-Diaz X, Kwicklis M, van Asten F, Ratnapriya R, Mehta P, Hamel A, Mahrotra S, Segrè A, Kiel C, Strunz T, Weber B, Chew E, Hernandez D, Montezuma S, Ferrington D, Swaroop A. QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration. RESEARCH SQUARE 2023:rs.3.rs-3011096. [PMID: 37398472 PMCID: PMC10312909 DOI: 10.21203/rs.3.rs-3011096/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
DNA methylation (DNAm) provides a crucial epigenetic mark linking genetic variations to environmental influence. We analyzed array-based DNAm profiles of 160 human retinas with co-measured RNA-seq and > 8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 mQTLs and 12,505 eQTLs) and 13,747 eQTMs (DNAm loci affecting gene expression), with over one-third specific to the retina. mQTLs and eQTMs show non-random distribution and enrichment of biological processes related to synapse, mitochondria, and catabolism. Summary data-based Mendelian randomization and colocalization analyses identify 87 target genes where methylation and gene-expression changes likely mediate the genotype effect on age-related macular degeneration (AMD). Integrated pathway analysis reveals epigenetic regulation of immune response and metabolism including the glutathione pathway and glycolysis. Our study thus defines key roles of genetic variations driving methylation changes, prioritizes epigenetic control of gene expression, and suggests frameworks for regulation of AMD pathology by genotype-environment interaction in retina.
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Affiliation(s)
| | | | | | | | | | - Puja Mehta
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Andrew Hamel
- Department of Ophthalmology, Massachusetts Eye and Ear
| | | | | | | | | | | | - Emily Chew
- National Eye Institute/National Institutes of Health
| | | | | | | | - Anand Swaroop
- National Eye Institute, National Institutes of Health
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33
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Xu Y, Gomez-Pinedo U, Liu J, Hong D, Xu J. Editorial: Current advances in genetic presentations of dementia and aging, volume II. Front Aging Neurosci 2023; 15:1202532. [PMID: 37323143 PMCID: PMC10264766 DOI: 10.3389/fnagi.2023.1202532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Affiliation(s)
- Yuzhen Xu
- Department of Rehabilitation, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
| | - Ulises Gomez-Pinedo
- Laboratory of Neurobiology, Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - Jun Liu
- Department of Neurology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Daojun Hong
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Xu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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34
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Jacome Burbano MS, Robin JD, Bauwens S, Martin M, Donati E, Martínez L, Lin P, Sacconi S, Magdinier F, Gilson E. Non-canonical telomere protection role of FOXO3a of human skeletal muscle cells regulated by the TRF2-redox axis. Commun Biol 2023; 6:561. [PMID: 37231173 DOI: 10.1038/s42003-023-04903-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 05/02/2023] [Indexed: 05/27/2023] Open
Abstract
Telomeric repeat binding factor 2 (TRF2) binds to telomeres and protects chromosome ends against the DNA damage response and senescence. Although the expression of TRF2 is downregulated upon cellular senescence and in various aging tissues, including skeletal muscle tissues, very little is known about the contribution of this decline to aging. We previously showed that TRF2 loss in myofibers does not trigger telomere deprotection but mitochondrial dysfunction leading to an increased level of reactive oxygen species. We show here that this oxidative stress triggers the binding of FOXO3a to telomeres where it protects against ATM activation, revealing a previously unrecognized telomere protective function of FOXO3a, to the best of our knowledge. We further showed in transformed fibroblasts and myotubes that the telomere properties of FOXO3a are dependent on the C-terminal segment of its CR2 domain (CR2C) but independent of its Forkhead DNA binding domain and of its CR3 transactivation domain. We propose that these non-canonical properties of FOXO3a at telomeres play a role downstream of the mitochondrial signaling induced by TRF2 downregulation to regulate skeletal muscle homeostasis and aging.
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Affiliation(s)
| | - Jérôme D Robin
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Faculté de médecine Nice, Nice, France
| | - Serge Bauwens
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Faculté de médecine Nice, Nice, France
| | - Marjorie Martin
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Faculté de médecine Nice, Nice, France
| | - Emma Donati
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Faculté de médecine Nice, Nice, France
| | - Lucia Martínez
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Faculté de médecine Nice, Nice, France
| | - Peipei Lin
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Faculté de médecine Nice, Nice, France
- Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, International Research Project in Hematology, Cancer and Aging, RuiJin Hospital, Shanghai Jiao Tong University School, Shanghai, China
| | - Sabrina Sacconi
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Faculté de médecine Nice, Nice, France
- Peripheral Nervous System, Muscle and ALS, Neuromuscular & ALS Center of Reference, FHU Oncoage, Nice University Hospital, Pasteur 2, Nice, France
| | | | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Faculté de médecine Nice, Nice, France.
- Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
- Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, International Research Project in Hematology, Cancer and Aging, RuiJin Hospital, Shanghai Jiao Tong University School, Shanghai, China.
- Department of Genetics, CHU; FHU OncoAge, Nice, France.
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35
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Zhang L, Park JJ, Dong MB, Arsala D, Xia S, Chen J, Sosa D, Atlas JE, Long M, Chen S. Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system. Genome Biol Evol 2023; 15:evad081. [PMID: 37170918 PMCID: PMC10210621 DOI: 10.1093/gbe/evad081] [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: 09/28/2022] [Revised: 04/24/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
T cells are a type of white blood cell that play a critical role in the immune response against foreign pathogens through a process called T Cell Adaptive Immunity (TCAI). However, the evolution of the genes and nucleotide sequences involved in TCAI is not well understood. To investigate this, we performed comparative studies of gene annotations and genome assemblies of 28 vertebrate species and identified sets of human genes that are involved in TCAI, carcinogenesis, and ageing. We found that these gene sets share interaction pathways which may have contributed to the evolution of longevity in the vertebrate lineage leading to humans. Our human gene age dating analyses revealed that there was rapid origination of genes with TCAI-related functions prior to the Cretaceous eutherian radiation and these new genes mainly encode negative regulators. We identified no new TCAI-related genes after the divergence of placental mammals, but we did detect an extensive number of amino acid substitutions under strong positive selection in recently evolved human immunity genes suggesting they are co-evolving with adaptive immunity. More specifically, we observed that antigen processing and presentation and checkpoint genes are significantly enriched among new genes evolving under positive selection. These observations reveal an evolutionary process of T Cell Adaptive Immunity that were associated with rapid gene duplication in the early stages of vertebrates and subsequent sequence changes in TCAI-related genes. These processes together suggest an early genetic construction of the vertebrate immune system and subsequent molecular adaptation to diverse antigens.
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Affiliation(s)
- Li Zhang
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
| | - Jonathan J Park
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
| | - Matthew B Dong
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
- Immunobiology Program, The Anlyan Center, New Haven, Connecticut, USA
- Department of Immunobiology, The Anlyan Center, New Haven, Connecticut, USA
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Jianhai Chen
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Jared E Atlas
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Sidi Chen
- System Biology Institute, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, Connecticut, USA
- Yale M.D.-Ph.D. Program, New Haven, Connecticut, USA
- Immunobiology Program, The Anlyan Center, New Haven, Connecticut, USA
- Yale Comprehensive Cancer Center, New Haven, Connecticut, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
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36
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Yamada S, Ko T, Ito M, Sassa T, Nomura S, Okuma H, Sato M, Imasaki T, Kikkawa S, Zhang B, Yamada T, Seki Y, Fujita K, Katoh M, Kubota M, Hatsuse S, Katagiri M, Hayashi H, Hamano M, Takeda N, Morita H, Takada S, Toyoda M, Uchiyama M, Ikeuchi M, Toyooka K, Umezawa A, Yamanishi Y, Nitta R, Aburatani H, Komuro I. TEAD1 trapping by the Q353R-Lamin A/C causes dilated cardiomyopathy. SCIENCE ADVANCES 2023; 9:eade7047. [PMID: 37058558 PMCID: PMC10104473 DOI: 10.1126/sciadv.ade7047] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Mutations in the LMNA gene encoding Lamin A and C (Lamin A/C), major components of the nuclear lamina, cause laminopathies including dilated cardiomyopathy (DCM), but the underlying molecular mechanisms have not been fully elucidated. Here, by leveraging single-cell RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), protein array, and electron microscopy analysis, we show that insufficient structural maturation of cardiomyocytes owing to trapping of transcription factor TEA domain transcription factor 1 (TEAD1) by mutant Lamin A/C at the nuclear membrane underlies the pathogenesis of Q353R-LMNA-related DCM. Inhibition of the Hippo pathway rescued the dysregulation of cardiac developmental genes by TEAD1 in LMNA mutant cardiomyocytes. Single-cell RNA-seq of cardiac tissues from patients with DCM with the LMNA mutation confirmed the dysregulated expression of TEAD1 target genes. Our results propose an intervention for transcriptional dysregulation as a potential treatment of LMNA-related DCM.
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Affiliation(s)
- Shintaro Yamada
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Toshiyuki Ko
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masamichi Ito
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Advanced Clinical Science and Therapeutics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tatsuro Sassa
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Seitaro Nomura
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiromichi Okuma
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Tsuyoshi Imasaki
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Satoshi Kikkawa
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Bo Zhang
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Takanobu Yamada
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Yuka Seki
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kanna Fujita
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Manami Katoh
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Masayuki Kubota
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Hatsuse
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mikako Katagiri
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiromu Hayashi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Momoko Hamano
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Norifumi Takeda
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Morita
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Tokyo 157-8535, Japan
| | - Masashi Toyoda
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Tokyo 157-8535, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masashi Ikeuchi
- Division of Biofunctional Restoration, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Setagaya-ku, Tokyo 157-8535, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Ryo Nitta
- Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Meguro-ku, Tokyo 153-8904, Japan
| | - Issei Komuro
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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37
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Balmorez T, Sakazaki A, Murakami S. Genetic Networks of Alzheimer's Disease, Aging, and Longevity in Humans. Int J Mol Sci 2023; 24:ijms24065178. [PMID: 36982253 PMCID: PMC10049434 DOI: 10.3390/ijms24065178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 03/30/2023] Open
Abstract
Human genomic analysis and genome-wide association studies (GWAS) have identified genes that are risk factors for early and late-onset Alzheimer's disease (AD genes). Although the genetics of aging and longevity have been extensively studied, previous studies have focused on a specific set of genes that have been shown to contribute to or are a risk factor for AD. Thus, the connections among the genes involved in AD, aging, and longevity are not well understood. Here, we identified the genetic interaction networks (referred to as pathways) of aging and longevity within the context of AD by using a gene set enrichment analysis by Reactome that cross-references more than 100 bioinformatic databases to allow interpretation of the biological functions of gene sets through a wide variety of gene networks. We validated the pathways with a threshold of p-value < 1.00 × 10-5 using the databases to extract lists of 356 AD genes, 307 aging-related (AR) genes, and 357 longevity genes. There was a broad range of biological pathways involved in AR and longevity genes shared with AD genes. AR genes identified 261 pathways within the threshold of p < 1.00 × 10-5, of which 26 pathways (10% of AR gene pathways) were further identified by overlapping genes among AD and AR genes. The overlapped pathways included gene expression (p = 4.05 × 10-11) including ApoE, SOD2, TP53, and TGFB1 (p = 2.84 × 10-10); protein metabolism and SUMOylation, including E3 ligases and target proteins (p = 1.08 × 10-7); ERBB4 signal transduction (p = 2.69 × 10-6); the immune system, including IL-3 and IL-13 (p = 3.83 × 10-6); programmed cell death (p = 4.36 × 10-6); and platelet degranulation (p = 8.16 × 10-6), among others. Longevity genes identified 49 pathways within the threshold, of which 12 pathways (24% of longevity gene pathways) were further identified by overlapping genes among AD and longevity genes. They include the immune system, including IL-3 and IL-13 (p = 7.64 × 10-8), plasma lipoprotein assembly, remodeling and clearance (p < 4.02 × 10-6), and the metabolism of fat-soluble vitamins (p = 1.96 × 10-5). Thus, this study provides shared genetic hallmarks of aging, longevity, and AD backed up by statistical significance. We discuss the significant genes involved in these pathways, including TP53, FOXO, SUMOylation, IL4, IL6, APOE, and CEPT, and suggest that mapping the gene network pathways provide a useful basis for further medical research on AD and healthy aging.
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Affiliation(s)
- Timothy Balmorez
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, USA
| | - Amy Sakazaki
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, USA
| | - Shin Murakami
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University California, Vallejo, CA 94592, USA
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38
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LaLonde-Paul D, Mouttham L, Promislow DEL, Castelhano MG. Banking on a new understanding: translational opportunities from veterinary biobanks. GeroScience 2023:10.1007/s11357-023-00763-z. [PMID: 36890420 PMCID: PMC10400517 DOI: 10.1007/s11357-023-00763-z] [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: 05/25/2022] [Accepted: 01/03/2023] [Indexed: 03/10/2023] Open
Abstract
Current advances in geroscience are due in part to the discovery of biomarkers with high predictive ability in short-lived laboratory animals such as flies and mice. These model species, however, do not always adequately reflect human physiology and disease, highlighting the need for a more comprehensive and relevant model of human aging. Domestic dogs offer a solution to this obstacle, as they share many aspects not only of the physiological and pathological trajectories of their human counterpart, but also of their environment. Furthermore, they age at a considerably faster rate. Studying aging in the companion dog provides an opportunity to better understand the biological and environmental determinants of healthy lifespan in our pets, and to translate those findings to human aging. Biobanking, the systematic collection, processing, storage, and distribution of biological material and associated data has contributed to basic, clinical, and translational research by streamlining the management of high-quality biospecimens for biomarker discovery and validation. In this review, we discuss how veterinary biobanks can support research on aging, particularly when integrated into large-scale longitudinal studies. As an example of this concept, we introduce the Dog Aging Project Biobank.
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Affiliation(s)
- D LaLonde-Paul
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - L Mouttham
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - D E L Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - M G Castelhano
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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39
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Johnson AA, Cuellar TL. Glycine and aging: Evidence and mechanisms. Ageing Res Rev 2023; 87:101922. [PMID: 37004845 DOI: 10.1016/j.arr.2023.101922] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023]
Abstract
The restriction of calories, branched-chain amino acids, and methionine have all been shown to extend lifespan in model organisms. Recently, glycine was shown to significantly boost longevity in genetically heterogenous mice. This simple amino acid similarly extends lifespan in rats and improves health in mammalian models of age-related disease. While compelling data indicate that glycine is a pro-longevity molecule, divergent mechanisms may underlie its effects on aging. Glycine is abundant in collagen, a building block for glutathione, a precursor to creatine, and an acceptor for the enzyme Glycine N-methyltransferase (GNMT). A review of the literature strongly implicates GNMT, which clears methionine from the body by taking a methyl group from S-adenosyl-L-methionine and methylating glycine to form sarcosine. In flies, Gnmt is required for reduced insulin/insulin-like growth factor 1 signaling and caloric restriction to fully extend lifespan. The geroprotector spermidine requires Gnmt to upregulate autophagy genes and boost longevity. Moreover, the overexpression of Gnmt is sufficient to extend lifespan and reduce methionine levels. Sarcosine, or methylglycine, declines with age in multiple species and is capable of inducing autophagy both in vitro and in vivo. Taken all together, existing evidence suggests that glycine prolongs life by mimicking methionine restriction and activating autophagy.
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40
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Ung CY, Correia C, Billadeau DD, Zhu S, Li H. Manifold epigenetics: A conceptual model that guides engineering strategies to improve whole-body regenerative health. Front Cell Dev Biol 2023; 11:1122422. [PMID: 36866271 PMCID: PMC9971008 DOI: 10.3389/fcell.2023.1122422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Despite the promising advances in regenerative medicine, there is a critical need for improved therapies. For example, delaying aging and improving healthspan is an imminent societal challenge. Our ability to identify biological cues as well as communications between cells and organs are keys to enhance regenerative health and improve patient care. Epigenetics represents one of the major biological mechanisms involving in tissue regeneration, and therefore can be viewed as a systemic (body-wide) control. However, how epigenetic regulations concertedly lead to the development of biological memories at the whole-body level remains unclear. Here, we review the evolving definitions of epigenetics and identify missing links. We then propose our Manifold Epigenetic Model (MEMo) as a conceptual framework to explain how epigenetic memory arises and discuss what strategies can be applied to manipulate the body-wide memory. In summary we provide a conceptual roadmap for the development of new engineering approaches to improve regenerative health.
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Affiliation(s)
- Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | | | - Shizhen Zhu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States,*Correspondence: Shizhen Zhu, ; Hu Li,
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States,*Correspondence: Shizhen Zhu, ; Hu Li,
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41
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Yang BA, Larouche JA, Sabin KM, Fraczek PM, Parker SCJ, Aguilar CA. Three-dimensional chromatin re-organization during muscle stem cell aging. Aging Cell 2023; 22:e13789. [PMID: 36727578 PMCID: PMC10086523 DOI: 10.1111/acel.13789] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world's population continues to increase. The regeneration of damaged skeletal muscle is mediated by muscle stem cells, but in old age muscle stem cells become functionally attenuated. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.
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Affiliation(s)
- Benjamin A Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Jacqueline A Larouche
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Kaitlyn M Sabin
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Paula M Fraczek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephen C J Parker
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
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42
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Zhang J, Wang S, Liu B. New Insights into the Genetics and Epigenetics of Aging Plasticity. Genes (Basel) 2023; 14:genes14020329. [PMID: 36833255 PMCID: PMC9956228 DOI: 10.3390/genes14020329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/14/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Biological aging is characterized by irreversible cell cycle blockade, a decreased capacity for tissue regeneration, and an increased risk of age-related diseases and mortality. A variety of genetic and epigenetic factors regulate aging, including the abnormal expression of aging-related genes, increased DNA methylation levels, altered histone modifications, and unbalanced protein translation homeostasis. The epitranscriptome is also closely associated with aging. Aging is regulated by both genetic and epigenetic factors, with significant variability, heterogeneity, and plasticity. Understanding the complex genetic and epigenetic mechanisms of aging will aid the identification of aging-related markers, which may in turn aid the development of effective interventions against this process. This review summarizes the latest research in the field of aging from a genetic and epigenetic perspective. We analyze the relationships between aging-related genes, examine the possibility of reversing the aging process by altering epigenetic age.
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Affiliation(s)
- Jie Zhang
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), School of Basic Medical Sciences, Shenzhen University, Shenzhen 518000, China
| | - Shixiao Wang
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), School of Basic Medical Sciences, Shenzhen University, Shenzhen 518000, China
| | - Baohua Liu
- Shenzhen Key Laboratory for Systemic Aging and Intervention (SKL-SAI), School of Basic Medical Sciences, Shenzhen University, Shenzhen 518000, China
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, School of Basic Medical Sciences, Medical School, Lihu Campus, Shenzhen University, Shenzhen 518000, China
- Correspondence: ; Tel.: +86-75586674609
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43
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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: 1214] [Impact Index Per Article: 1214.0] [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.
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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.
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44
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Treaster S, Deelen J, Daane JM, Murabito J, Karasik D, Harris MP. Convergent genomics of longevity in rockfishes highlights the genetics of human life span variation. SCIENCE ADVANCES 2023; 9:eadd2743. [PMID: 36630509 PMCID: PMC9833670 DOI: 10.1126/sciadv.add2743] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 12/09/2022] [Indexed: 05/16/2023]
Abstract
Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, which range in longevity from 11 to over 205 years. Multiple shifts in rockfish longevity have occurred independently and in a short evolutionary time frame, thus empowering convergence analyses. Our analyses reveal a common network of genes under convergent evolution, encompassing established aging regulators such as insulin signaling, yet also identify flavonoid (aryl-hydrocarbon) metabolism as a pathway modulating longevity. The selective pressures on these pathways indicate the ancestral state of rockfishes was long lived and that the changes in short-lived lineages are adaptive. These pathways were also used to explore genome-wide association studies of human longevity, identifying the aryl-hydrocarbon metabolism pathway to be significantly associated with human survival to the 99th percentile. This evolutionary intersection defines and cross-validates a previously unappreciated genetic architecture that associates with the evolution of longevity across vertebrates.
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Affiliation(s)
- Stephen Treaster
- Department of Orthopaedic Surgery, Boston Children’s Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joris Deelen
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Köln, Germany
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, Netherlands
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Jacob M. Daane
- Department of Biology and Biochemistry, University of Houston, Houston TX, USA
| | - Joanne Murabito
- Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Marcus Institute for Aging Research, Hebrew Senior Life, Boston, MA, USA
| | - Matthew P. Harris
- Department of Orthopaedic Surgery, Boston Children’s Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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45
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Xu W, Luo Y, Yin J, Huang M, Luo F. Targeting AMPK signaling by polyphenols: a novel strategy for tackling aging. Food Funct 2023; 14:56-73. [PMID: 36524530 DOI: 10.1039/d2fo02688k] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aging is an inevitable biological process and is accompanied by a gradual decline of physiological functions, such as the incidence of age-related diseases. Aging becomes a major burden and challenge for society to prevent or delay the occurrence and development of these age-related diseases. AMPK is a key regulator of intracellular energy and participates in the adaptation of calorie restriction. It is also an important mediator of nutritionally sensitive pathways that regulate the biological effects of nutrient active ingredients. AMPK can limit proliferation and activate autophagy. Recent studies have shown that nutritional intervention can delay aging and lessen age-related diseases in many animal and even human models. Polyphenols function as a natural antidote and are important anti-inflammatory and antioxidant agents in human diets. Polyphenols can prevent age-related diseases because they regulate complex networks of cellular processes such as oxidative damage, inflammation, cellular aging, and autophagy, and have also attracted wide attention as a potential beneficial substance for longevity. In this review, we systemically summarized the progress of targeting AMPK signaling by dietary polyphenols in aging prevention. Polyphenols can reduce oxidative stress and inflammatory response, and maintain the steady state of energy. Polyphenols can also modulate sirtuins/NAD+, nutrient-sensing, proteostasis, mitochondrial function, autophagy and senescence via targeting AMPK signaling. Therefore, targeting the AMPK signaling pathway by dietary polyphenols may be a novel anti-aging strategy.
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Affiliation(s)
- Wei Xu
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha, Hunan 410004, China. .,Hunan Food and Drug Vocational College, Department of Food Science and Engineering, Changsha, Hunan 410208, China
| | - Yi Luo
- Department of Clinic Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Jiaxin Yin
- Hunan Food and Drug Vocational College, Department of Food Science and Engineering, Changsha, Hunan 410208, China
| | - Mengzhen Huang
- Hunan Food and Drug Vocational College, Department of Food Science and Engineering, Changsha, Hunan 410208, China
| | - Feijun Luo
- Hunan Key Laboratory of Grain-oil Deep Process and Quality Control, Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Central South University of Forestry and Technology, Changsha, Hunan 410004, China.
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46
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López-Otín C, Pietrocola F, Roiz-Valle D, Galluzzi L, Kroemer G. Meta-hallmarks of aging and cancer. Cell Metab 2023; 35:12-35. [PMID: 36599298 DOI: 10.1016/j.cmet.2022.11.001] [Citation(s) in RCA: 104] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 11/07/2022] [Indexed: 01/05/2023]
Abstract
Both aging and cancer are characterized by a series of partially overlapping "hallmarks" that we subject here to a meta-analysis. Several hallmarks of aging (i.e., genomic instability, epigenetic alterations, chronic inflammation, and dysbiosis) are very similar to specific cancer hallmarks and hence constitute common "meta-hallmarks," while other features of aging (i.e., telomere attrition and stem cell exhaustion) act likely to suppress oncogenesis and hence can be viewed as preponderantly "antagonistic hallmarks." Disabled macroautophagy and cellular senescence are two hallmarks of aging that exert context-dependent oncosuppressive and pro-tumorigenic effects. Similarly, the equivalence or antagonism between aging-associated deregulated nutrient-sensing and cancer-relevant alterations of cellular metabolism is complex. The agonistic and antagonistic relationship between the processes that drive aging and cancer has bearings for the age-related increase and oldest age-related decrease of cancer morbidity and mortality, as well as for the therapeutic management of malignant disease in the elderly.
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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.
| | - Federico Pietrocola
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - David Roiz-Valle
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA; Sandra and Edward Meyer Cancer Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris Cité, 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.
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47
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Marino N, Putignano G, Cappilli S, Chersoni E, Santuccione A, Calabrese G, Bischof E, Vanhaelen Q, Zhavoronkov A, Scarano B, Mazzotta AD, Santus E. Towards AI-driven longevity research: An overview. FRONTIERS IN AGING 2023; 4:1057204. [PMID: 36936271 PMCID: PMC10018490 DOI: 10.3389/fragi.2023.1057204] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023]
Abstract
While in the past technology has mostly been utilized to store information about the structural configuration of proteins and molecules for research and medical purposes, Artificial Intelligence is nowadays able to learn from the existing data how to predict and model properties and interactions, revealing important knowledge about complex biological processes, such as aging. Modern technologies, moreover, can rely on a broader set of information, including those derived from the next-generation sequencing (e.g., proteomics, lipidomics, and other omics), to understand the interactions between human body and the external environment. This is especially relevant as external factors have been shown to have a key role in aging. As the field of computational systems biology keeps improving and new biomarkers of aging are being developed, artificial intelligence promises to become a major ally of aging research.
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Affiliation(s)
- Nicola Marino
- Women’s Brain Project (WBP), Gunterhausen, Switzerland
- *Correspondence: Nicola Marino,
| | | | - Simone Cappilli
- Dermatology, Catholic University of the Sacred Heart, Rome, Italy
- UOC of Dermatology, Department of Abdominal and Endocrine Metabolic Medical and Surgical Sciences, A. Gemelli University Hospital Foundation-IRCCS, Rome, Italy
| | - Emmanuele Chersoni
- Department of Chinese and Bilingual Studies, The Hong Kong Polytechnic University, Hong Kong, China
| | | | - Giuliana Calabrese
- Department of Translational Medicine and Surgery, CatholicUniversity of the Sacred Heart, Rome, Italy
| | - Evelyne Bischof
- Insilico Medicine Hong Kong Ltd., New Territories, Hong Kong SAR, China
| | - Quentin Vanhaelen
- Insilico Medicine Hong Kong Ltd., New Territories, Hong Kong SAR, China
| | - Alex Zhavoronkov
- Insilico Medicine Hong Kong Ltd., New Territories, Hong Kong SAR, China
| | - Bryan Scarano
- Department of Translational Medicine and Surgery, CatholicUniversity of the Sacred Heart, Rome, Italy
| | - Alessandro D. Mazzotta
- Department of Digestive, Oncological and Metabolic Surgery, Institute Mutualiste Montsouris, Paris, France
- Biorobotics Institute, Scuola Superiore Sant’anna, Pisa, Italy
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48
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Chang ZS, He ZM, Xia JB. FoxO3 Regulates the Progress and Development of Aging and Aging-Related Diseases. Curr Mol Med 2023; 23:991-1006. [PMID: 36239722 DOI: 10.2174/1566524023666221014140817] [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: 06/20/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/22/2022]
Abstract
Aging is an inevitable risk factor for many diseases, including cardiovascular diseases, neurodegenerative diseases, cancer, and diabetes. Investigation into the molecular mechanisms involved in aging and longevity will benefit the treatment of age-dependent diseases and the development of preventative medicine for agingrelated diseases. Current evidence has revealed that FoxO3, encoding the transcription factor (FoxO)3, a key transcription factor that integrates different stimuli in the intrinsic and extrinsic pathways and is involved in cell differentiation, protein homeostasis, stress resistance and stem cell status, plays a regulatory role in longevity and in age-related diseases. However, the precise mechanisms by which the FoxO3 transcription factor modulates aging and promotes longevity have been unclear until now. Here, we provide a brief overview of the mechanisms by which FoxO3 mediates signaling in pathways involved in aging and aging-related diseases, as well as the current knowledge on the role of the FoxO3 transcription factor in the human lifespan and its clinical prospects. Ultimately, we conclude that FoxO3 signaling pathways, including upstream and downstream molecules, may be underlying therapeutic targets in aging and age-related diseases.
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Affiliation(s)
- Zao-Shang Chang
- Department of Physiology, School of Basic Medical Sciences, Shaoyang University, Shaoyang 422000, Hunan, China
| | - Zhi-Ming He
- Department of Physiology, School of Basic Medical Sciences, Shaoyang University, Shaoyang 422000, Hunan, China
| | - Jing-Bo Xia
- Guangdong Provincial Key Laboratory of Physical Activity and Health Promotion, Guangzhou Sport University, Guangzhou 510500, Guangdong, China
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49
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Kunizheva SS, Volobaev VP, Plotnikova MY, Kupriyanova DA, Kuznetsova IL, Tyazhelova TV, Rogaev EI. Current Trends and Approaches to the Search for Genetic Determinants of Aging and Longevity. RUSS J GENET+ 2022; 58:1427-1443. [PMID: 36590179 PMCID: PMC9794410 DOI: 10.1134/s1022795422120067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/29/2022]
Abstract
Aging is a natural process of extinction of the body and the main aspect that determines the life expectancy for individuals who have survived to the post-reproductive period. The process of aging is accompanied by certain physiological, immune, and metabolic changes in the body, as well as the development of age-related diseases. The contribution of genetic factors to human life expectancy is estimated at about 25-30%. Despite the success in identifying genes and metabolic pathways that may be involved in the life extension process in model organisms, the key question remains to what extent these data can be extrapolated to humans, for example, because of the complexity of its biological and sociocultural systems, as well as possible species differences in life expectancy and causes of mortality. New molecular genetic methods have significantly expanded the possibilities for searching for genetic factors of human life expectancy and identifying metabolic pathways of aging, the interaction of genes and transcription factors, the regulation of gene expression at the level of transcription, and epigenetic modifications. The review presents the latest research and current strategies for studying the genetic basis of human aging and longevity: the study of individual candidate genes in genetic population studies, variations identified by the GWAS method, immunogenetic differences in aging, and genomic studies to identify factors of "healthy aging." Understanding the mechanisms of the interaction between factors affecting the life expectancy and the possibility of their regulation can become the basis for developing comprehensive measures to achieve healthy longevity. Supplementary Information The online version contains supplementary material available at 10.1134/S1022795422120067.
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Affiliation(s)
- S. S. Kunizheva
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
- Moscow State University, 119234 Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - V. P. Volobaev
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - M. Yu. Plotnikova
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
- Moscow State University, 119234 Moscow, Russia
| | - D. A. Kupriyanova
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - I. L. Kuznetsova
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - T. V. Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E. I. Rogaev
- Center for Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Sochi, Russia
- Moscow State University, 119234 Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
- University of Massachusetts Chan Medical School, 01545 Shrewsbury, MA United States
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Teulière J, Bernard C, Corel E, Lapointe FJ, Martens J, Lopez P, Bapteste E. Network analyses unveil ageing-associated pathways evolutionarily conserved from fungi to animals. GeroScience 2022; 45:1059-1080. [PMID: 36508078 PMCID: PMC9886728 DOI: 10.1007/s11357-022-00704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
The genetic roots of the diverse paces and shapes of ageing and of the large variations in longevity observed across the tree of life are poorly understood. Indeed, pathways associated with ageing/longevity are incompletely known, both in terms of their constitutive genes/proteins and of their molecular interactions. Moreover, there is limited overlap between the genes constituting these pathways across mammals. Yet, dedicated comparative analyses might still unravel evolutionarily conserved, important pathways associated with longevity or ageing. Here, we used an original strategy with a double evolutionary and systemic focus to analyse protein interactions associated with ageing or longevity during the evolution of five species of Opisthokonta. We ranked these proteins and interactions based on their evolutionary conservation and centrality in past and present protein-protein interaction (PPI) networks, providing a big systemic picture of the evolution of ageing and longevity pathways that identified which pathways emerged in which Opisthokonta lineages, were conserved, and/or central. We confirmed that longevity/ageing-associated proteins (LAPs), be they pro- or anti-longevity, are highly central in extant PPI, consistently with the antagonistic pleiotropy theory of ageing, and identified key antagonistic regulators of ageing/longevity, 52 of which with homologues in humans. While some highly central LAPs were evolutionarily conserved for over a billion years, we report a clear transition in the functionally important components of ageing/longevity within bilaterians. We also predicted 487 novel evolutionarily conserved LAPs in humans, 54% of which are more central than mTOR, and 138 of which are druggable, defining new potential targets for anti-ageing treatments in humans.
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Affiliation(s)
- Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Charles Bernard
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eduardo Corel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - François-Joseph Lapointe
- grid.14848.310000 0001 2292 3357Département de Sciences Biologiques, Complexe Des Sciences, Université de Montréal, Montréal, QC Canada
| | - Johannes Martens
- Sciences, Normes, Démocratie (SND), Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d’Histoire Naturelle, EPHE, Université Des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université Des Antilles, Paris, France.
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