1
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Martens DS, Lammertyn EJ, Goeminne PC, Colpaert K, Proesmans M, Vanaudenaerde BM, Nawrot TS, Dupont LJ. Leukocyte telomere length and attrition in association with disease severity in cystic fibrosis patients. Aging (Albany NY) 2024; 16:11809-11823. [PMID: 39213174 PMCID: PMC11386922 DOI: 10.18632/aging.206093] [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: 12/19/2023] [Accepted: 07/15/2024] [Indexed: 09/04/2024]
Abstract
Cystic fibrosis (CF) is characterized by chronic airway inflammation and premature aging. The link with leukocyte telomere length (LTL) as a marker of biological aging is unclear. We studied disease severity and LTL in 168 CF patients of which 85 patients had a second retrospective LTL assessment. A higher FEV1 was associated with longer LTL, with a stronger effect in men (5.08% longer LTL) compared to women (0.41% longer LTL). A higher FEV1/FVC ratio was associated with 7.05% (P=0.017) longer LTL in men. CF asthma, as defined by the treatment with inhaled corticosteroids, was associated with -6.65% shorter LTL (P=0.028). Men homozygous for the ΔF508 genotype showed a -10.48% (P=0.026) shorter LTL compared to heterozygotes. A genotype-specific non-linear association between LTL shortening and chronological age was observed. Stronger age-related LTL shortening was observed in patients homozygous for the ΔF508 genotype (P-interaction= 0.044). This work showed that disease severity in CF patients negatively influences LTL, with slightly more pronounced effects in men. The homozygous genotype for ΔF508 may play a role in LTL attrition in CF patients. Understanding factors in CF patients that accelerate biological aging provides insights into mechanisms that can extend the overall life quality in CF-diseased.
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Affiliation(s)
- Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Elise J Lammertyn
- Department of Chronic Diseases and Metabolism (CHROMETA), Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | | | - Kristine Colpaert
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Marijke Proesmans
- Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Flanders, Belgium
| | - Bart M Vanaudenaerde
- Department of Chronic Diseases and Metabolism (CHROMETA), Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Lieven J Dupont
- Department of Chronic Diseases and Metabolism (CHROMETA), Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven, Belgium
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
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2
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Castilho RM, Castilho LS, Palomares BH, Squarize CH. Determinants of Chromatin Organization in Aging and Cancer-Emerging Opportunities for Epigenetic Therapies and AI Technology. Genes (Basel) 2024; 15:710. [PMID: 38927646 PMCID: PMC11202709 DOI: 10.3390/genes15060710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
This review article critically examines the pivotal role of chromatin organization in gene regulation, cellular differentiation, disease progression and aging. It explores the dynamic between the euchromatin and heterochromatin, coded by a complex array of histone modifications that orchestrate essential cellular processes. We discuss the pathological impacts of chromatin state misregulation, particularly in cancer and accelerated aging conditions such as progeroid syndromes, and highlight the innovative role of epigenetic therapies and artificial intelligence (AI) in comprehending and harnessing the histone code toward personalized medicine. In the context of aging, this review explores the use of AI and advanced machine learning (ML) algorithms to parse vast biological datasets, leading to the development of predictive models for epigenetic modifications and providing a framework for understanding complex regulatory mechanisms, such as those governing cell identity genes. It supports innovative platforms like CEFCIG for high-accuracy predictions and tools like GridGO for tailored ChIP-Seq analysis, which are vital for deciphering the epigenetic landscape. The review also casts a vision on the prospects of AI and ML in oncology, particularly in the personalization of cancer therapy, including early diagnostics and treatment optimization for diseases like head and neck and colorectal cancers by harnessing computational methods, AI advancements and integrated clinical data for a transformative impact on healthcare outcomes.
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Affiliation(s)
- Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
| | - Leonard S. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
| | - Bruna H. Palomares
- Oral Diagnosis Department, Piracicaba School of Dentistry, State University of Campinas, Piracicaba 13414-903, Sao Paulo, Brazil;
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
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3
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Deb S, Berei J, Miliavski E, Khan MJ, Broder TJ, Akurugo TA, Lund C, Fleming SE, Hillwig R, Ross J, Puri N. The Effects of Smoking on Telomere Length, Induction of Oncogenic Stress, and Chronic Inflammatory Responses Leading to Aging. Cells 2024; 13:884. [PMID: 38891017 PMCID: PMC11172003 DOI: 10.3390/cells13110884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/11/2024] [Accepted: 05/18/2024] [Indexed: 06/20/2024] Open
Abstract
Telomeres, potential biomarkers of aging, are known to shorten with continued cigarette smoke exposure. In order to further investigate this process and its impact on cellular stress and inflammation, we used an in vitro model with cigarette smoke extract (CSE) and observed the downregulation of telomere stabilizing TRF2 and POT1 genes after CSE treatment. hTERT is a subunit of telomerase and a well-known oncogenic marker, which is overexpressed in over 85% of cancers and may contribute to lung cancer development in smokers. We also observed an increase in hTERT and ISG15 expression levels after CSE treatment, as well as increased protein levels revealed by immunohistochemical staining in smokers' lung tissue samples compared to non-smokers. The effects of ISG15 overexpression were further studied by quantifying IFN-γ, an inflammatory protein induced by ISG15, which showed greater upregulation in smokers compared to non-smokers. Similar changes in gene expression patterns for TRF2, POT1, hTERT, and ISG15 were observed in blood and buccal swab samples from smokers compared to non-smokers. The results from this study provide insight into the mechanisms behind smoking causing telomere shortening and how this may contribute to the induction of inflammation and/or tumorigenesis, which may lead to comorbidities in smokers.
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Affiliation(s)
- Shreya Deb
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Joseph Berei
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Edward Miliavski
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Muhammad J. Khan
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Taylor J. Broder
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Thomas A. Akurugo
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Cody Lund
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
| | - Sara E. Fleming
- Department of Pathology, UW Health SwedishAmerican Hospital, Rockford, IL 61107, USA;
| | - Robert Hillwig
- Department of Health Sciences Education, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA;
| | - Joseph Ross
- Department of Family and Community Medicine, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA;
| | - Neelu Puri
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL 61107, USA; (S.D.); (J.B.); (E.M.); (M.J.K.); (T.J.B.); (T.A.A.); (C.L.)
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4
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Bierhoff H. [Genetics, epigenetics, and environmental factors in life expectancy-What role does nature-versus-nurture play in aging?]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2024; 67:521-527. [PMID: 38637469 PMCID: PMC11093831 DOI: 10.1007/s00103-024-03873-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: 11/01/2023] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
In Germany and worldwide, the average age of the population is continuously rising. With this general increase in chronological age, the focus on biological age, meaning the actual health and fitness status, is becoming more and more important. The key question is to what extent the age-related decline in fitness is genetically predetermined or malleable by environmental factors and lifestyle.Many epigenetic studies in aging research have provided interesting insights in this nature-versus-nurture debate. In most model organisms, aging is associated with specific epigenetic changes, which can be countered by certain interventions like moderate caloric restriction or increased physical activity. Since these interventions also have positive effects on lifespan and health, epigenetics appears to be the interface between environmental factors and the aging process. This notion is supported by the fact that an epigenetic drift occurs through the life course of identical twins, which is related to the different manifestations of aging symptoms. Furthermore, biological age can be determined with high precision based on DNA methylation patterns, further emphasizing the importance of epigenetics in aging.This article provides an overview of the importance of genetic and epigenetic parameters for life expectancy. A major focus will be on the possibilities of maintaining a young epigenome through lifestyle and environmental factors, thereby slowing down biological aging.
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Affiliation(s)
- Holger Bierhoff
- Institut für Biochemie und Biophysik, Friedrich-Schiller-Universität Jena, Hans-Knöll-Straße 2, 07745, Jena, Deutschland.
- Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut (FLI), Jena, Deutschland.
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5
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Dubey SK, Dubey R, Prajapati SC, Jung K, Mohan K, Liu X, Roney J, Tian W, Abney J, Giarmarco MM, Hernandez AG, Liu J, Kleinman ME. Histone deficiency and hypoacetylation in the aging retinal pigment epithelium. Aging Cell 2024; 23:e14108. [PMID: 38408164 PMCID: PMC11113634 DOI: 10.1111/acel.14108] [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: 11/08/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/28/2024] Open
Abstract
Histones serve as a major carrier of epigenetic information in the form of post-translational modifications which are vital for controlling gene expression, maintaining cell identity, and ensuring proper cellular function. Loss of histones in the aging genome can drastically impact the epigenetic landscape of the cell leading to altered chromatin structure and changes in gene expression profiles. In this study, we investigated the impact of age-related changes on histone levels and histone acetylation in the retinal pigment epithelium (RPE) and retina of mice. We observed a global reduction of histones H1, H2A, H2B, H3, and H4 in aged RPE/choroid but not in the neural retina. Transcriptomic analyses revealed significant downregulation of histones in aged RPE/choroid including crucial elements of the histone locus body (HLB) complex involved in histone pre-mRNA processing. Knockdown of HINFP, a key HLB component, in human RPE cells induced histone loss, senescence, and the upregulation of senescence-associated secretory phenotype (SASP) markers. Replicative senescence and chronological aging in human RPE cells similarly resulted in progressive histone loss and acquisition of the SASP. Immunostaining of human retina sections revealed histone loss in RPE with age. Acetyl-histone profiling in aged mouse RPE/choroid revealed a specific molecular signature with loss of global acetyl-histone levels, including H3K14ac, H3K56ac, and H4K16ac marks. These findings strongly demonstrate histone loss as a unique feature of RPE aging and provide critical insights into the potential mechanisms linking histone dynamics, cellular senescence, and aging.
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Affiliation(s)
- Sushil K. Dubey
- Department of SurgeryEast Tennessee State UniversityJohnson CityTennesseeUSA
| | - Rashmi Dubey
- Department of SurgeryEast Tennessee State UniversityJohnson CityTennesseeUSA
| | - Subhash C. Prajapati
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Kyungsik Jung
- Department of SurgeryEast Tennessee State UniversityJohnson CityTennesseeUSA
| | - Kabhilan Mohan
- Department of SurgeryEast Tennessee State UniversityJohnson CityTennesseeUSA
| | - Xinan Liu
- Department of Computer ScienceUniversity of KentuckyLexingtonKentuckyUSA
| | - Jacob Roney
- Department of Ophthalmology and Visual SciencesUniversity of KentuckyLexingtonKentuckyUSA
| | - Wenjian Tian
- Department of SurgeryEast Tennessee State UniversityJohnson CityTennesseeUSA
| | - Jennifer Abney
- Department of Ophthalmology and Visual SciencesUniversity of KentuckyLexingtonKentuckyUSA
| | | | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology CenterUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Jinze Liu
- Department of BiostatisticsVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Mark E. Kleinman
- Department of SurgeryEast Tennessee State UniversityJohnson CityTennesseeUSA
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6
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Yamamoto Y, Takahashi RU, Kinehara M, Yano K, Kuramoto T, Shimamoto A, Tahara H. Downregulation of Histone H3.3 Induces p53-Dependent Cellular Senescence in Human Diploid Fibroblasts. Genes (Basel) 2024; 15:543. [PMID: 38790171 PMCID: PMC11121134 DOI: 10.3390/genes15050543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Cellular senescence is an irreversible growth arrest that acts as a barrier to cancer initiation and progression. Histone alteration is one of the major events during replicative senescence. However, little is known about the function of H3.3 in cellular senescence. Here we found that the downregulation of H3.3 induced growth suppression with senescence-like phenotypes such as senescence-associated heterochromatin foci (SAHF) and β-galactosidase (SA-β-gal) activity. Furthermore, H3.3 depletion induced senescence-like phenotypes with the p53/p21-depedent pathway. In addition, we identified miR-22-3p, tumor suppressive miRNA, as an upstream regulator of the H3F3B (H3 histone, family 3B) gene which is the histone variant H3.3 and replaces conventional H3 in active genes. Therefore, our results reveal for the first time the molecular mechanisms for cellular senescence which are regulated by H3.3 abundance. Taken together, our studies suggest that H3.3 exerts functional roles in regulating cellular senescence and is a promising target for cancer therapy.
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Affiliation(s)
- Yuki Yamamoto
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
| | - Ryou-u Takahashi
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
| | - Masaki Kinehara
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
| | - Kimiyoshi Yano
- Laboratory of Genome Stress Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan;
| | - Tatsuya Kuramoto
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
| | - Akira Shimamoto
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo Onoda 756-0884, Japan;
| | - Hidetoshi Tahara
- Department of Cellular and Molecular Biology, Basic Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan; (Y.Y.); (R.-u.T.)
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7
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Keller D, Stinus S, Umlauf D, Gourbeyre E, Biot E, Olivier N, Mahou P, Beaurepaire E, Andrey P, Crabbe L. Non-random spatial organization of telomeres varies during the cell cycle and requires LAP2 and BAF. iScience 2024; 27:109343. [PMID: 38510147 PMCID: PMC10951912 DOI: 10.1016/j.isci.2024.109343] [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: 08/22/2023] [Revised: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Spatial genome organization within the nucleus influences major biological processes and is impacted by the configuration of linear chromosomes. Here, we applied 3D spatial statistics and modeling on high-resolution telomere and centromere 3D-structured illumination microscopy images in cancer cells. We found a multi-scale organization of telomeres that dynamically evolved from a mixed clustered-and-regular distribution in early G1 to a purely regular distribution as cells progressed through the cell cycle. In parallel, our analysis revealed two pools of peripheral and internal telomeres, the proportions of which were inverted during the cell cycle. We then conducted a targeted screen using MadID to identify the molecular pathways driving or maintaining telomere anchoring to the nuclear envelope observed in early G1. Lamina-associated polypeptide (LAP) proteins were found transiently localized to telomeres in anaphase, a stage where LAP2α initiates the reformation of the nuclear envelope, and impacted telomere redistribution in the next interphase together with their partner barrier-to-autointegration factor (BAF).
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Affiliation(s)
- Debora Keller
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Sonia Stinus
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - David Umlauf
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Edith Gourbeyre
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Eric Biot
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Nicolas Olivier
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, École polytechnique, CNRS, INSERM, IP Paris, 91128 Palaiseau, France
| | - Philippe Andrey
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Laure Crabbe
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
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8
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Jin K, McCoy BM, Goldman EA, Usova V, Tkachev V, Chitsazan AD, Kakebeen A, Jeffery U, Creevy KE, Wills A, Snyder‐Mackler N, Promislow DEL. DNA methylation and chromatin accessibility predict age in the domestic dog. Aging Cell 2024; 23:e14079. [PMID: 38263575 PMCID: PMC11019125 DOI: 10.1111/acel.14079] [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: 11/10/2021] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Across mammals, the epigenome is highly predictive of chronological age. These "epigenetic clocks," most of which have been built using DNA methylation (DNAm) profiles, have gained traction as biomarkers of aging and organismal health. While the ability of DNAm to predict chronological age has been repeatedly demonstrated, the ability of other epigenetic features to predict age remains unclear. Here, we use two types of epigenetic information-DNAm, and chromatin accessibility as measured by ATAC-seq-to develop age predictors in peripheral blood mononuclear cells sampled from a population of domesticated dogs. We measured DNAm and ATAC-seq profiles for 71 dogs, building separate predictive clocks from each, as well as the combined dataset. We also use fluorescence-assisted cell sorting to quantify major lymphoid populations for each sample. We found that chromatin accessibility can accurately predict chronological age (R2 ATAC = 26%), though less accurately than the DNAm clock (R2 DNAm = 33%), and the clock built from the combined datasets was comparable to both (R2 combined = 29%). We also observed various populations of CD62L+ T cells significantly correlated with dog age. Finally, we found that all three clocks selected features that were in or near at least two protein-coding genes: BAIAP2 and SCARF2, both previously implicated in processes related to cognitive or neurological impairment. Taken together, these results highlight the potential of chromatin accessibility as a complementary epigenetic resource for modeling and investigating biologic age.
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Affiliation(s)
- Kelly Jin
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Brianah M. McCoy
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | | | - Viktoria Usova
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Victor Tkachev
- Division of Pediatric Hematology/OncologyBoston Children's HospitalBostonMassachusettsUSA
- Dana Farber Cancer InstituteBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Alex D. Chitsazan
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Anneke Kakebeen
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Unity Jeffery
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Kate E. Creevy
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Andrea Wills
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Noah Snyder‐Mackler
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Daniel E. L. Promislow
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
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9
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Mason CE, Sierra MA, Feng HJ, Bailey SM. Telomeres and aging: on and off the planet! Biogerontology 2024; 25:313-327. [PMID: 38581556 PMCID: PMC10998805 DOI: 10.1007/s10522-024-10098-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2024] [Indexed: 04/08/2024]
Abstract
Improving human healthspan in our rapidly aging population has never been more imperative. Telomeres, protective "caps" at the ends of linear chromosomes, are essential for maintaining genome stability of eukaryotic genomes. Due to their physical location and the "end-replication problem" first envisioned by Dr. Alexey Olovnikov, telomeres shorten with cell division, the implications of which are remarkably profound. Telomeres are hallmarks and molecular drivers of aging, as well as fundamental integrating components of the cumulative effects of genetic, lifestyle, and environmental factors that erode telomere length over time. Ongoing telomere attrition and the resulting limit to replicative potential imposed by cellular senescence serves a powerful tumor suppressor function, and also underlies aging and a spectrum of age-related degenerative pathologies, including reduced fertility, dementias, cardiovascular disease and cancer. However, very little data exists regarding the extraordinary stressors and exposures associated with long-duration space exploration and eventual habitation of other planets, nor how such missions will influence telomeres, reproduction, health, disease risk, and aging. Here, we briefly review our current understanding, which has advanced significantly in recent years as a result of the NASA Twins Study, the most comprehensive evaluation of human health effects associated with spaceflight ever conducted. Thus, the Twins Study is at the forefront of personalized space medicine approaches for astronauts and sets the stage for subsequent missions. We also extrapolate from current understanding to future missions, highlighting potential biological and biochemical strategies that may enable human survival, and consider the prospect of longevity in the extreme environment of space.
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Affiliation(s)
- Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Maria A Sierra
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Henry J Feng
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.
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10
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Yang KB, Rasouly A, Epshtein V, Martinez C, Nguyen T, Shamovsky I, Nudler E. Persistence of backtracking by human RNA polymerase II. Mol Cell 2024; 84:897-909.e4. [PMID: 38340716 DOI: 10.1016/j.molcel.2024.01.019] [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: 08/25/2023] [Revised: 11/20/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
RNA polymerase II (RNA Pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome-wide distribution of more persistent backtracking are unknown. Consequently, we developed a method to directly sequence the extruded, "backtracked" 3' RNA. Our data show that RNA Pol II slides backward more than 20 nt in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where RNA Pol II pauses near promoters and intron-exon junctions and is enriched in genes involved in translation, replication, and development, where gene expression is decreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, and the resolution of such events is likely required for timely expression during cell division. These results demonstrate that persistent backtracking can potentially affect diverse gene expression programs.
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Affiliation(s)
- Kevin B Yang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Aviram Rasouly
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Criseyda Martinez
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Thao Nguyen
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA.
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11
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Das A, Giri AK, Bhattacharjee P. Targeting 'histone mark': Advanced approaches in epigenetic regulation of telomere dynamics in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195007. [PMID: 38237857 DOI: 10.1016/j.bbagrm.2024.195007] [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: 08/01/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Telomere integrity is required for the maintenance of genome stability and prevention of oncogenic transformation of cells. Recent evidence suggests the presence of epigenetic modifications as an important regulator of mammalian telomeres. Telomeric and subtelomeric regions are rich in epigenetic marks that regulate telomere length majorly through DNA methylation and post-translational histone modifications. Specific histone modifying enzymes play an integral role in establishing telomeric histone codes necessary for the maintenance of structural integrity. Alterations of crucial histone moieties and histone modifiers cause deregulations in the telomeric chromatin leading to carcinogenic manifestations. This review delves into the significance of histone modifications and their influence on telomere dynamics concerning cancer. Additionally, it highlights the existing research gaps that hold the potential to drive the development of therapeutic interventions targeting the telomere epigenome.
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Affiliation(s)
- Ankita Das
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India; Department of Zoology, University of Calcutta, Kolkata 700019, India
| | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India.
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12
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Dubey SK, Dubey R, Kleinman ME. Unraveling Histone Loss in Aging and Senescence. Cells 2024; 13:320. [PMID: 38391933 PMCID: PMC10886805 DOI: 10.3390/cells13040320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
As the global population experiences a notable surge in aging demographics, the need to understand the intricate molecular pathways exacerbated by age-related stresses, including epigenetic dysregulation, becomes a priority. Epigenetic mechanisms play a critical role in driving age-related diseases through altered gene expression, genomic instability, and irregular chromatin remodeling. In this review, we focus on histones, a central component of the epigenome, and consolidate the key findings of histone loss and genome-wide redistribution as fundamental processes contributing to aging and senescence. The review provides insights into novel histone expression profiles, nucleosome occupancy, disruptions in higher-order chromatin architecture, and the emergence of noncanonical histone variants in the aging cellular landscape. Furthermore, we explore the current state of our understanding of the molecular mechanisms of histone deficiency in aging cells. Specific emphasis is placed on highlighting histone degradation pathways in the cell and studies that have explored potential strategies to mitigate histone loss or restore histone levels in aging cells. Finally, in addressing future perspectives, the insights gained from this review hold profound implications for advancing strategies that actively intervene in modulating histone expression profiles in the context of cellular aging and identifying potential therapeutic targets for alleviating a multitude of age-related diseases.
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Affiliation(s)
| | | | - Mark Ellsworth Kleinman
- Department of Surgery, East Tennessee State University, Johnson City, TN 37614, USA; (S.K.D.); (R.D.)
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13
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Sichani AS, Khoddam S, Shakeri S, Tavakkoli Z, Jafroodi AR, Dabbaghipour R, Sisakht M, Fallahi J. Partial Reprogramming as a Method for Regenerating Neural Tissues in Aged Organisms. Cell Reprogram 2024; 26:10-23. [PMID: 38381402 DOI: 10.1089/cell.2023.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Aging causes numerous age-related diseases, leading the human species to death. Nevertheless, rejuvenating strategies based on cell epigenetic modifications are a possible approach to counteract disease progression while getting old. Cell reprogramming of adult somatic cells toward pluripotency ought to be a promising tool for age-related diseases. However, researchers do not have control over this process as cells lose their fate, and cause potential cancerous cells or unexpected cell phenotypes. Direct and partial reprogramming were introduced in recent years with distinctive applications. Although direct reprogramming makes cells lose their identity, it has various applications in regeneration medicine. Temporary and regulated in vivo overexpression of Yamanaka factors has been shown in several experimental contexts to be achievable and is used to rejuvenate mice models. This regeneration can be accomplished by altering the epigenetic adult cell signature to the signature of a younger cell. The greatest advantage of partial reprogramming is that this method does not allow cells to lose their identity when they are resetting their epigenetic clock. It is a regimen of short-term Oct3/4, Sox2, Klf4, and c-Myc expression in vivo that prevents full reprogramming to the pluripotent state and avoids both tumorigenesis and the presence of unwanted undifferentiated cells. We know that many neurological age-related diseases, such as Alzheimer's disease, stroke, dementia, and Parkinson's disease, are the main cause of death in the last decades of life. Therefore, scientists have a special tendency regarding neuroregeneration methods to increase human life expectancy.
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Affiliation(s)
- Ali Saber Sichani
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Somayeh Khoddam
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shayan Shakeri
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Tavakkoli
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arad Ranji Jafroodi
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Dabbaghipour
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Sisakht
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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14
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Dhillon VS, Shahid M, Deo P, Fenech M. Reduced SIRT1 and SIRT3 and Lower Antioxidant Capacity of Seminal Plasma Is Associated with Shorter Sperm Telomere Length in Oligospermic Men. Int J Mol Sci 2024; 25:718. [PMID: 38255792 PMCID: PMC10815409 DOI: 10.3390/ijms25020718] [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: 11/24/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Infertility affects millions of couples worldwide and has a profound impact not only on their families, but also on communities. Telomere attrition has been associated with infertility, DNA damage and fragmentation. Oxidative stress has been shown to affect sperm DNA integrity and telomere length. Sirtuins such as SIRT1 and SIRT3 are involved in aging and oxidative stress response. The aim of the present study is to determine the role of SIRT1 and SIRT3 in regulating oxidative stress, telomere shortening, and their association with oligospermia. Therefore, we assessed the protein levels of SIRT1 and SIRT3, total antioxidant capacity (TAC), superoxide dismutase (SOD), malondialdehyde (MDA) and catalase activity (CAT) in the seminal plasma of 272 patients with oligospermia and 251 fertile men. We also measured sperm telomere length (STL) and leukocyte telomere length (LTL) using a standard real-time quantitative PCR assay. Sperm chromatin and protamine deficiency were also measured as per standard methods. Our results for oligospermic patients demonstrate significant reductions in semen parameters, shorter STL and LTL, lower levels of SOD, TAC, CAT, SIRT1 and SIRT3 levels, and also significant protamine deficiency and higher levels of MDA and DNA fragmentation. We conclude that a shorter TL in sperms and leukocytes is associated with increased oxidative stress that also accounts for high levels of DNA fragmentation in sperms. Our results support the hypothesis that various sperm parameters in the state of oligospermia are associated with or caused by reduced levels of SIRT1 and SIRT3 proteins.
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Affiliation(s)
- Varinderpal S. Dhillon
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (P.D.); (M.F.)
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Permal Deo
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (P.D.); (M.F.)
| | - Michael Fenech
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (P.D.); (M.F.)
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15
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De Luca SN, Vlahos R. Targeting accelerated pulmonary ageing to treat chronic obstructive pulmonary disease-induced neuropathological comorbidities. Br J Pharmacol 2024; 181:3-20. [PMID: 37828646 PMCID: PMC10952708 DOI: 10.1111/bph.16263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/06/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a major incurable health burden, ranking as the third leading cause of death worldwide, mainly driven by cigarette smoking. COPD is characterised by persistent airway inflammation, lung function decline and premature ageing with the presence of pulmonary senescent cells. This review proposes that cellular senescence, a state of stable cell cycle arrest linked to ageing, induced by inflammation and oxidative stress in COPD, extends beyond the lungs and affects the systemic circulation. This pulmonary senescent profile will reach other organs via extracellular vesicles contributing to brain inflammation and damage, and increasing the risk of neurological comorbidities, such as stroke, cerebral small vessel disease and Alzheimer's disease. The review explores the role of cellular senescence in COPD-associated brain conditions and investigates the relationship between cellular senescence and circadian rhythm in COPD. Additionally, it discusses potential therapies, including senomorphic and senolytic treatments, as novel strategies to halt or improve the progression of COPD.
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Affiliation(s)
- Simone N. De Luca
- Centre for Respiratory Science and Health, School of Health & Biomedical SciencesRMIT UniversityMelbourneVictoriaAustralia
| | - Ross Vlahos
- Centre for Respiratory Science and Health, School of Health & Biomedical SciencesRMIT UniversityMelbourneVictoriaAustralia
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16
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Yang KB, Rasouly A, Epshtein V, Martinez C, Nguyen T, Shamovsky I, Nudler E. Persistence of backtracking by human RNA polymerase II. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571520. [PMID: 38168453 PMCID: PMC10760130 DOI: 10.1101/2023.12.13.571520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
RNA polymerase II (pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome wide distribution of more persistent backtracking is unknown. Consequently, we developed a novel method to directly sequence the extruded, "backtracked" 3' RNA. Our data shows that pol II slides backwards more than 20 nucleotides in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where pol II pauses near promoters and intron-exon junctions, and is enriched in genes involved in translation, replication, and development, where gene expression is decreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, and the resolution of such events is likely required for timely expression during cell division. These results demonstrate that persistent backtracking has the potential to affect diverse gene expression programs.
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17
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Lu YR, Tian X, Sinclair DA. The Information Theory of Aging. NATURE AGING 2023; 3:1486-1499. [PMID: 38102202 DOI: 10.1038/s43587-023-00527-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/02/2023] [Indexed: 12/17/2023]
Abstract
Information storage and retrieval is essential for all life. In biology, information is primarily stored in two distinct ways: the genome, comprising nucleic acids, acts as a foundational blueprint and the epigenome, consisting of chemical modifications to DNA and histone proteins, regulates gene expression patterns and endows cells with specific identities and functions. Unlike the stable, digital nature of genetic information, epigenetic information is stored in a digital-analog format, susceptible to alterations induced by diverse environmental signals and cellular damage. The Information Theory of Aging (ITOA) states that the aging process is driven by the progressive loss of youthful epigenetic information, the retrieval of which via epigenetic reprogramming can improve the function of damaged and aged tissues by catalyzing age reversal.
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Affiliation(s)
- Yuancheng Ryan Lu
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xiao Tian
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - David A Sinclair
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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18
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Suganuma T, Workman JL. Chromatin balances cell redox and energy homeostasis. Epigenetics Chromatin 2023; 16:46. [PMID: 38017471 PMCID: PMC10683155 DOI: 10.1186/s13072-023-00520-8] [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: 08/16/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Chromatin plays a central role in the conversion of energy in cells: alteration of chromatin structure to make DNA accessible consumes energy, and compaction of chromatin preserves energy. Alteration of chromatin structure uses energy sources derived from carbon metabolism such as ATP and acetyl-CoA; conversely, chromatin compaction and epigenetic modification feedback to metabolism and energy homeostasis by controlling gene expression and storing metabolites. Coordination of these dual chromatin events must be flexibly modulated in response to environmental changes such as during development and exposure to stress. Aging also alters chromatin structure and the coordination of metabolism, chromatin dynamics, and other cell processes. Noncoding RNAs and other RNA species that associate directly with chromatin or with chromatin modifiers contribute to spatiotemporal control of transcription and energy conversion. The time required for generating the large amounts of RNAs and chromatin modifiers observed in super-enhancers may be critical for regulation of transcription and may be impacted by aging. Here, taking into account these factors, we review alterations of chromatin that are fundamental to cell responses to metabolic changes due to stress and aging to maintain redox and energy homeostasis. We discuss the relationship between spatiotemporal control of energy and chromatin function, as this emerging concept must be considered to understand how cell homeostasis is maintained.
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Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA.
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
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19
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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20
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Jing Y, Jiang X, Ji Q, Wu Z, Wang W, Liu Z, Guillen-Garcia P, Esteban CR, Reddy P, Horvath S, Li J, Geng L, Hu Q, Wang S, Belmonte JCI, Ren J, Zhang W, Qu J, Liu GH. Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation. Cell Stem Cell 2023; 30:1452-1471.e10. [PMID: 37832549 DOI: 10.1016/j.stem.2023.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 08/04/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Our understanding of the molecular basis for cellular senescence remains incomplete, limiting the development of strategies to ameliorate age-related pathologies by preventing stem cell senescence. Here, we performed a genome-wide CRISPR activation (CRISPRa) screening using a human mesenchymal precursor cell (hMPC) model of the progeroid syndrome. We evaluated targets whose activation antagonizes cellular senescence, among which SOX5 outperformed as a top hit. Through decoding the epigenomic landscapes remodeled by overexpressing SOX5, we uncovered its role in resetting the transcription network for geroprotective genes, including HMGB2. Mechanistically, SOX5 binding elevated the enhancer activity of HMGB2 with increased levels of H3K27ac and H3K4me1, raising HMGB2 expression so as to promote rejuvenation. Furthermore, gene therapy with lentiviruses carrying SOX5 or HMGB2 rejuvenated cartilage and alleviated osteoarthritis in aged mice. Our study generated a comprehensive list of rejuvenators, pinpointing SOX5 as a potent driver for rejuvenation both in vitro and in vivo.
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Affiliation(s)
- Yaobin Jing
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qianzhao Ji
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zeming Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Wei Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Pedro Guillen-Garcia
- Department of Traumatology and Research Unit, Clinica CEMTRO, 28035 Madrid, Spain
| | - Concepcion Rodriguez Esteban
- Altos Labs, Inc., San Diego, CA 94022, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Pradeep Reddy
- Altos Labs, Inc., San Diego, CA 94022, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Steve Horvath
- Altos Labs, Inc., San Diego, CA 94022, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 10833, USA
| | - Jingyi Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Lingling Geng
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Qinchao Hu
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou 510060, China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou 510060, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China; Chongqing Renji Hospital, University of Chinese Academy of Sciences, Chongqing 400062, China
| | - Juan Carlos Izpisua Belmonte
- Altos Labs, Inc., San Diego, CA 94022, USA; Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jie Ren
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Weiqi Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100190, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
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21
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Qian J, Zhou X, Tanaka K, Takahashi A. Alteration in the chromatin landscape during the DNA damage response: Continuous rotation of the gear driving cellular senescence and aging. DNA Repair (Amst) 2023; 131:103572. [PMID: 37742405 DOI: 10.1016/j.dnarep.2023.103572] [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: 06/26/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
The DNA damage response (DDR) is a crucial biological mechanism for maintaining cellular homeostasis in living organisms. This complex process involves a cascade of signaling pathways that orchestrate the sensing and processing of DNA lesions. Perturbations in this process may cause DNA repair failure, genomic instability, and irreversible cell cycle arrest, known as cellular senescence, potentially culminating in tumorigenesis. Persistent DDR exerts continuous and cumulative pressure on global chromatin dynamics, resulting in altered chromatin structure and perturbed epigenetic regulations, which are highly associated with cellular senescence and aging. Sustained DDR activation and heterochromatin changes further promote senescence-associated secretory phenotype (SASP), which is responsible for aging-related diseases and cancer development. In this review, we discuss the diverse mechanisms by which DDR leads to cellular senescence and triggers SASP, together with the evidence for DDR-induced chromatin remodeling and epigenetic regulation in relation to aging.
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Affiliation(s)
- Jianghao Qian
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi 980-8575, Japan
| | - Xiangyu Zhou
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Kozo Tanaka
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi 980-8575, Japan
| | - Akiko Takahashi
- Division of Cellular Senescence, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; Cancer Cell Communication Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan.
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22
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Emerson FJ, Lee SS. Chromatin: the old and young of it. Front Mol Biosci 2023; 10:1270285. [PMID: 37877123 PMCID: PMC10591336 DOI: 10.3389/fmolb.2023.1270285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Aging affects nearly all aspects of our cells, from our DNA to our proteins to how our cells handle stress and communicate with each other. Age-related chromatin changes are of particular interest because chromatin can dynamically respond to the cellular and organismal environment, and many modifications at chromatin are reversible. Changes at chromatin occur during aging, and evidence from model organisms suggests that chromatin factors could play a role in modulating the aging process itself, as altering proteins that work at chromatin often affect the lifespan of yeast, worms, flies, and mice. The field of chromatin and aging is rapidly expanding, and high-resolution genomics tools make it possible to survey the chromatin environment or track chromatin factors implicated in longevity with precision that was not previously possible. In this review, we discuss the state of chromatin and aging research. We include examples from yeast, Drosophila, mice, and humans, but we particularly focus on the commonly used aging model, the worm Caenorhabditis elegans, in which there are many examples of chromatin factors that modulate longevity. We include evidence of both age-related changes to chromatin and evidence of specific chromatin factors linked to longevity in core histones, nuclear architecture, chromatin remodeling, and histone modifications.
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Affiliation(s)
| | - Siu Sylvia Lee
- Lee Lab, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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23
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Sung S, Kim E, Niida H, Kim C, Lee J. Distinct characteristics of two types of alternative lengthening of telomeres in mouse embryonic stem cells. Nucleic Acids Res 2023; 51:9122-9143. [PMID: 37496110 PMCID: PMC10516625 DOI: 10.1093/nar/gkad617] [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: 09/24/2022] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023] Open
Abstract
Telomere length must be maintained in actively dividing cells to avoid cellular arrest or death. In the absence of telomerase activity, activation of alternative lengthening of telomeres (ALT) allows the maintenance of telomeric length and prolongs the cellular lifespan. Our previous studies have established two types of ALT survivors from mouse embryonic stem cells. The key differences between these ALT survivors are telomere-constituting sequences: non-telomeric sequences and canonical telomeric repeats, with each type of ALT survivors being referred to as type I and type II, respectively. We explored how the characteristics of the two types of ALT lines reflect their fates using multi-omics approaches. The most notable gene expression signatures of type I and type II ALT cell lines were chromatin remodelling and DNA repair, respectively. Compared with type II cells, type I ALT cells accumulated more mutations and demonstrated persistent telomere instability. These findings indicate that cells of the same origin have separate routes for survival, thus providing insights into the plasticity of crisis-suffering cells and cancers.
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Affiliation(s)
- Sanghyun Sung
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
| | - Eunkyeong Kim
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Chuna Kim
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Gwahak-ro 125, Daejeon 34141, Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Junho Lee
- Department of Biological Sciences, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Gwanak-ro 1, Seoul 08826, Korea
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24
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López-Gil L, Pascual-Ahuir A, Proft M. Genomic Instability and Epigenetic Changes during Aging. Int J Mol Sci 2023; 24:14279. [PMID: 37762580 PMCID: PMC10531692 DOI: 10.3390/ijms241814279] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Aging is considered the deterioration of physiological functions along with an increased mortality rate. This scientific review focuses on the central importance of genomic instability during the aging process, encompassing a range of cellular and molecular changes that occur with advancing age. In particular, this revision addresses the genetic and epigenetic alterations that contribute to genomic instability, such as telomere shortening, DNA damage accumulation, and decreased DNA repair capacity. Furthermore, the review explores the epigenetic changes that occur with aging, including modifications to histones, DNA methylation patterns, and the role of non-coding RNAs. Finally, the review discusses the organization of chromatin and its contribution to genomic instability, including heterochromatin loss, chromatin remodeling, and changes in nucleosome and histone abundance. In conclusion, this review highlights the fundamental role that genomic instability plays in the aging process and underscores the need for continued research into these complex biological mechanisms.
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Affiliation(s)
- Lucía López-Gil
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
| | - Markus Proft
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
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25
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Plesa AM, Shadpour M, Boyden E, Church GM. Transcriptomic reprogramming for neuronal age reversal. Hum Genet 2023; 142:1293-1302. [PMID: 37004545 PMCID: PMC10066999 DOI: 10.1007/s00439-023-02529-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/24/2023] [Indexed: 04/04/2023]
Abstract
Aging is a progressive multifaceted functional decline of a biological system. Chronic age-related conditions such as neurodegenerative diseases are leading causes of death worldwide, and they are becoming a pressing problem for our society. To address this global challenge, there is a need for novel, safe, and effective rejuvenation therapies aimed at reversing age-related phenotypes and improving human health. With gene expression being a key determinant of cell identity and function, and in light of recent studies reporting rejuvenation effects through genetic perturbations, we propose an age reversal strategy focused on reprogramming the cell transcriptome to a youthful state. To this end, we suggest using transcriptomic data from primary human cells to predict rejuvenation targets and develop high-throughput aging assays, which can be used in large perturbation screens. We propose neural cells as particularly relevant targets for rejuvenation due to substantial impact of neurodegeneration on human frailty. Of all cell types in the brain, we argue that glutamatergic neurons, neuronal stem cells, and oligodendrocytes represent the most impactful and tractable targets. Lastly, we provide experimental designs for anti-aging reprogramming screens that will likely enable the development of neuronal age reversal therapies, which hold promise for dramatically improving human health.
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Affiliation(s)
- Alexandru M. Plesa
- Department of Genetics, Harvard Medical School, Boston, MA USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA USA
| | - Michael Shadpour
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA USA
- Department of Biological Engineering, MIT, Cambridge, MA USA
| | - Ed Boyden
- Department of Biological Engineering, MIT, Cambridge, MA USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA USA
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26
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Bi J, Wang D, Zhu F, Lu X, Xie Y, Liu H, Wang M, He X, Jiang Y, Liu K, Zhao M, Wang T, Li J. Epigenetic Iinsights into the Senescence of Porcine Fetal Fibroblasts induced by Passaging. Cell Cycle 2023; 22:1597-1613. [PMID: 37338871 PMCID: PMC10361148 DOI: 10.1080/15384101.2023.2222521] [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: 12/21/2022] [Revised: 02/13/2023] [Accepted: 03/07/2023] [Indexed: 06/21/2023] Open
Abstract
Epigenetic status of fetal fibroblasts (FFs) is one of the crucial factors accounted for the success of somatic cell nuclear transfer and gene editing, which might inevitably be affected by passaging. But few systematic studies have been performed on the epigenetic status of passaged aging cells. Therefore, FFs from large white pig were in vitro passaged to the 5, 10, and 15 (F5, F10, and F15) passages in the present study to investigate the potential alteration of epigenetic status. Results indicated the senescence of FFs occurs with the passaging, as assessed by the weakened growth rate, increased β-gal expression, and so on. For the epigenetic status of FFs, the higher level both of DNA methylation and H3K4me1, H3K4me2, H3K4me3 was observed at F10, but the lowest level was observed at F15. However, the fluorescence intensity of m6A was significantly higher in F15, but lower (p < 0.05) in F10, and the related mRNA expression in F15 was significantly higher than F5. Further, RNA-Seq indicated a considerable difference in the expression pattern of F5, F10, and F15 FFs. Among differentially expressed genes, not only the genes involved in cell senescence were changed, but also the upregulated expression of Dnmt1, Dnmt3b, Tet1 and dysregulated expression of histone methyltransferases-related genes were detected in F10 FFs. In addition, most genes related to m6A such as METTL3, YTHDF2, and YTHDC1 were significantly different in F5, F10, and F15 FFs. In conclusion, the epigenetic status of FFs was affected by being passaged from F5 to F15.
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Affiliation(s)
- Jiaying Bi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Dayu Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fuquan Zhu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinyue Lu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yan Xie
- Taixing Animal Husbandry and Veterinary Center, Taizhou, Jiangsu Province, China
| | - Huijun Liu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang Province, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang Province, China
| | - Xu He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuan Jiang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ke Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Mingyue Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Tingzhang Wang
- Taixing Animal Husbandry and Veterinary Center, Taizhou, Jiangsu Province, China
| | - Juan Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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27
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Giroud J, Bouriez I, Paulus H, Pourtier A, Debacq-Chainiaux F, Pluquet O. Exploring the Communication of the SASP: Dynamic, Interactive, and Adaptive Effects on the Microenvironment. Int J Mol Sci 2023; 24:10788. [PMID: 37445973 DOI: 10.3390/ijms241310788] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Cellular senescence is a complex cell state that can occur during physiological ageing or after exposure to stress signals, regardless of age. It is a dynamic process that continuously evolves in a context-dependent manner. Senescent cells interact with their microenvironment by producing a heterogenous and plastic secretome referred to as the senescence-associated secretory phenotype (SASP). Hence, understanding the cross-talk between SASP and the microenvironment can be challenging due to the complexity of signal exchanges. In this review, we first aim to update the definition of senescence and its associated biomarkers from its discovery to the present day. We detail the regulatory mechanisms involved in the expression of SASP at multiple levels and develop how SASP can orchestrate microenvironment modifications, by focusing on extracellular matrix modifications, neighboring cells' fate, and intercellular communications. We present hypotheses on how these microenvironmental events may affect dynamic changes in SASP composition in return. Finally, we discuss the various existing approaches to targeting SASP and clarify what is currently known about the biological effects of these modified SASPs on the cellular environment.
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Affiliation(s)
- Joëlle Giroud
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
- University of Lille, CNRS, Inserm, Pasteur Institute of Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France
| | - Inès Bouriez
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Hugo Paulus
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Albin Pourtier
- University of Lille, CNRS, Inserm, Pasteur Institute of Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France
| | - Florence Debacq-Chainiaux
- Laboratory of Biochemistry and Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, 5000 Namur, Belgium
| | - Olivier Pluquet
- University of Lille, CNRS, Inserm, Pasteur Institute of Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, 59000 Lille, France
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28
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Liu Z, Liang Q, Ren Y, Guo C, Ge X, Wang L, Cheng Q, Luo P, Zhang Y, Han X. Immunosenescence: molecular mechanisms and diseases. Signal Transduct Target Ther 2023; 8:200. [PMID: 37179335 PMCID: PMC10182360 DOI: 10.1038/s41392-023-01451-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/24/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Infection susceptibility, poor vaccination efficacy, age-related disease onset, and neoplasms are linked to innate and adaptive immune dysfunction that accompanies aging (known as immunosenescence). During aging, organisms tend to develop a characteristic inflammatory state that expresses high levels of pro-inflammatory markers, termed inflammaging. This chronic inflammation is a typical phenomenon linked to immunosenescence and it is considered the major risk factor for age-related diseases. Thymic involution, naïve/memory cell ratio imbalance, dysregulated metabolism, and epigenetic alterations are striking features of immunosenescence. Disturbed T-cell pools and chronic antigen stimulation mediate premature senescence of immune cells, and senescent immune cells develop a proinflammatory senescence-associated secretory phenotype that exacerbates inflammaging. Although the underlying molecular mechanisms remain to be addressed, it is well documented that senescent T cells and inflammaging might be major driving forces in immunosenescence. Potential counteractive measures will be discussed, including intervention of cellular senescence and metabolic-epigenetic axes to mitigate immunosenescence. In recent years, immunosenescence has attracted increasing attention for its role in tumor development. As a result of the limited participation of elderly patients, the impact of immunosenescence on cancer immunotherapy is unclear. Despite some surprising results from clinical trials and drugs, it is necessary to investigate the role of immunosenescence in cancer and other age-related diseases.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China
| | - Qimeng Liang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 4500052, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Xiaoyong Ge
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China.
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29
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Bao H, Cao J, Chen M, Chen M, Chen W, Chen X, Chen Y, Chen Y, Chen Y, Chen Z, Chhetri JK, Ding Y, Feng J, Guo J, Guo M, He C, Jia Y, Jiang H, Jing Y, Li D, Li J, Li J, Liang Q, Liang R, Liu F, Liu X, Liu Z, Luo OJ, Lv J, Ma J, Mao K, Nie J, Qiao X, Sun X, Tang X, Wang J, Wang Q, Wang S, Wang X, Wang Y, Wang Y, Wu R, Xia K, Xiao FH, Xu L, Xu Y, Yan H, Yang L, Yang R, Yang Y, Ying Y, Zhang L, Zhang W, Zhang W, Zhang X, Zhang Z, Zhou M, Zhou R, Zhu Q, Zhu Z, Cao F, Cao Z, Chan P, Chen C, Chen G, Chen HZ, Chen J, Ci W, Ding BS, Ding Q, Gao F, Han JDJ, Huang K, Ju Z, Kong QP, Li J, Li J, Li X, Liu B, Liu F, Liu L, Liu Q, Liu Q, Liu X, Liu Y, Luo X, Ma S, Ma X, Mao Z, Nie J, Peng Y, Qu J, Ren J, Ren R, Song M, Songyang Z, Sun YE, Sun Y, Tian M, Wang S, Wang S, Wang X, Wang X, Wang YJ, Wang Y, Wong CCL, Xiang AP, Xiao Y, Xie Z, Xu D, Ye J, Yue R, Zhang C, Zhang H, Zhang L, Zhang W, Zhang Y, Zhang YW, Zhang Z, Zhao T, Zhao Y, Zhu D, Zou W, Pei G, Liu GH. Biomarkers of aging. SCIENCE CHINA. LIFE SCIENCES 2023; 66:893-1066. [PMID: 37076725 PMCID: PMC10115486 DOI: 10.1007/s11427-023-2305-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/27/2023] [Indexed: 04/21/2023]
Abstract
Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant.
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Affiliation(s)
- Hainan Bao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mengting Chen
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Min Chen
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wei Chen
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xiao Chen
- Department of Nuclear Medicine, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Yanhao Chen
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yutian Chen
- The Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zhiyang Chen
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China
| | - Jagadish K Chhetri
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Yingjie Ding
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junlin Feng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jun Guo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China
| | - Mengmeng Guo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Chuting He
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Yujuan Jia
- Department of Neurology, First Affiliated Hospital, Shanxi Medical University, Taiyuan, 030001, China
| | - Haiping Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Ying Jing
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Dingfeng Li
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyi Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Qinhao Liang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
| | - Rui Liang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China
| | - Feng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Zuojun Liu
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Jianwei Lv
- School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Jingyi Ma
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Kehang Mao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China
| | - Jiawei Nie
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinpei Sun
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China
| | - Xiaoqiang Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianfang Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyuan Wang
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China
| | - Xuan Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Yuhan Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Rimo Wu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China
| | - Kai Xia
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Fu-Hui Xiao
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yingying Xu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
| | - Haoteng Yan
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Liang Yang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Ruici Yang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuanxin Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yilin Ying
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China
| | - Le Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Weiwei Zhang
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China
| | - Wenwan Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xing Zhang
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Min Zhou
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China
| | - Rui Zhou
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Qingchen Zhu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhengmao Zhu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Feng Cao
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, 100853, China.
| | - Zhongwei Cao
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Piu Chan
- National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Guobing Chen
- Department of Microbiology and Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China.
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, Guangzhou, 510000, China.
| | - Hou-Zao Chen
- Department of Biochemistryand Molecular Biology, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
| | - Jun Chen
- Peking University Research Center on Aging, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, Department of Integration of Chinese and Western Medicine, School of Basic Medical Science, Peking University, Beijing, 100191, China.
| | - Weimin Ci
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
| | - Bi-Sen Ding
- State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Qiurong Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Feng Gao
- Key Laboratory of Ministry of Education, School of Aerospace Medicine, Fourth Military Medical University, Xi'an, 710032, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Kai Huang
- Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Clinical Research Center of Metabolic and Cardiovascular Disease, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Key Laboratory of Metabolic Abnormalities and Vascular Aging, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Zhenyu Ju
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Ageing and Regenerative Medicine, Jinan University, Guangzhou, 510632, China.
| | - Qing-Peng Kong
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- State Key Laboratory of Genetic Resources and Evolution, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Key Laboratory of Healthy Aging Study, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- Hunan Key Laboratory of Aging Biology, Xiangya Hospital, Central South University, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Jian Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, China.
| | - Xin Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Baohua Liu
- School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen, 518060, China.
| | - Feng Liu
- Metabolic Syndrome Research Center, The Second Xiangya Hospital, Central South Unversity, Changsha, 410011, China.
| | - Lin Liu
- Department of Genetics and Cell Biology, College of Life Science, Nankai University, Tianjin, 300071, China.
- Haihe Laboratory of Cell Ecosystem, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Institute of Translational Medicine, Tianjin Union Medical Center, Nankai University, Tianjin, 300000, China.
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, China.
| | - Qiang Liu
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230036, China.
| | - Qiang Liu
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
- Tianjin Institute of Immunology, Tianjin Medical University, Tianjin, 300070, China.
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
| | - Yong Liu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China.
| | - Xianghang Luo
- Department of Endocrinology, Endocrinology Research Center, Xiangya Hospital of Central South University, Changsha, 410008, China.
| | - Shuai Ma
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Jing Nie
- The State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Yaojin Peng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ruibao Ren
- Shanghai Institute of Hematology, State Key Laboratory for Medical Genomics, National Research Center for Translational Medicine (Shanghai), International Center for Aging and Cancer, Collaborative Innovation Center of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Center for Aging and Cancer, Hainan Medical University, Haikou, 571199, China.
| | - Moshi Song
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Institute of Healthy Aging Research, Sun Yat-sen University, Guangzhou, 510275, China.
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
| | - Yi Eve Sun
- Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China.
| | - Yu Sun
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA, 98195, USA.
| | - Mei Tian
- Human Phenome Institute, Fudan University, Shanghai, 201203, China.
| | - Shusen Wang
- Research Institute of Transplant Medicine, Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, 300384, China.
| | - Si Wang
- Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
| | - Xia Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
| | - Xiaoning Wang
- Institute of Geriatrics, The second Medical Center, Beijing Key Laboratory of Aging and Geriatrics, National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Yan-Jiang Wang
- Department of Neurology and Center for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Yunfang Wang
- Hepatobiliary and Pancreatic Center, Medical Research Center, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China.
| | - Catherine C L Wong
- Clinical Research Institute, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, 100730, China.
| | - Andy Peng Xiang
- Center for Stem Cell Biologyand Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, 510080, China.
- National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Yichuan Xiao
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Zhengwei Xie
- Peking University International Cancer Institute, Health Science Center, Peking University, Beijing, 100101, China.
- Beijing & Qingdao Langu Pharmaceutical R&D Platform, Beijing Gigaceuticals Tech. Co. Ltd., Beijing, 100101, China.
| | - Daichao Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Jing Ye
- Department of Geriatrics, Medical Center on Aging of Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital, Shanghai, 200025, China.
| | - Rui Yue
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Cuntai Zhang
- Gerontology Center of Hubei Province, Wuhan, 430000, China.
- Institute of Gerontology, Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Liang Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yong Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Yun-Wu Zhang
- Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, School of Medicine, Xiamen University, Xiamen, 361102, China.
| | - Zhuohua Zhang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical Genetics, Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, 410078, China.
- Department of Neurosciences, Hengyang Medical School, University of South China, Hengyang, 421001, China.
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
- Research Unit of New Techniques for Live-cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Dahai Zhu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Weiguo Zou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Gang Pei
- Shanghai Key Laboratory of Signaling and Disease Research, Laboratory of Receptor-Based Biomedicine, The Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, 200070, China.
| | - Guang-Hui Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
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30
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la Torre A, Lo Vecchio F, Greco A. Epigenetic Mechanisms of Aging and Aging-Associated Diseases. Cells 2023; 12:cells12081163. [PMID: 37190071 DOI: 10.3390/cells12081163] [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: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.
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Affiliation(s)
- Annamaria la Torre
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Filomena Lo Vecchio
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Antonio Greco
- Complex Unit of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
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31
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Sen P, Donahue G, Li C, Egervari G, Yang N, Lan Y, Robertson N, Shah PP, Kerkhoven E, Schultz DC, Adams PD, Berger SL. Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging. NATURE AGING 2023; 3:402-417. [PMID: 37117791 PMCID: PMC10165726 DOI: 10.1038/s43587-023-00384-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2023] [Indexed: 04/30/2023]
Abstract
Mammalian aging is characterized by the progressive loss of tissue function and increased risk for disease. Accumulation of senescent cells in aging tissues partly contributes to this decline, and targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. The fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal aberrant transcription initiation inside genes during senescence and aging that co-occurs with changes in the chromatin landscape. Interventions that alter these spurious transcripts have profound consequences on cellular health, primarily affecting intracellular signal transduction pathways. We propose that age-related spurious transcription promotes a noisy transcriptome and degradation of coherent transcriptional networks.
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Affiliation(s)
- Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Greg Donahue
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine Li
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabor Egervari
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neil Robertson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Parisha P Shah
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erik Kerkhoven
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David C Schultz
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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32
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Rabjohns EM, Rampersad RR, Ghosh A, Hurst K, Eudy AM, Brozowski JM, Lee HH, Ren Y, Mirando A, Gladman J, Bowser JL, Berg K, Wani S, Ralston SH, Hilton MJ, Tarrant TK. Aged G Protein-Coupled Receptor Kinase 3 (Grk3)-Deficient Mice Exhibit Enhanced Osteoclastogenesis and Develop Bone Lesions Analogous to Human Paget's Disease of Bone. Cells 2023; 12:981. [PMID: 37048054 PMCID: PMC10093054 DOI: 10.3390/cells12070981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
Paget's Disease of Bone (PDB) is a metabolic bone disease that is characterized by dysregulated osteoclast function leading to focal abnormalities of bone remodeling. It can lead to pain, fracture, and bone deformity. G protein-coupled receptor kinase 3 (GRK3) is an important negative regulator of G protein-coupled receptor (GPCR) signaling. GRK3 is known to regulate GPCR function in osteoblasts and preosteoblasts, but its regulatory function in osteoclasts is not well defined. Here, we report that Grk3 expression increases during osteoclast differentiation in both human and mouse primary cells and established cell lines. We also show that aged mice deficient in Grk3 develop bone lesions similar to those seen in human PDB and other Paget's Disease mouse models. We show that a deficiency in Grk3 expression enhances osteoclastogenesis in vitro and proliferation of hematopoietic osteoclast precursors in vivo but does not affect the osteoclast-mediated bone resorption function or cellular senescence pathway. Notably, we also observe decreased Grk3 expression in peripheral blood mononuclear cells of patients with PDB compared with age- and gender-matched healthy controls. Our data suggest that GRK3 has relevance to the regulation of osteoclast differentiation and that it may have relevance to the pathogenesis of PDB and other metabolic bone diseases associated with osteoclast activation.
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Affiliation(s)
- Emily M. Rabjohns
- Division of Rheumatology and Immunology, Duke University Department of Medicine, Durham, NC 27710, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rishi R. Rampersad
- Division of Rheumatology and Immunology, Duke University Department of Medicine, Durham, NC 27710, USA
| | - Arin Ghosh
- College of Arts and Sciences, Duke University, Durham, NC 27510, USA
| | - Katlyn Hurst
- College of Arts and Sciences, Duke University, Durham, NC 27510, USA
| | - Amanda M. Eudy
- Division of Rheumatology and Immunology, Duke University Department of Medicine, Durham, NC 27710, USA
| | - Jaime M. Brozowski
- Division of Rheumatology and Immunology, Duke University Department of Medicine, Durham, NC 27710, USA
| | - Hyun Ho Lee
- Division of Rheumatology and Immunology, Duke University Department of Medicine, Durham, NC 27710, USA
| | - Yinshi Ren
- Department of Orthopaedic Surgery, University of Texas Southwestern, Dallas, TX 75390, USA
- Scottish Rite Hospital, Dallas, TX 75219, USA
- Department of Orthopedics, Duke University, Durham, NC 27710, USA
| | - Anthony Mirando
- Department of Orthopedics, Duke University, Durham, NC 27710, USA
| | - Justin Gladman
- Pratt School of Engineering, Duke University, Durham, NC 27710, USA
| | - Jessica L. Bowser
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kathryn Berg
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sachin Wani
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Stuart H. Ralston
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Teresa K. Tarrant
- Division of Rheumatology and Immunology, Duke University Department of Medicine, Durham, NC 27710, USA
- Durham Veterans Hospital, Durham, NC 27710, USA
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Nassour J, Aguiar LG, Correia A, Schmidt TT, Mainz L, Przetocka S, Haggblom C, Tadepalle N, Williams A, Shokhirev MN, Akincilar SC, Tergaonkar V, Shadel GS, Karlseder J. Telomere-to-mitochondria signalling by ZBP1 mediates replicative crisis. Nature 2023; 614:767-773. [PMID: 36755096 PMCID: PMC9946831 DOI: 10.1038/s41586-023-05710-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2023] [Indexed: 02/10/2023]
Abstract
Cancers arise through the accumulation of genetic and epigenetic alterations that enable cells to evade telomere-based proliferative barriers and achieve immortality. One such barrier is replicative crisis-an autophagy-dependent program that eliminates checkpoint-deficient cells with unstable telomeres and other cancer-relevant chromosomal aberrations1,2. However, little is known about the molecular events that regulate the onset of this important tumour-suppressive barrier. Here we identified the innate immune sensor Z-DNA binding protein 1 (ZBP1) as a regulator of the crisis program. A crisis-associated isoform of ZBP1 is induced by the cGAS-STING DNA-sensing pathway, but reaches full activation only when associated with telomeric-repeat-containing RNA (TERRA) transcripts that are synthesized from dysfunctional telomeres. TERRA-bound ZBP1 oligomerizes into filaments on the outer mitochondrial membrane of a subset of mitochondria, where it activates the innate immune adapter protein mitochondrial antiviral-signalling protein (MAVS). We propose that these oligomerization properties of ZBP1 serve as a signal amplification mechanism, where few TERRA-ZBP1 interactions are sufficient to launch a detrimental MAVS-dependent interferon response. Our study reveals a mechanism for telomere-mediated tumour suppression, whereby dysfunctional telomeres activate innate immune responses through mitochondrial TERRA-ZBP1 complexes to eliminate cells destined for neoplastic transformation.
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Affiliation(s)
- Joe Nassour
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Adriana Correia
- The Salk Institute for Biological Studies, La Jolla, CA, USA
- Departamento de Biologia Vegetal, Faculdade de Ciências da Universidade de Lisboa (FCUL), Lisbon, Portugal
| | | | - Laura Mainz
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sara Przetocka
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Candy Haggblom
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - April Williams
- The Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Semih C Akincilar
- A*STAR Division of Cancer Genetics, Institute of Molecular and Cell Biology (IMCB), Singapore, Singapore
- Therapeutics Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), Singapore, Singapore
| | - Vinay Tergaonkar
- A*STAR Division of Cancer Genetics, Institute of Molecular and Cell Biology (IMCB), Singapore, Singapore
- Therapeutics Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Gerald S Shadel
- The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Jan Karlseder
- The Salk Institute for Biological Studies, La Jolla, CA, USA.
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34
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Protasoni M, Serrano M. Targeting Mitochondria to Control Ageing and Senescence. Pharmaceutics 2023; 15:352. [PMID: 36839673 PMCID: PMC9960816 DOI: 10.3390/pharmaceutics15020352] [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: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/24/2023] Open
Abstract
Ageing is accompanied by a progressive impairment of cellular function and a systemic deterioration of tissues and organs, resulting in increased vulnerability to multiple diseases. Here, we review the interplay between two hallmarks of ageing, namely, mitochondrial dysfunction and cellular senescence. The targeting of specific mitochondrial features in senescent cells has the potential of delaying or even reverting the ageing process. A deeper and more comprehensive understanding of mitochondrial biology in senescent cells is necessary to effectively face this challenge. Here, we discuss the main alterations in mitochondrial functions and structure in both ageing and cellular senescence, highlighting the differences and similarities between the two processes. Moreover, we describe the treatments available to target these pathways and speculate on possible future directions of anti-ageing and anti-senescence therapies targeting mitochondria.
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Affiliation(s)
- Margherita Protasoni
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Cambridge Institute of Science, Altos Labs, Granta Park, Cambridge CB21 6GP, UK
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35
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Ayala-Guerrero L, Claudio-Galeana S, Furlan-Magaril M, Castro-Obregón S. Chromatin Structure from Development to Ageing. Subcell Biochem 2023; 102:7-51. [PMID: 36600128 DOI: 10.1007/978-3-031-21410-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Nuclear structure influences genome architecture, which contributes to determine patterns of gene expression. Global changes in chromatin dynamics are essential during development and differentiation, and are one of the hallmarks of ageing. This chapter describes the molecular dynamics of chromatin structure that occur during development and ageing. In the first part, we introduce general information about the nuclear lamina, the chromatin structure, and the 3D organization of the genome. Next, we detail the molecular hallmarks found during development and ageing, including the role of DNA and histone modifications, 3D genome dynamics, and changes in the nuclear lamina. Within the chapter we discuss the implications that genome structure has on the mechanisms that drive development and ageing, and the physiological consequences when these mechanisms fail.
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Affiliation(s)
- Lorelei Ayala-Guerrero
- Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico
| | - Sherlyn Claudio-Galeana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico
| | - Mayra Furlan-Magaril
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
| | - Susana Castro-Obregón
- Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
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36
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Tabibzadeh S. Resolving Geroplasticity to the Balance of Rejuvenins and Geriatrins. Aging Dis 2022; 13:1664-1714. [PMID: 36465174 PMCID: PMC9662275 DOI: 10.14336/ad.2022.0414] [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: 03/19/2022] [Accepted: 04/14/2022] [Indexed: 09/29/2024] Open
Abstract
According to the cell centric hypotheses, the deficits that drive aging occur within cells by age dependent progressive damage to organelles, telomeres, biologic signaling pathways, bioinformational molecules, and by exhaustion of stem cells. Here, we amend these hypotheses and propose an eco-centric model for geroplasticity (aging plasticity including aging reversal). According to this model, youth and aging are plastic and require constant maintenance, and, respectively, engage a host of endogenous rejuvenating (rejuvenins) and gero-inducing [geriatrin] factors. Aging in this model is akin to atrophy that occurs as a result of damage or withdrawal of trophic factors. Rejuvenins maintain and geriatrins adversely impact cellular homeostasis, cell fitness, and proliferation, stem cell pools, damage response and repair. Rejuvenins reduce and geriatrins increase the age-related disorders, inflammatory signaling, and senescence and adjust the epigenetic clock. When viewed through this perspective, aging can be successfully reversed by supplementation with rejuvenins and by reducing the levels of geriatrins.
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Affiliation(s)
- Siamak Tabibzadeh
- Frontiers in Bioscience Research Institute in Aging and Cancer, Irvine, CA 92618, USA
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37
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Maurya VK, Szwarc MM, Lonard DM, Gibbons WE, Wu SP, O’Malley BW, DeMayo FJ, Lydon JP. Decidualization of human endometrial stromal cells requires steroid receptor coactivator-3. FRONTIERS IN REPRODUCTIVE HEALTH 2022; 4:1033581. [PMID: 36505394 PMCID: PMC9730893 DOI: 10.3389/frph.2022.1033581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Steroid receptor coactivator-3 (SRC-3; also known as NCOA3 or AIB1) is a member of the multifunctional p160/SRC family of coactivators, which also includes SRC-1 and SRC-2. Clinical and cell-based studies as well as investigations on mice have demonstrated pivotal roles for each SRC in numerous physiological and pathophysiological contexts, underscoring their functional pleiotropy. We previously demonstrated the critical involvement of SRC-2 in murine embryo implantation as well as in human endometrial stromal cell (HESC) decidualization, a cellular transformation process required for trophoblast invasion and ultimately placentation. We show here that, like SRC-2, SRC-3 is expressed in the epithelial and stromal cellular compartments of the human endometrium during the proliferative and secretory phase of the menstrual cycle as well as in cultured HESCs. We also found that SRC-3 depletion in cultured HESCs results in a significant attenuation in the induction of a wide-range of established biomarkers of decidualization, despite exposure of these cells to a deciduogenic stimulus and normal progesterone receptor expression. These molecular findings are supported at the cellular level by the inability of HESCs to morphologically transform from a stromal fibroblastoid cell to an epithelioid decidual cell when endogenous SRC-3 levels are markedly reduced. To identify genes, signaling pathways and networks that are controlled by SRC-3 and potentially important for hormone-dependent decidualization, we performed RNA-sequencing on HESCs in which SRC-3 levels were significantly reduced at the time of administering the deciduogenic stimulus. Comparing HESC controls with HESCs deficient in SRC-3, gene enrichment analysis of the differentially expressed gene set revealed an overrepresentation of genes involved in chromatin remodeling, cell proliferation/motility, and programmed cell death. These predictive bioanalytic results were confirmed by the demonstration that SRC-3 is required for the expansion, migratory and invasive activities of the HESC population, cellular properties that are required in vivo in the formation or functioning of the decidua. Collectively, our results support SRC-3 as an important coregulator in HESC decidualization. Since perturbation of normal homeostatic levels of SRC-3 is linked with common gynecological disorders diagnosed in reproductive age women, this endometrial coregulator-along with its new molecular targets described here-may open novel clinical avenues in the diagnosis and/or treatment of a non-receptive endometrium, particularly in patients presenting non-aneuploid early pregnancy loss.
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Affiliation(s)
- Vineet K. Maurya
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Maria M. Szwarc
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - David M. Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - William E. Gibbons
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, United States
| | - San-Pin Wu
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States
| | - Bert W. O’Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Francesco J. DeMayo
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States
| | - John P. Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States,Correspondence: John P. Lydon
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38
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Wang K, Liu H, Hu Q, Wang L, Liu J, Zheng Z, Zhang W, Ren J, Zhu F, Liu GH. Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct Target Ther 2022; 7:374. [PMID: 36336680 PMCID: PMC9637765 DOI: 10.1038/s41392-022-01211-8] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Aging is accompanied by the decline of organismal functions and a series of prominent hallmarks, including genetic and epigenetic alterations. These aging-associated epigenetic changes include DNA methylation, histone modification, chromatin remodeling, non-coding RNA (ncRNA) regulation, and RNA modification, all of which participate in the regulation of the aging process, and hence contribute to aging-related diseases. Therefore, understanding the epigenetic mechanisms in aging will provide new avenues to develop strategies to delay aging. Indeed, aging interventions based on manipulating epigenetic mechanisms have led to the alleviation of aging or the extension of the lifespan in animal models. Small molecule-based therapies and reprogramming strategies that enable epigenetic rejuvenation have been developed for ameliorating or reversing aging-related conditions. In addition, adopting health-promoting activities, such as caloric restriction, exercise, and calibrating circadian rhythm, has been demonstrated to delay aging. Furthermore, various clinical trials for aging intervention are ongoing, providing more evidence of the safety and efficacy of these therapies. Here, we review recent work on the epigenetic regulation of aging and outline the advances in intervention strategies for aging and age-associated diseases. A better understanding of the critical roles of epigenetics in the aging process will lead to more clinical advances in the prevention of human aging and therapy of aging-related diseases.
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Affiliation(s)
- Kang Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Huicong Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Qinchao Hu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
- Hospital of Stomatology, Sun Yat-sen University, 510060, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lingna Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Jiaqing Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Zikai Zheng
- University of Chinese Academy of Sciences, 100049, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, 100049, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jie Ren
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Fangfang Zhu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 200030, Shanghai, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, 100053, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China.
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39
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Blessing WA, Digesu CS, Liu R, Mahvi DA, Tal-Mason A, Kumar A, Hachey KJ, Colby AH, Korunes-Miller JT, Agar N, Regan MS, Shih A, Raut CP, Grinstaff MW, Colson YL. Sustained Supratherapeutic Paclitaxel Delivery Enhances Irreversible Sarcoma Cell Death. Mol Cancer Ther 2022; 21:1663-1673. [PMID: 36031342 PMCID: PMC9633561 DOI: 10.1158/1535-7163.mct-21-0750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/26/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022]
Abstract
Risk of locoregional recurrence after sarcoma resection is high, increasing both morbidity and mortality. Intraoperative implantation of paclitaxel (PTX)-eluting polymer films locally delivers sustained, supratherapeutic PTX concentrations to the tumor bed that are not clinically feasible with systemic therapy, thereby reducing recurrence and improving survival in a murine model of recurrent sarcoma. However, the biology underlying increased efficacy of PTX-eluting films is unknown and provides the impetus for this work. In vitro PTX efficacy is time and dose dependent with prolonged exposure significantly decreasing PTX IC50 values for human chondrosarcoma (CS-1) cells (153.9 nmol/L at 4 hours vs. 14.2 nmol/L at 30 hours, P = 0.0001). High-dose PTX significantly inhibits proliferation with in vivo PTX films delivering a dose >130 μmol/L directly to the tumor thereby irreversibly arresting cell cycle and inducing apoptosis in CS-1 as well as patient-derived liposarcoma (LP6) and leiomyosarcoma (LMS20). Supratherapeutic PTX upregulates the expression of p21 in G2-M arrested cells, and irreversibly induces apoptosis followed by cell death, within 4 hours of exposure. Microarray analyses corroborate the finding of poor DNA integrity commonly observed as a final step of apoptosis in CS-1 cells and tumor. Unlike low PTX concentrations at the tumor bed during systemic delivery, supratherapeutic concentrations achieved with PTX-eluting films markedly decrease sarcoma lethality in vivo and offer an alternative paradigm to prevent recurrence.
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Affiliation(s)
- William A. Blessing
- Division of Thoracic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Christopher S. Digesu
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Rong Liu
- Division of Thoracic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - David A. Mahvi
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Aya Tal-Mason
- Division of Thoracic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Anil Kumar
- Division of Thoracic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | - Aaron H. Colby
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston, MA
| | - Jenny T. Korunes-Miller
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston, MA
| | - Natalie Agar
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Michael S. Regan
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Angela Shih
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Chandrajit P. Raut
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mark W. Grinstaff
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, Boston, MA
| | - Yolonda L. Colson
- Division of Thoracic Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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40
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Zhang Y, Amaral ML, Zhu C, Grieco SF, Hou X, Lin L, Buchanan J, Tong L, Preissl S, Xu X, Ren B. Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain. Cell Res 2022; 32:1008-1021. [PMID: 36207411 PMCID: PMC9652396 DOI: 10.1038/s41422-022-00719-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/21/2022] [Indexed: 01/31/2023] Open
Abstract
Loss of heterochromatin has been implicated as a cause of pre-mature aging and age-associated decline in organ functions in mammals; however, the specific cell types and gene loci affected by this type of epigenetic change have remained unclear. To address this knowledge gap, we probed chromatin accessibility at single-cell resolution in the brains, hearts, skeletal muscles, and bone marrows from young, middle-aged, and old mice, and assessed age-associated changes at 353,126 candidate cis-regulatory elements (cCREs) across 32 major cell types. Unexpectedly, we detected increased chromatin accessibility within specific heterochromatin domains in old mouse excitatory neurons. The gain of chromatin accessibility at these genomic loci was accompanied by the cell-type-specific loss of heterochromatin and activation of LINE1 elements. Immunostaining further confirmed the loss of the heterochromatin mark H3K9me3 in the excitatory neurons but not in inhibitory neurons or glial cells. Our results reveal the cell-type-specific changes in chromatin landscapes in old mice and shed light on the scope of heterochromatin loss in mammalian aging.
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Affiliation(s)
- Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- School of Life Sciences, Westlake University, Hangzhou, China.
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Chenxu Zhu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Steven Francis Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Lin Lin
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Liqi Tong
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA.
- The Center for Neural Circuit Mapping, University of California, Irvine, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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41
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Jäger K, Mensch J, Grimmig ME, Neuner B, Gorzelniak K, Türkmen S, Demuth I, Hartmann A, Hartmann C, Wittig F, Sporbert A, Hermann A, Fuellen G, Möller S, Walter M. A conserved long-distance telomeric silencing mechanism suppresses mTOR signaling in aging human fibroblasts. SCIENCE ADVANCES 2022; 8:eabk2814. [PMID: 35977016 PMCID: PMC9385144 DOI: 10.1126/sciadv.abk2814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Telomeres are repetitive nucleotide sequences at the ends of each chromosome. It has been hypothesized that telomere attrition evolved as a tumor suppressor mechanism in large long-lived species. Long telomeres can silence genes millions of bases away through a looping mechanism called telomere position effect over long distances (TPE-OLD). The function of this silencing mechanism is unknown. We determined a set of 2322 genes with high positional conservation across replicatively aging species that includes known and candidate TPE-OLD genes that may mitigate potentially harmful effects of replicative aging. Notably, we identified PPP2R2C as a tumor suppressor gene, whose up-regulation by TPE-OLD in aged human fibroblasts leads to dephosphorylation of p70S6 kinase and mammalian target of rapamycin suppression. A mechanistic link between telomeres and a tumor suppressor mechanism supports the hypothesis that replicative aging fulfills a tumor suppressor function and motivates previously unknown antitumor and antiaging strategies.
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Affiliation(s)
- Kathrin Jäger
- Institute of Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, University of Rostock, Rostock, Germany
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Berlin, Germany
| | - Juliane Mensch
- Institute of Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, University of Rostock, Rostock, Germany
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Berlin, Germany
| | - Maria Elisabeth Grimmig
- Institute of Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Bruno Neuner
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Anesthesiology and Intensive Care Medicine, Berlin, Germany
| | - Kerstin Gorzelniak
- Unfallkrankenhaus Berlin, Institute of Laboratory Medicine, Berlin, Germany
| | - Seval Türkmen
- LNS Hematooncogenetics, National Center of Genetics Luxembourg, Dudelange, Luxemburg
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Genetics and Human Genetics, Berlin, Germany
| | - Ilja Demuth
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Endocrinology and Metabolism, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, BCRT - Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Alexander Hartmann
- Institute of Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Christiane Hartmann
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, Rostock University Medical Center, University of Rostock, 18147 Rostock, Germany
| | - Felix Wittig
- Institute of Pharmacology and Toxicology, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Anje Sporbert
- Advanced Light Microscopy, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Andreas Hermann
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, Rostock University Medical Center, University of Rostock, 18147 Rostock, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Rostock/Greifswald, Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, Rostock, Germany
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Steffen Möller
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Michael Walter
- Institute of Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, University of Rostock, Rostock, Germany
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Berlin, Germany
- Corresponding author.
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Svoboda LK, Perera BPU, Morgan RK, Polemi KM, Pan J, Dolinoy DC. Toxicoepigenetics and Environmental Health: Challenges and Opportunities. Chem Res Toxicol 2022; 35:1293-1311. [PMID: 35876266 PMCID: PMC9812000 DOI: 10.1021/acs.chemrestox.1c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The rapidly growing field of toxicoepigenetics seeks to understand how toxicant exposures interact with the epigenome to influence disease risk. Toxicoepigenetics is a promising field of environmental health research, as integrating epigenetics into the field of toxicology will enable a more thorough evaluation of toxicant-induced disease mechanisms as well as the elucidation of the role of the epigenome as a biomarker of exposure and disease and possible mediator of exposure effects. Likewise, toxicoepigenetics will enhance our knowledge of how environmental exposures, lifestyle factors, and diet interact to influence health. Ultimately, an understanding of how the environment impacts the epigenome to cause disease may inform risk assessment, permit noninvasive biomonitoring, and provide potential opportunities for therapeutic intervention. However, the translation of research from this exciting field into benefits for human and animal health presents several challenges and opportunities. Here, we describe four significant areas in which we see opportunity to transform the field and improve human health by reducing the disease burden caused by environmental exposures. These include (1) research into the mechanistic role for epigenetic change in environment-induced disease, (2) understanding key factors influencing vulnerability to the adverse effects of environmental exposures, (3) identifying appropriate biomarkers of environmental exposures and their associated diseases, and (4) determining whether the adverse effects of environment on the epigenome and human health are reversible through pharmacologic, dietary, or behavioral interventions. We then highlight several initiatives currently underway to address these challenges.
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Affiliation(s)
- Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katelyn M Polemi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Junru Pan
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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Sikder S, Arunkumar G, Melters DP, Dalal Y. Breaking the aging epigenetic barrier. Front Cell Dev Biol 2022; 10:943519. [PMID: 35966762 PMCID: PMC9366916 DOI: 10.3389/fcell.2022.943519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Aging is an inexorable event occurring universally for all organisms characterized by the progressive loss of cell function. However, less is known about the key events occurring inside the nucleus in the process of aging. The advent of chromosome capture techniques and extensive modern sequencing technologies have illuminated a rather dynamic structure of chromatin inside the nucleus. As cells advance along their life cycle, chromatin condensation states alter which leads to a different epigenetic landscape, correlated with modified gene expression. The exact factors mediating these changes in the chromatin structure and function remain elusive in the context of aging cells. The accumulation of DNA damage, reactive oxygen species and loss of genomic integrity as cells cease to divide can contribute to a tumor stimulating environment. In this review, we focus on genomic and epigenomic changes occurring in an aged cell which can contribute to age-related tumor formation.
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Affiliation(s)
| | | | | | - Yamini Dalal
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, United States
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Tan SYX, Zhang J, Tee WW. Epigenetic Regulation of Inflammatory Signaling and Inflammation-Induced Cancer. Front Cell Dev Biol 2022; 10:931493. [PMID: 35757000 PMCID: PMC9213816 DOI: 10.3389/fcell.2022.931493] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Epigenetics comprise a diverse array of reversible and dynamic modifications to the cell’s genome without implicating any DNA sequence alterations. Both the external environment surrounding the organism, as well as the internal microenvironment of cells and tissues, contribute to these epigenetic processes that play critical roles in cell fate specification and organismal development. On the other hand, dysregulation of epigenetic activities can initiate and sustain carcinogenesis, which is often augmented by inflammation. Chronic inflammation, one of the major hallmarks of cancer, stems from proinflammatory cytokines that are secreted by tumor and tumor-associated cells in the tumor microenvironment. At the same time, inflammatory signaling can establish positive and negative feedback circuits with chromatin to modulate changes in the global epigenetic landscape. In this review, we provide an in-depth discussion of the interconnected crosstalk between epigenetics and inflammation, specifically how epigenetic mechanisms at different hierarchical levels of the genome control inflammatory gene transcription, which in turn enact changes within the cell’s epigenomic profile, especially in the context of inflammation-induced cancer.
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Affiliation(s)
- Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Aguado J, Gómez-Inclán C, Leeson HC, Lavin MF, Shiloh Y, Wolvetang EJ. The hallmarks of aging in Ataxia-Telangiectasia. Ageing Res Rev 2022; 79:101653. [PMID: 35644374 DOI: 10.1016/j.arr.2022.101653] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/28/2022] [Accepted: 05/24/2022] [Indexed: 01/10/2023]
Abstract
Ataxia-telangiectasia (A-T) is caused by absence of the catalytic activity of ATM, a protein kinase that plays a central role in the DNA damage response, many branches of cellular metabolism, redox and mitochondrial homeostasis, and cell cycle regulation. A-T is a complex disorder characterized mainly by progressive cerebellar degeneration, immunodeficiency, radiation sensitivity, genome instability, and predisposition to cancer. It is increasingly recognized that the premature aging component of A-T is an important driver of this disease, and A-T is therefore an attractive model to study the aging process. This review outlines the current state of knowledge pertaining to the molecular and cellular signatures of aging in A-T and proposes how these new insights can guide novel therapeutic approaches for A-T.
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Affiliation(s)
- Julio Aguado
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Queensland 4072, Australia.
| | - Cecilia Gómez-Inclán
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Queensland 4072, Australia
| | - Hannah C Leeson
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Queensland 4072, Australia
| | - Martin F Lavin
- University of Queensland Centre for Clinical Research, The University of Queensland, Herston, Brisbane, Australia
| | - Yosef Shiloh
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Queensland 4072, Australia.
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Lyu Y, Ge Y. Toward Elucidating Epigenetic and Metabolic Regulation of Stem Cell Lineage Plasticity in Skin Aging. Front Cell Dev Biol 2022; 10:903904. [PMID: 35663405 PMCID: PMC9160930 DOI: 10.3389/fcell.2022.903904] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Skin is the largest organ in human body, harboring a plethora of cell types and serving as the organismal barrier. Skin aging such as wrinkling and hair graying is graphically pronounced, and the molecular mechanisms behind these phenotypic manifestations are beginning to unfold. As in many other organs and tissues, epigenetic and metabolic deregulations have emerged as key aging drivers. Particularly in the context of the skin epithelium, the epigenome and metabolome coordinately shape lineage plasticity and orchestrate stem cell function during aging. Our review discusses recent studies that proposed molecular mechanisms that drive the degeneration of hair follicles, a major appendage of the skin. By focusing on skin while comparing it to model organisms and adult stem cells of other tissues, we summarize literature on genotoxic stress, nutritional sensing, metabolic rewiring, mitochondrial activity, and epigenetic regulations of stem cell plasticity. Finally, we speculate about the rejuvenation potential of rate-limiting upstream signals during aging and the dominant role of the tissue microenvironment in dictating aged epithelial stem cell function.
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Affiliation(s)
| | - Yejing Ge
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Alsagaby SA. Transcriptomics-Based Investigation of Molecular Mechanisms Underlying Apoptosis Induced by ZnO Nanoparticles in Human Diffuse Large B-Cell Lymphoma. Int J Nanomedicine 2022; 17:2261-2281. [PMID: 35611214 PMCID: PMC9124502 DOI: 10.2147/ijn.s355408] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/29/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Zinc oxide nanoparticles (ZnO NPs) show anti-cancer activity. Diffuse Large B-cell Lymphoma (DLBCL) is a type of B-cell malignancies with unsatisfying treatment outcomes. This study was set to assess the potential of ZnO NPs to selectively induce apoptosis in human DLBCL cells (OCI-LY3), and to describe possible molecular mechanisms of action. Methods The impact of ZnO NPs on DLBCL cells and normal peripheral blood mononuclear cells (PBMCs) was studied using cytotoxicity assay and flow-cytometry. Transcriptomics analysis was conducted to identify ZnO NPs-dependent changes in the transcriptomic profiles of DLBCL cells. Results ZnO NPs selectively induced apoptosis in DLBCL cells, and caused changes in their transcriptomes. Deferential gene expression (DGE) with fold change (FC) ≥3 and p ≤ 0.008 with corrected p ≤ 0.05 was identified for 528 genes; 125 genes were over-expressed and 403 genes were under-expressed in ZnO NPs-treated DLBCL cells. The over-expressed genes involved in biological processes and pathways like stress response to metal ion, cellular response to zinc ion, metallothioneins bind metals, oxidative stress, and negative regulation of growth. In contrast, the under-expressed genes were implicated in DNA packaging complex, signaling by NOTCH, negative regulation of gene expression by epigenetic, signaling by WNT, M phase of cell cycle, and telomere maintenance. Setting the FC to ≥1.5 with p ≤ 0.05 and corrected p ≤ 0.1 showed ZnO NPs to induce over-expression of anti-oxidant genes and under-expression of oncogenes; target B-cell receptor (BCR) signaling pathway and NF-κB pathway; and promote apoptosis by intrinsic and extrinsic pathways. Discussion Overall, ZnO NPs selectively induced apoptosis in DLBCL cells, and possible molecular mechanisms of action were described.
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Affiliation(s)
- Suliman A Alsagaby
- Department of Medical Laboratories Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah, 11932, Saudi Arabia
- Correspondence: Suliman A Alsagaby, Email
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Gill D, Parry A, Santos F, Okkenhaug H, Todd CD, Hernando-Herraez I, Stubbs TM, Milagre I, Reik W. Multi-omic rejuvenation of human cells by maturation phase transient reprogramming. eLife 2022; 11:e71624. [PMID: 35390271 PMCID: PMC9023058 DOI: 10.7554/elife.71624] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of somatic cell reprogramming, which suggests full reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first "maturation phase transient reprogramming" (MPTR) method, where reprogramming factors are selectively expressed until this rejuvenation point then withdrawn. Applying MPTR to dermal fibroblasts from middle-aged donors, we found that cells temporarily lose and then reacquire their fibroblast identity, possibly as a result of epigenetic memory at enhancers and/or persistent expression of some fibroblast genes. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome was rejuvenated to a similar extent, including H3K9me3 levels and the DNA methylation ageing clock. The magnitude of rejuvenation instigated by MPTR appears substantially greater than that achieved in previous transient reprogramming protocols. In addition, MPTR fibroblasts produced youthful levels of collagen proteins, and showed partial functional rejuvenation of their migration speed. Finally, our work suggests that optimal time windows exist for rejuvenating the transcriptome and the epigenome. Overall, we demonstrate that it is possible to separate rejuvenation from complete pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.
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Affiliation(s)
- Diljeet Gill
- Epigenetics Programme, Babraham InstituteCambridgeUnited Kingdom
| | - Aled Parry
- Epigenetics Programme, Babraham InstituteCambridgeUnited Kingdom
| | - Fátima Santos
- Epigenetics Programme, Babraham InstituteCambridgeUnited Kingdom
| | | | | | | | | | - Inês Milagre
- Laboratory for Epigenetic Mechanisms/Chromosome Dynamics Lab, Instituto Gulbenkian de CiênciaOeirasPortugal
| | - Wolf Reik
- Epigenetics Programme, Babraham InstituteCambridgeUnited Kingdom
- Wellcome Trust Sanger Institute, HinxtonCambridgeUnited Kingdom
- Centre for Trophoblast Research, University of CambridgeCambridgeUnited Kingdom
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Shabanov GA, Rybchenko AA, Lugovaya YA, Vdovenko SI. Biological Age Estimation Based on the Spectral Analysis of the Bioelectrical Activity of the Human Brain. ADVANCES IN GERONTOLOGY 2022. [DOI: 10.1134/s207905702201012x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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50
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Crouch J, Shvedova M, Thanapaul RJRS, Botchkarev V, Roh D. Epigenetic Regulation of Cellular Senescence. Cells 2022; 11:672. [PMID: 35203320 PMCID: PMC8870565 DOI: 10.3390/cells11040672] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Senescence is a complex cellular stress response that abolishes proliferative capacity and generates a unique secretory pattern that is implicated in organismal aging and age-related disease. How a cell transitions to a senescent state is multifactorial and often requires transcriptional regulation of multiple genes. Epigenetic alterations to DNA and chromatin are powerful regulators of genome architecture and gene expression, and they play a crucial role in mediating the induction and maintenance of senescence. This review will highlight the changes in chromatin, DNA methylation, and histone alterations that establish and maintain cellular senescence, alongside the specific epigenetic regulation of the senescence-associated secretory phenotype (SASP).
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Affiliation(s)
- Jack Crouch
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Maria Shvedova
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Rex Jeya Rajkumar Samdavid Thanapaul
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Vladimir Botchkarev
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Daniel Roh
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
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