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Wang H, Zhang Y, Wang Z, Zhang L, Guo M, Cao C, Xiao H. Deciphering Nucleic Acid Binding Proteome of Mouse Immune Organs Reveals Hub Proteins for Aging. Mol Cell Proteomics 2023; 22:100611. [PMID: 37391046 PMCID: PMC10412848 DOI: 10.1016/j.mcpro.2023.100611] [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: 02/23/2023] [Revised: 05/24/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023] Open
Abstract
Profiling the nucleic acid-binding proteins (NABPs) during aging process is critical to elucidate its roles in biological systems as well as transcriptional and translational regulation. Here, we developed a comprehensive strategy to survey the NABPs of mouse immune organs by using single cell preparation and selective capture technology-based proteomics. Our approach provided a global view of tissue NABPs from different organs under normal physiological conditions with extraction specificity of 70 to 90%. Through quantitative proteomics analysis of mouse spleen and thymus at 1, 4, 12, 24, 48, and 72 weeks, we investigated the molecular features of aging-related NABPs. A total of 2674 proteins were quantified in all six stages, demonstrating distinct and time-specific expression pattern of NABPs. Thymus and spleen exhibited unique aging signatures, and differential proteins and pathways were enriched across the mouse lifespan. Three core modules and 16 hub proteins associated with aging were revealed through weighted gene correlation network analysis. Significant candidates were screened for immunoassay verification, and six hub proteins were confirmed. The integrated strategy pertains the capability to decipher the dynamic functions of NABPs in aging physiology and benefit further mechanism research.
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Affiliation(s)
- Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Miao Guo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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2
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Choucair K, Naqash AR, Nebhan CA, Nipp R, Johnson DB, Saeed A. Immune Checkpoint Inhibitors: The Unexplored Landscape of Geriatric Oncology. Oncologist 2022; 27:778-789. [PMID: 35781739 PMCID: PMC9438919 DOI: 10.1093/oncolo/oyac119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer is classically considered a disease of aging, with over half of all new cancer diagnoses occurring in patients over the age of 65 years. Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, yet the participation of older adults with cancer in ICI trials has been suboptimal, particularly at the extremes of age. Despite significant improvement in treatment response and an improved toxicity profile when compared with conventional cytotoxic chemotherapies, many cancers develop resistance to ICIs, and these drugs are not free of toxicities. This becomes particularly important in the setting of older adults with cancer, who are generally frailer and harbor more comorbidities than do their younger counterparts. Immunosenescence, a concept involving age-related changes in immune function, may also play a role in differential responses to ICI treatment in older patients. Data on ICI treatment response in older adult with cancers remains inconclusive, with multiple studies revealing conflicting results. The molecular mechanisms underlying response to ICIs in older cancer patients are poorly understood, and predictors of response that can delineate responders from non-responders remain to be elucidated. In this review, we explore the unique geriatric oncology population by analyzing existing retrospective datasets, and we also sought to highlight potential cellular, inflammatory, and molecular changes associated with aging as potential biomarkers for response to ICIs.
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Affiliation(s)
- Khalil Choucair
- University of Kansas School of Medicine-Wichita, Department of Internal Medicine, Wichita, KS, USA
| | - Abdul Rafeh Naqash
- The University of Oklahoma College of Medicine, Department of Internal Medicine, Division of Hematology/Oncology; Stephenson Cancer Center, Oklahoma City, OK, USA
| | - Caroline A Nebhan
- Vanderbilt University Medical Center, Department of Medicine, Division of Hematology/Oncology, Nashville, TN, USA
| | - Ryan Nipp
- The University of Oklahoma College of Medicine, Department of Internal Medicine, Division of Hematology/Oncology; Stephenson Cancer Center, Oklahoma City, Oklahoma, USA
| | - Douglas B Johnson
- Vanderbilt University Medical Center, Department of Medicine, Division of Hematology/Oncology, Nashville, Tennessee, USA
| | - Anwaar Saeed
- Kansas University Cancer Center, Department of Medicine, Division of Medical Oncology, Kansas City, KS, USA
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3
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Catarinella G, Nicoletti C, Bracaglia A, Procopio P, Salvatori I, Taggi M, Valle C, Ferri A, Canipari R, Puri PL, Latella L. SerpinE1 drives a cell-autonomous pathogenic signaling in Hutchinson-Gilford progeria syndrome. Cell Death Dis 2022; 13:737. [PMID: 36028501 PMCID: PMC9418244 DOI: 10.1038/s41419-022-05168-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 01/21/2023]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare, fatal disease caused by Lamin A mutation, leading to altered nuclear architecture, loss of peripheral heterochromatin and deregulated gene expression. HGPS patients eventually die by coronary artery disease and cardiovascular alterations. Yet, how deregulated transcriptional networks at the cellular level impact on the systemic disease phenotype is currently unclear. A genome-wide analysis of gene expression in cultures of primary HGPS fibroblasts identified SerpinE1, also known as Plasminogen Activator Inhibitor (PAI-1), as central gene that propels a cell-autonomous pathogenic signaling from the altered nuclear lamina. Indeed, siRNA-mediated downregulation and pharmacological inhibition of SerpinE1 by TM5441 could revert key pathological features of HGPS in patient-derived fibroblasts, including re-activation of cell cycle progression, reduced DNA damage signaling, decreased expression of pro-fibrotic genes and recovery of mitochondrial defects. These effects were accompanied by the correction of nuclear abnormalities. These data point to SerpinE1 as a novel potential effector and target for therapeutic interventions in HGPS pathogenesis.
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Affiliation(s)
| | - Chiara Nicoletti
- grid.479509.60000 0001 0163 8573Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Andrea Bracaglia
- grid.417778.a0000 0001 0692 3437IRCCS Fondazione Santa Lucia, Rome, Italy ,grid.6530.00000 0001 2300 0941PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Paola Procopio
- grid.417778.a0000 0001 0692 3437IRCCS Fondazione Santa Lucia, Rome, Italy ,grid.10253.350000 0004 1936 9756Present Address: BPC, Pharmakologisches Institut, Philipps-Universität Marburg, Marburg, Germany
| | - Illari Salvatori
- grid.417778.a0000 0001 0692 3437IRCCS Fondazione Santa Lucia, Rome, Italy ,grid.7841.aDepartment of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy
| | - Marilena Taggi
- grid.7841.aDAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Rome, Italy
| | - Cristiana Valle
- grid.417778.a0000 0001 0692 3437IRCCS Fondazione Santa Lucia, Rome, Italy ,grid.5326.20000 0001 1940 4177Institute of Translational Pharmacology, National Research Council of Italy, Rome, Italy
| | - Alberto Ferri
- grid.417778.a0000 0001 0692 3437IRCCS Fondazione Santa Lucia, Rome, Italy ,grid.5326.20000 0001 1940 4177Institute of Translational Pharmacology, National Research Council of Italy, Rome, Italy
| | - Rita Canipari
- grid.7841.aDAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Rome, Italy
| | - Pier Lorenzo Puri
- grid.479509.60000 0001 0163 8573Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037 USA
| | - Lucia Latella
- grid.417778.a0000 0001 0692 3437IRCCS Fondazione Santa Lucia, Rome, Italy ,grid.5326.20000 0001 1940 4177Institute of Translational Pharmacology, National Research Council of Italy, Rome, Italy
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4
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Gil L, Niño SA, Guerrero C, Jiménez-Capdeville ME. Phospho-Tau and Chromatin Landscapes in Early and Late Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms221910283. [PMID: 34638632 PMCID: PMC8509045 DOI: 10.3390/ijms221910283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 12/25/2022] Open
Abstract
Cellular identity is determined through complex patterns of gene expression. Chromatin, the dynamic structure containing genetic information, is regulated through epigenetic modulators, mainly by the histone code. One of the main challenges for the cell is maintaining functionality and identity, despite the accumulation of DNA damage throughout the aging process. Replicative cells can remain in a senescent state or develop a malign cancer phenotype. In contrast, post-mitotic cells such as pyramidal neurons maintain extraordinary functionality despite advanced age, but they lose their identity. This review focuses on tau, a protein that protects DNA, organizes chromatin, and plays a crucial role in genomic stability. In contrast, tau cytosolic aggregates are considered hallmarks of Alzheimer´s disease (AD) and other neurodegenerative disorders called tauopathies. Here, we explain AD as a phenomenon of chromatin dysregulation directly involving the epigenetic histone code and a progressive destabilization of the tau–chromatin interaction, leading to the consequent dysregulation of gene expression. Although this destabilization could be lethal for post-mitotic neurons, tau protein mediates profound cellular transformations that allow for their temporal survival.
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Affiliation(s)
- Laura Gil
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain;
| | - Sandra A. Niño
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma, de San Luis Potosí 78210, Mexico;
| | - Carmen Guerrero
- Banco de Cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain;
| | - María E. Jiménez-Capdeville
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma, de San Luis Potosí 78210, Mexico;
- Correspondence: ; Tel.: +52-444-826-2366
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5
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Ravel-Godreuil C, Massiani-Beaudoin O, Mailly P, Prochiantz A, Joshi RL, Fuchs J. Perturbed DNA methylation by Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death. iScience 2021; 24:102756. [PMID: 34278264 PMCID: PMC8264156 DOI: 10.1016/j.isci.2021.102756] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/14/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Age is a major risk factor for neurodegenerative diseases like Parkinson's disease, but few studies have explored the contribution of key hallmarks of aging, namely DNA methylation changes and heterochromatin destructuration, in the neurodegenerative process. Here, we investigated the consequences of viral overexpression of Gadd45b, a multifactorial protein involved in DNA demethylation, in the mouse midbrain. Gadd45b overexpression induced global and stable changes in DNA methylation, particularly in introns of genes related to neuronal functions, as well as on LINE-1 transposable elements. This was paralleled by disorganized heterochromatin, increased DNA damage, and vulnerability to oxidative stress. LINE-1 de-repression, a potential source of DNA damage, preceded Gadd45b-induced neurodegeneration, whereas prolonged Gadd45b expression deregulated expression of genes related to heterochromatin maintenance, DNA methylation, or Parkinson's disease. Our data indicates that aging-related alterations contribute to dopaminergic neuron degeneration with potential implications for Parkinson's disease.
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Affiliation(s)
- Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Mailly
- Orion Imaging Facility, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Labex Memolife, Université PSL, Paris, France
| | - Alain Prochiantz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Rajiv L. Joshi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
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6
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Gil L, Niño SA, Capdeville G, Jiménez-Capdeville ME. Aging and Alzheimer's disease connection: Nuclear Tau and lamin A. Neurosci Lett 2021; 749:135741. [PMID: 33610669 DOI: 10.1016/j.neulet.2021.135741] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/12/2021] [Accepted: 02/11/2021] [Indexed: 12/24/2022]
Abstract
Age-related pathologies like Alzheimer`s disease (AD) imply cellular responses directed towards repairing DNA damage. Postmitotic neurons show progressive accumulation of oxidized DNA during decades of brain aging, which is especially remarkable in AD brains. The characteristic cytoskeletal pathology of AD neurons is brought about by the progressive changes that neurons undergo throughout aging, and their irreversible nuclear transformation initiates the disease. This review focusses on critical molecular events leading to the loss of plasticity that underlies cognitive deficits in AD. During healthy neuronal aging, nuclear Tau participates in the regulation of the structure and function of the chromatin. The aberrant cell cycle reentry initiated for DNA repair triggers a cascade of events leading to the dysfunctional AD neuron, whereby Tau protein exits the nucleus leading to chromatin disorganization. Lamin A, which is not typically expressed in neurons, appears at the transformation from senile to AD neurons and contributes to halting the consequences of cell cycle reentry and nuclear Tau exit, allowing the survival of the neuron. Nevertheless, this irreversible nuclear transformation alters the nucleic acid and protein synthesis machinery as well as the nuclear lamina and cytoskeleton structures, leading to neurofibrillary tangles formation and final neurodegeneration.
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Affiliation(s)
- Laura Gil
- Departamento de Genética, Escuela de Medicina, Universidad "Alfonso X el Sabio", Madrid, Spain
| | - Sandra A Niño
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, Mexico
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7
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Lee JR, Choe SH, Kim YH, Cho HM, Park HR, Lee HE, Jin YB, Kim JS, Jeong KJ, Park SJ, Huh JW. Longitudinal profiling of the blood transcriptome in an African green monkey aging model. Aging (Albany NY) 2020; 13:846-864. [PMID: 33290253 PMCID: PMC7834999 DOI: 10.18632/aging.202190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
African green monkeys (AGMs, Chlorocebus aethiops) are Old World monkeys which are used as experimental models in biomedical research. Recent technological advances in next generation sequencing are useful for unraveling the genetic mechanisms underlying senescence, aging, and age-related disease. To elucidate the normal aging mechanisms in older age, the blood transcriptomes of nine healthy, aged AGMs (15‒23 years old), were analyzed over two years. We identified 910‒1399 accumulated differentially expressed genes (DEGs) in each individual, which increased with age. Aging-related DEGs were sorted across the three time points. A major proportion of the aging-related DEGs belonged to gene ontology (GO) categories involved in translation and rRNA metabolic processes. Next, we sorted common aging-related DEGs across three time points over two years. Common aging-related DEGs belonged to GO categories involved in translation, cellular component biogenesis, rRNA metabolic processes, cellular component organization, biogenesis, and RNA metabolic processes. Furthermore, we identified 29 candidate aging genes that were upregulated across the time series analysis. These candidate aging genes were linked to protein synthesis. This study describes a changing gene expression pattern in AGMs during aging using longitudinal transcriptome sequencing. The candidate aging genes identified here may be potential targets for the treatment of aging.
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Affiliation(s)
- Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56216, Republic of Korea
| | - Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Hye-Ri Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee-Eun Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Yeung Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Ji-Su Kim
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56216, Republic of Korea
| | - Kang Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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8
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Yang Z, Jiang H. A chromatin perspective on metabolic and genotoxic impacts on hematopoietic stem and progenitor cells. Cell Mol Life Sci 2020; 77:4031-4047. [PMID: 32318759 PMCID: PMC7541408 DOI: 10.1007/s00018-020-03522-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023]
Abstract
Fate determination in self-renewal and differentiation of hematopoietic stem and progenitor cells (HSCs and HPCs) is ultimately controlled by gene expression, which is profoundly influenced by the global and local chromatin state. Cellular metabolism directly influences the chromatin state through the dynamic regulation of the enzymatic activities that modify DNA and histones, but also generates genotoxic metabolites that can damage DNA and thus pose threat to the genome integrity. On the other hand, mechanisms modulating the chromatin state impact metabolism by regulating the expression and activities of key metabolic enzymes. Moreover, through regulating either DNA damage response directly or expression of genes involved in this process, chromatin modulators play active and crucial roles in guarding the genome integrity, breaching of which results in defective HSPC function. Therefore, HSPC function is regulated by the dynamic and two-way interactions between metabolism and chromatin. Here, we review recent advances that provide a chromatin perspective on the major impacts the metabolic and genotoxic factors can have on HSPC function and fate determination.
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Affiliation(s)
- Zhenhua Yang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
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9
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Maruthapandi M, Saravanan A, Luong JHT, Gedanken A. Antimicrobial Properties of Polyaniline and Polypyrrole Decorated with Zinc-Doped Copper Oxide Microparticles. Polymers (Basel) 2020; 12:polym12061286. [PMID: 32512800 PMCID: PMC7362252 DOI: 10.3390/polym12061286] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023] Open
Abstract
Polyaniline (PANI) and polypyrrole (PPY) were synthesized by carbon dots (CDs) under UV irradiation and then sonicated together with zinc acetate and copper acetate to form the PANI-Zn@CuO and PPY-Zn@Cu composites. The former consisted of agglomerated spherical particles with diameters of 1–5 µm, whereas the latter displayed irregular stick shapes with similar diameters. The bacterial potency of the composites against Escherichia coli and Staphylococcus aureus was enhanced remarkably with Zn doping in the CuO matrix, designated as Zn0.11Cu0.89O, at 0.144 mg/mL. The cell death was mainly attributed to the release of reactive oxygen species (ROS) that would severely damage DNA, proteins, and lipids. Bacteria could adhere to neutral surfaces of the composites by van der Waals attractive forces. The binding event disrupted the native surface charge of bacterial cells to induce cell lysis and result in eventual cell death.
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Affiliation(s)
- Moorthy Maruthapandi
- Bar-Ilan Institute for Nanotechnology and Advanced Materials, Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel; (M.M.); (A.S.)
| | - Arumugam Saravanan
- Bar-Ilan Institute for Nanotechnology and Advanced Materials, Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel; (M.M.); (A.S.)
| | - John H. T. Luong
- School of Chemistry, University College Cork, Cork T12 YN60, Ireland;
| | - Aharon Gedanken
- Bar-Ilan Institute for Nanotechnology and Advanced Materials, Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel; (M.M.); (A.S.)
- Correspondence: ; Tel.: +972-3-5318315; Fax: +972-3-7384053
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10
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Mueller AL, McNamara MS, Sinclair DA. Why does COVID-19 disproportionately affect older people? Aging (Albany NY) 2020; 12:9959-9981. [PMID: 32470948 PMCID: PMC7288963 DOI: 10.18632/aging.103344] [Citation(s) in RCA: 578] [Impact Index Per Article: 144.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022]
Abstract
The severity and outcome of coronavirus disease 2019 (COVID-19) largely depends on a patient's age. Adults over 65 years of age represent 80% of hospitalizations and have a 23-fold greater risk of death than those under 65. In the clinic, COVID-19 patients most commonly present with fever, cough and dyspnea, and from there the disease can progress to acute respiratory distress syndrome, lung consolidation, cytokine release syndrome, endotheliitis, coagulopathy, multiple organ failure and death. Comorbidities such as cardiovascular disease, diabetes and obesity increase the chances of fatal disease, but they alone do not explain why age is an independent risk factor. Here, we present the molecular differences between young, middle-aged and older people that may explain why COVID-19 is a mild illness in some but life-threatening in others. We also discuss several biological age clocks that could be used in conjunction with genetic tests to identify both the mechanisms of the disease and individuals most at risk. Finally, based on these mechanisms, we discuss treatments that could increase the survival of older people, not simply by inhibiting the virus, but by restoring patients' ability to clear the infection and effectively regulate immune responses.
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Affiliation(s)
- Amber L. Mueller
- Glenn Center for Biology of Aging Research, Blavatnik Institute, Harvard Medical School, Boston, MA 20115, USA
| | - Maeve S. McNamara
- Glenn Center for Biology of Aging Research, Blavatnik Institute, Harvard Medical School, Boston, MA 20115, USA
| | - David A. Sinclair
- Glenn Center for Biology of Aging Research, Blavatnik Institute, Harvard Medical School, Boston, MA 20115, USA
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11
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Hishikawa A, Hayashi K, Abe T, Kaneko M, Yokoi H, Azegami T, Nakamura M, Yoshimoto N, Kanda T, Sakamaki Y, Itoh H. Decreased KAT5 Expression Impairs DNA Repair and Induces Altered DNA Methylation in Kidney Podocytes. Cell Rep 2020; 26:1318-1332.e4. [PMID: 30699357 DOI: 10.1016/j.celrep.2019.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 11/18/2018] [Accepted: 12/28/2018] [Indexed: 01/19/2023] Open
Abstract
Altered DNA methylation plays an important role in the onset and progression of kidney disease. However, little is known about how the changes arise in disease states. Here, we report that KAT5-mediated DNA damage repair is essential for the maintenance of kidney podocytes and is associated with DNA methylation status. Podocyte-specific KAT5-knockout mice develop severe albuminuria with increased DNA double-strand breaks (DSBs), increased DNA methylation of the nephrin promoter region, and decreased nephrin expression. Podocyte KAT5 expression is decreased, whereas DNA DSBs and DNA methylation are increased in diabetic nephropathy; moreover, KAT5 restoration by gene transfer attenuates albuminuria. Furthermore, KAT5 decreases DNA DSBs and DNA methylation at the same nephrin promoter region, which indicates that KAT5-mediated DNA repair may be related to DNA methylation status. These results suggest a concept in which an environment of DNA damage repair, which occurs with decreased KAT5, may affect DNA methylation status.
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Affiliation(s)
- Akihito Hishikawa
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kaori Hayashi
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Takaya Abe
- Animal Resource Development Unit and Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, Hyogo 650-0047, Japan
| | - Mari Kaneko
- Animal Resource Development Unit and Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, Hyogo 650-0047, Japan
| | - Hideki Yokoi
- Department of Nephrology, Kyoto University Graduate School of Medicine, 54 Shogoin Kawahara-cho, Sakyo, Kyoto 606-8507, Japan
| | - Tatsuhiko Azegami
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Mari Nakamura
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Norifumi Yoshimoto
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Takeshi Kanda
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yusuke Sakamaki
- Department of Internal Medicine, Tokyo Dental College Hospital, 5-11-13 Sugano, Ichikawa-shi, Chiba 272-8513, Japan
| | - Hiroshi Itoh
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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12
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Gil L, Niño SA, Chi-Ahumada E, Rodríguez-Leyva I, Guerrero C, Rebolledo AB, Arias JA, Jiménez-Capdeville ME. Perinuclear Lamin A and Nucleoplasmic Lamin B2 Characterize Two Types of Hippocampal Neurons through Alzheimer's Disease Progression. Int J Mol Sci 2020; 21:E1841. [PMID: 32155994 PMCID: PMC7084765 DOI: 10.3390/ijms21051841] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Recent reports point to a nuclear origin of Alzheimer's disease (AD). Aged postmitotic neurons try to repair their damaged DNA by entering the cell cycle. This aberrant cell cycle re-entry involves chromatin modifications where nuclear Tau and the nuclear lamin are involved. The purpose of this work was to elucidate their participation in the nuclear pathological transformation of neurons at early AD. METHODOLOGY The study was performed in hippocampal paraffin embedded sections of adult, senile, and AD brains at I-VI Braak stages. We analyzed phospho-Tau, lamins A, B1, B2, and C, nucleophosmin (B23) and the epigenetic marker H4K20me3 by immunohistochemistry. RESULTS Two neuronal populations were found across AD stages, one is characterized by a significant increase of Lamin A expression, reinforced perinuclear Lamin B2, elevated expression of H4K20me3 and nuclear Tau loss, while neurons with nucleoplasmic Lamin B2 constitute a second population. CONCLUSIONS The abnormal cell cycle reentry in early AD implies a fundamental neuronal transformation. This implies the reorganization of the nucleo-cytoskeleton through the expression of the highly regulated Lamin A, heterochromatin repression and building of toxic neuronal tangles. This work demonstrates that nuclear Tau and lamin modifications in hippocampal neurons are crucial events in age-related neurodegeneration.
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Affiliation(s)
- Laura Gil
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain; (L.G.)
| | - Sandra A. Niño
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Erika Chi-Ahumada
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | | | - Carmen Guerrero
- Banco de cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - Ana Belén Rebolledo
- Banco de cerebros (Biobanco), Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - José A. Arias
- Departamento de Genética, Escuela de Medicina, Universidad “Alfonso X el Sabio”, 28691 Madrid, Spain; (L.G.)
| | - María E. Jiménez-Capdeville
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
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13
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The Development of Epigenetics in the Study of Disease Pathogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1253:57-94. [PMID: 32445091 DOI: 10.1007/978-981-15-3449-2_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The study of epigenetics has its roots in the study of organism change over time and response to environmental change, although over the past several decades the definition has been formalized to include heritable alterations in gene expression that are not a result of alterations in underlying DNA sequence. In this chapter, we discuss first the history and milestones in the 100+ years of epigenetic study, including early discoveries of DNA methylation, histone posttranslational modification, and noncoding RNA. We then discuss how epigenetics has changed the way that we think of both health and disease, offering as examples studies examining the epigenetic contributions to aging, including the recent development of an epigenetic "clock", and explore how antiaging therapies may work through epigenetic modifications. We then discuss a nonpathogenic role for epigenetics in the clinic: epigenetic biomarkers. We conclude by offering two examples of modern state-of-the-art integrated multi-omics studies of epigenetics in disease pathogenesis, one which sought to capture shared mechanisms among multiple diseases, and another which used epigenetic big data to better understand the pathogenesis of a single tissue from one disease.
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14
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Bonath F, Domingo-Prim J, Tarbier M, Friedländer MR, Visa N. Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks. Nucleic Acids Res 2019; 46:11869-11882. [PMID: 30418607 PMCID: PMC6294500 DOI: 10.1093/nar/gky1107] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022] Open
Abstract
Recent studies suggest that transcription takes place at DNA double-strand breaks (DSBs), that transcripts at DSBs are processed by Drosha and Dicer into damage-induced small RNAs (diRNAs), and that diRNAs are required for DNA repair. However, diRNAs have been mostly detected in reporter constructs or repetitive sequences, and their existence at endogenous loci has been questioned by recent reports. Using the homing endonuclease I-PpoI, we have investigated diRNA production in genetically unperturbed human and mouse cells. I-PpoI is an ideal tool to clarify the requirements for diRNA production because it induces DSBs in different types of loci: the repetitive 28S locus, unique genes and intergenic loci. We show by extensive sequencing that the rDNA locus produces substantial levels of diRNAs, whereas unique genic and intergenic loci do not. Further characterization of diRNAs emerging from the 28S locus reveals the existence of two diRNA subtypes. Surprisingly, Drosha and its partner DGCR8 are dispensable for diRNA production and only one diRNAs subtype depends on Dicer processing. Furthermore, we provide evidence that diRNAs are incorporated into Argonaute. Our findings provide direct evidence for diRNA production at endogenous loci in mammalian cells and give insights into RNA processing at DSBs.
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Affiliation(s)
- Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Judit Domingo-Prim
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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15
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DNA methylation dynamics in aging: how far are we from understanding the mechanisms? Mech Ageing Dev 2018; 174:3-17. [DOI: 10.1016/j.mad.2017.12.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 02/07/2023]
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16
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Lenart P, Novak J, Bienertova-Vasku J. PIWI-piRNA pathway: Setting the pace of aging by reducing DNA damage. Mech Ageing Dev 2018; 173:29-38. [PMID: 29580825 DOI: 10.1016/j.mad.2018.03.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/02/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
Transposable elements (TEs) are powerful drivers of genome evolutionary dynamics but are principally deleterious to the host organism by compromising the integrity and function of the genome. The transposition of TEs may result in mutations and DNA damage. DNA double-strand breaks (DSBs), which may be caused by the transposition, are one of the processes directly linked to aging. TEs may thus be considered to constitute an internal source of aging and the frequency of transposition may, in turn, be considered to affect the pace of aging. The PIWI-piRNA pathway is a widespread strategy used by most animals to effectively suppress transposition. Interestingly, the PIWI-piRNA pathway is expressed predominantly in the animal germline, a more or less continuous immortal lineage set aside after the first few cell divisions of a developing embryo. Recent findings further imply that the PIWI-piRNA pathway and TE suppression constitute an important mechanism regulating aging. This article discusses the proposed role of the PIWI-piRNA pathway in setting the pace of aging as well as the possible mechanisms underlying this process.
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Affiliation(s)
- Peter Lenart
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A18, 625 00, Brno, Czech Republic; Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, Building A29, 625 00, Brno, Czech Republic
| | - Jan Novak
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A18, 625 00, Brno, Czech Republic
| | - Julie Bienertova-Vasku
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A18, 625 00, Brno, Czech Republic; Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, Building A29, 625 00, Brno, Czech Republic.
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17
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Warmoes M, Lam SW, van der Groep P, Jaspers JE, Smolders YHCM, de Boer L, Pham TV, Piersma SR, Rottenberg S, Boven E, Jonkers J, van Diest PJ, Jimenez CR. Secretome proteomics reveals candidate non-invasive biomarkers of BRCA1 deficiency in breast cancer. Oncotarget 2018; 7:63537-63548. [PMID: 27566577 PMCID: PMC5325383 DOI: 10.18632/oncotarget.11535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/13/2016] [Indexed: 11/25/2022] Open
Abstract
Breast cancer arising in female BRCA1 mutation carriers is characterized by an aggressive phenotype and early age of onset. We performed tandem mass spectrometry-based proteomics of secretomes and exosome-like extracellular vesicles from BRCA1-deficient and BRCA1-proficient murine breast tumor models to identify extracellular protein biomarkers, which can be used as an adjunct to current diagnostic modalities in patients with BRCA1-deficient breast cancer. We identified 2,107 proteins, of which 215 were highly enriched in the BRCA1-deficient secretome. We demonstrated that BRCA1-deficient secretome proteins could cluster most human BRCA1- and BRCA2-related breast carcinomas at the transcriptome level. Topoisomerase I (TOP1) and P-cadherin (CDH3) expression was investigated by immunohistochemistry on tissue microarrays of a large panel of 253 human breast carcinomas with and without BRCA1/2 mutations. We showed that expression of TOP1 and CDH3 was significantly increased in human BRCA1-related breast carcinomas relative to sporadic cases (p = 0.002 and p < 0.001, respectively). Multiple logistic regression showed that TOP1 (adjusted odds ratio [OR] 3.75; 95% confidence interval [95% CI], 1.85 - 7.71, p < 0.001) as well as CDH3 positivity (adjusted OR 2.45; 95% CI, 1.08 - 5.49, p = 0.032) were associated with BRCA1/2-related breast carcinomas after adjustment for triple-negative phenotype and age. In conclusion, proteome profiling of secretome using murine breast tumor models is a powerful strategy to identify non-invasive candidate biomarkers of BRCA1-deficient breast cancer. We demonstrate that TOP1 and CDH3 are closely associated to BRCA1-deficient breast cancer. These data merit further investigation for early detection of tumors arising in BRCA1 mutation carriers.
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Affiliation(s)
- Marc Warmoes
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Siu W Lam
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Petra van der Groep
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Internal Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Janneke E Jaspers
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yvonne H C M Smolders
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Leon de Boer
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Switzerland
| | - Epie Boven
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jos Jonkers
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Connie R Jimenez
- Oncoproteomics Laboratory, Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
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18
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Abstract
As the popular adage goes, all diseases run into old age and almost all physiological changes are associated with alterations in gene expression, irrespective of whether they are causal or consequential. Therefore, the quest for mechanisms that delay ageing and decrease age-associated diseases has propelled researchers to unravel regulatory factors that lead to changes in chromatin structure and function, which ultimately results in deregulated gene expression. It is therefore essential to bring together literature, which until recently has investigated gene expression and chromatin independently. With advances in biomedical research and the emergence of epigenetic regulators as potential therapeutic targets, enhancing our understanding of mechanisms that 'derail' transcription and identification of causal genes/pathways during ageing will have a significant impact. In this context, this chapter aims to not only summarize the key features of age-associated changes in epigenetics and transcription, but also identifies gaps in the field and proposes aspects that need to be investigated in the future.
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19
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Quénet D. Histone Variants and Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:1-39. [DOI: 10.1016/bs.ircmb.2017.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Guedj A, Geiger-Maor A, Galun E, Benyamini H, Nevo Y, Elgavish S, Amsalem H, Rachmilewitz J. Early age decline in DNA repair capacity in the liver: in depth profile of differential gene expression. Aging (Albany NY) 2017; 8:3131-3146. [PMID: 27922819 PMCID: PMC5191890 DOI: 10.18632/aging.101120] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/16/2016] [Indexed: 02/02/2023]
Abstract
Aging is associated with progressive decline in cell function and with increased
damage to macromolecular components. DNA damage, in the form of double-strand breaks
(DSBs), increases with age and in turn, contributes to the aging process and
age-related diseases. DNA strand breaks triggers a set of highly orchestrated
signaling events known as the DNA damage response (DDR), which coordinates DNA
repair. However, whether the accumulation of DNA damage with age is a result of
decreased repair capacity, remains to be determined. In our study we showed that with
age there is a decline in the resolution of foci containing γH2AX and pKAP-1
in diethylnitrosamine (DEN)-treated mouse livers, already evident at a remarkably
early age of 6-months. Considerable age-dependent differences in global gene
expression profiles in mice livers after exposure to DEN, further affirmed these age
related differences in the response to DNA damage. Functional analysis identified p53
as the most overrepresented pathway that is specifically enhanced and prolonged in
6-month-old mice. Collectively, our results demonstrated an early decline in DNA
damage repair that precedes ‘old age’, suggesting this may be a driving
force contributing to the aging process rather than a phenotypic consequence of old
age.
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Affiliation(s)
- Avital Guedj
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Anat Geiger-Maor
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eithan Galun
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Hadar Benyamini
- Bioinformatics Unit, of the I-CORE Computation Center, the Hebrew University and Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Yaval Nevo
- Bioinformatics Unit, of the I-CORE Computation Center, the Hebrew University and Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Sharona Elgavish
- Bioinformatics Unit, of the I-CORE Computation Center, the Hebrew University and Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Hagai Amsalem
- Department of Obstetrics and Gynecology, Hadassah University Hospital-Mount Scopus, Jerusalem, Israel
| | - Jacob Rachmilewitz
- Goldyne Savad Institute of Gene Therapy, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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21
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Abstract
During aging, the mechanisms that normally maintain health and stress resistance strikingly decline, resulting in decrepitude, frailty, and ultimately death. Exactly when and how this decline occurs is unknown. Changes in transcriptional networks and chromatin state lie at the heart of age-dependent decline. These epigenomic changes are not only observed during aging but also profoundly affect cellular function and stress resistance, thereby contributing to the progression of aging. We propose that the dysregulation of transcriptional and chromatin networks is a crucial component of aging. Understanding age-dependent epigenomic changes will yield key insights into how aging begins and progresses and should lead to the development of new therapeutics that delay or even reverse aging and age-related diseases.
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Affiliation(s)
- Lauren N Booth
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA.
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22
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Angelé-Martínez C, Nguyen KVT, Ameer FS, Anker JN, Brumaghim JL. Reactive oxygen species generation by copper(II) oxide nanoparticles determined by DNA damage assays and EPR spectroscopy. Nanotoxicology 2017; 11:278-288. [PMID: 28248593 DOI: 10.1080/17435390.2017.1293750] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Copper(II) oxide nanoparticles (NPCuO) have many industrial applications, but are highly cytotoxic because they generate reactive oxygen species (ROS). It is unknown whether the damaging ROS are generated primarily from copper leached from the nanoparticles, or whether the nanoparticle surface plays a significant role. To address this question, we separated nanoparticles from the supernatant containing dissolved copper, and measured their ability to damage plasmid DNA with addition of hydrogen peroxide, ascorbate, or both. While DNA damage from the supernatant (measured using an electrophoresis assay) can be explained solely by dissolved copper ions, damage by the nanoparticles in the presence of ascorbate is an order of magnitude higher than can be explained by dissolved copper and must, therefore, depend primarily upon the nanoparticle surface. DNA damage is time-dependent, with shorter incubation times resulting in higher EC50 values. Hydroxyl radical (•OH) is the main ROS generated by NPCuO/hydrogen peroxide as determined by EPR measurements; NPCuO/hydrogen peroxide/ascorbate conditions generate ascorbyl, hydroxyl, and superoxide radicals. Thus, NPCuO generate ROS through several mechanisms, likely including Fenton-like and Haber-Weiss reactions from the surface or dissolved copper ions. The same radical species were observed when NPCuO suspensions were replaced with the supernatant containing leached copper, washed NPCuO, or dissolved copper solutions. Overall, NPCuO generate significantly more ROS and DNA damage in the presence of ascorbate than can be explained simply from dissolved copper, and the NPCuO surface must play a large role.
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Affiliation(s)
| | - Khanh Van T Nguyen
- b School of Biotechnology, International University - Vietnam National University, Ho Chi Minh City , Vietnam
| | - Fathima S Ameer
- a Department of Chemistry , Clemson University , Clemson , SC , USA
| | - Jeffrey N Anker
- a Department of Chemistry , Clemson University , Clemson , SC , USA
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23
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Barzilai A, Schumacher B, Shiloh Y. Genome instability: Linking ageing and brain degeneration. Mech Ageing Dev 2017; 161:4-18. [DOI: 10.1016/j.mad.2016.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/23/2016] [Accepted: 03/26/2016] [Indexed: 02/06/2023]
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24
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Latchney SE, Calvi LM. The aging hematopoietic stem cell niche: Phenotypic and functional changes and mechanisms that contribute to hematopoietic aging. Semin Hematol 2016; 54:25-32. [PMID: 28088984 DOI: 10.1053/j.seminhematol.2016.10.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 11/11/2022]
Abstract
The hematopoietic system has the remarkable ability to provide a lifelong supply of mature cells that make up the entire blood and immune system. However, similar to other adult stem cell niches, the hematopoietic system is vulnerable to the detrimental effects of aging. This is a substantial health concern as the trend for population aging continues to increase. Identifying mechanisms that underlie hematopoietic aging is vital for understanding hematopoietic-related diseases. In this review, we first discuss the cellular hierarchy of the hematopoietic system and the components that make up the surrounding hematopoietic niche. We then provide an overview of the major phenotypes associated with hematopoietic aging and discuss recent research investigating cell-intrinsic and cell-extrinsic mechanisms of hematopoietic stem cell (HSCs) aging. We end by discussing the exciting new concept of possibly reversing the HSC aging process along with outstanding questions that remain to be answered.
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Affiliation(s)
- Sarah E Latchney
- Endocrine Metabolism Division, University of Rochester School of Medicine and Dentistry, Rochester NY
| | - Laura M Calvi
- Endocrine Metabolism Division, University of Rochester School of Medicine and Dentistry, Rochester NY; Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester NY.
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25
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Abstract
Aging is a universal phenomenon in metazoans, characterized by a general decline of the organism physiology associated with an increased risk of mortality and morbidity. Aging of an organism correlates with a decline in function of its cells, as shown for muscle, immune, and neuronal cells. As the DNA content of most cells within an organism remains largely identical throughout the life span, age-associated transcriptional changes must be achieved by epigenetic mechanisms. However, how aging may impact on the epigenetic state of cells is only beginning to be understood. In light of a growing number of studies demonstrating that noncoding RNAs can provide molecular signals that regulate expression of protein-coding genes and define epigenetic states of cells, we hypothesize that noncoding RNAs could play a direct role in inducing age-associated profiles of gene expression. In this context, the role of long noncoding RNAs (lncRNAs) as regulators of gene expression might be important for the overall transcriptional landscape observed in aged human cells. The possible functions of lncRNAs and other noncoding RNAs, and their roles in the regulation of aging-related cellular pathways will be analyzed.
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26
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Ribezzo F, Shiloh Y, Schumacher B. Systemic DNA damage responses in aging and diseases. Semin Cancer Biol 2016; 37-38:26-35. [PMID: 26773346 PMCID: PMC4886830 DOI: 10.1016/j.semcancer.2015.12.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 12/28/2015] [Accepted: 12/31/2015] [Indexed: 01/09/2023]
Abstract
The genome is constantly attacked by a variety of genotoxic insults. The causal role for DNA damage in aging and cancer is exemplified by genetic defects in DNA repair that underlie a broad spectrum of acute and chronic human disorders that are characterized by developmental abnormalities, premature aging, and cancer predisposition. The disease symptoms are typically tissue-specific with uncertain genotype-phenotype correlation. The cellular DNA damage response (DDR) has been extensively investigated ever since yeast geneticists discovered DNA damage checkpoint mechanisms, several decades ago. In recent years, it has become apparent that not only cell-autonomous but also systemic DNA damage responses determine the outcome of genome instability in organisms. Understanding the mechanisms of non-cell-autonomous DNA damage responses will provide important new insights into the role of genome instability in human aging and a host of diseases including cancer and might better explain the complex phenotypes caused by genome instability.
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Affiliation(s)
- Flavia Ribezzo
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD) Research Center, Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Genetic Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD) Research Center, Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany.
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27
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Kour S, Rath PC. Long noncoding RNAs in aging and age-related diseases. Ageing Res Rev 2016; 26:1-21. [PMID: 26655093 DOI: 10.1016/j.arr.2015.12.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/08/2015] [Accepted: 12/01/2015] [Indexed: 12/14/2022]
Abstract
Aging is the universal, intrinsic, genetically-controlled, evolutionarily-conserved and time-dependent intricate biological process characterised by the cumulative decline in the physiological functions and their coordination in an organism after the attainment of adulthood resulting in the imbalance of neurological, immunological and metabolic functions of the body. Various biological processes and mechanisms along with altered levels of mRNAs and proteins have been reported to be involved in the progression of aging. It is one of the major risk factors in the patho-physiology of various diseases and disorders. Recently, the discovery of pervasive transcription of a vast pool of heterogeneous regulatory noncoding RNAs (ncRNAs), including small ncRNAs (sncRNAs) and long ncRNAs (lncRNAs), in the mammalian genome have provided an alternative way to study and explore the missing links in the aging process, its mechanism(s) and related diseases in a whole new dimension. The involvement of small noncoding RNAs in aging and age-related diseases have been extensively studied and recently reviewed. However, lncRNAs, whose function is far less explored in relation to aging, have emerged as a class of major regulators of genomic functions. Here, we have described some examples of known as well as novel lncRNAs that have been implicated in the progression of the aging process and age-related diseases. This may further stimulate research on noncoding RNAs and the aging process.
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Affiliation(s)
- Sukhleen Kour
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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28
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Rangaraju S, Solis GM, Thompson RC, Gomez-Amaro RL, Kurian L, Encalada SE, Niculescu AB, Salomon DR, Petrascheck M. Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality. eLife 2015; 4:e08833. [PMID: 26623667 PMCID: PMC4720515 DOI: 10.7554/elife.08833] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 10/29/2015] [Indexed: 12/28/2022] Open
Abstract
Longevity mechanisms increase lifespan by counteracting the effects of aging. However, whether longevity mechanisms counteract the effects of aging continually throughout life, or whether they act during specific periods of life, preventing changes that precede mortality is unclear. Here, we uncover transcriptional drift, a phenomenon that describes how aging causes genes within functional groups to change expression in opposing directions. These changes cause a transcriptome-wide loss in mRNA stoichiometry and loss of co-expression patterns in aging animals, as compared to young adults. Using Caenorhabditis elegans as a model, we show that extending lifespan by inhibiting serotonergic signals by the antidepressant mianserin attenuates transcriptional drift, allowing the preservation of a younger transcriptome into an older age. Our data are consistent with a model in which inhibition of serotonergic signals slows age-dependent physiological decline and the associated rise in mortality levels exclusively in young adults, thereby postponing the onset of major mortality. DOI:http://dx.doi.org/10.7554/eLife.08833.001 All organisms age, leading to gradual declines in the body’s systems and eventually death. How certain genetic mutations and drugs delay the effects of aging and promote survival to an older age is a question many researchers are exploring. One way this problem is investigated is by looking at how the activity – or expression – of different genes changes during aging. Scientists interested in understanding aging and longevity often study a simple worm called Caenorhabditis elegans. This worm normally lives for about three weeks, and young C. elegans are able to produce offspring within days of hatching. This accelerated life cycle allows scientists to observe the entire lifespan of the worms. Over time, experiments have shown that DNA damage, changes in behavior and changes to gene expression are all markers of aging in the worms. Now, Rangaraju et al. describe how changes in gene expression patterns that begin early in the lives of C. elegans shorten their lifespan. Specifically, in groups of genes that work together, some genes increase expression, while others decrease expression with age. This phenomenon is called “transcriptional drift” and leads to an age-associated loss of coordination among groups of genes that help orchestrate specific tasks. Rangaraju et al. show that an antidepressant called mianserin prevents transcriptional drift in many of C. elegans’ genes: young worms treated with the drug resist the effects of aging on the transcriptome and maintain coordinated patterns of gene expression for longer. Maintaining coordinated patterns of gene expression postpones the onset of age-related bodily declines and extends the life of treated worms by extending the duration of young adulthood and postponing the onset of age-associated death. The drug also appears to protect against stress-induced changes in gene expression. This suggests that some of the age-related shifts in gene expression occur when cells fail to recover normal gene expression patterns after a stressful event. Questions that remain to be investigated in future studies are whether other longevity mechanisms also extend lifespan by preserving coordinated gene expression patterns, and whether other longevity mechanisms act by extending specific periods of life. DOI:http://dx.doi.org/10.7554/eLife.08833.002
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Affiliation(s)
- Sunitha Rangaraju
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States.,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, United States.,Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States.,Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Gregory M Solis
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States.,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, United States.,Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States.,Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Ryan C Thompson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, United States
| | - Rafael L Gomez-Amaro
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States.,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, United States.,Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States.,Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Leo Kurian
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Sandra E Encalada
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, United States.,Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States.,Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Alexander B Niculescu
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, United States
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, United States
| | - Michael Petrascheck
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States.,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, United States.,Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, United States.,Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, United States
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29
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Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nat Rev Mol Cell Biol 2015; 16:593-610. [PMID: 26373265 DOI: 10.1038/nrm4048] [Citation(s) in RCA: 389] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ageing is affected by both genetic and non-genetic factors. Here, we review the chromatin-based epigenetic changes that occur during ageing, the role of chromatin modifiers in modulating lifespan and the importance of epigenetic signatures as biomarkers of ageing. We also discuss how epigenome remodelling by environmental stimuli affects several aspects of transcription and genomic stability, with important consequences for longevity, and outline epigenetic differences between the 'mortal soma' and the 'immortal germ line'. Finally, we discuss the inheritance of characteristics of ageing and potential chromatin-based strategies to delay or reverse hallmarks of ageing or age-related diseases.
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30
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Jeon HJ, Kim YS, Park JS, Pyo JH, Na HJ, Kim IJ, Kim CM, Chung HY, Kim ND, Arking R, Yoo MA. Age-related change in γH2AX of Drosophila muscle: its significance as a marker for muscle damage and longevity. Biogerontology 2015; 16:503-16. [PMID: 25860864 DOI: 10.1007/s10522-015-9573-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/06/2015] [Indexed: 11/26/2022]
Abstract
Muscle aging is closely related to unhealthy late-life and organismal aging. Recently, the state of differentiated cells was shown to be critical to tissue homeostasis. Thus, understanding how fully differentiated muscle cells age is required for ensuring healthy aging. Adult Drosophila muscle is a useful model for exploring the aging process of fully differentiated cells. In this study, we investigated age-related changes of γH2AX, an indicator of DNA strand breaks, in adult Drosophila muscle to document whether its changes are correlated with muscle degeneration and lifespan. The results demonstrate that γH2AX accumulation increases in adult Drosophila thoracic and leg muscles with age. Analyses of short-, normal-, and long-lived strains indicate that the age-related increase of γH2AX is closely associated with the extent of muscle degeneration, cleaved caspase-3 and poly-ubiquitin aggregates, and longevity. Further analysis of muscle-specific knockdown of heterochromatin protein 1a revealed that the excessive γH2AX accumulation in thoracic and leg muscles induces accelerated degeneration and decreases longevity. These data suggest a strong correlation between age-related muscle damage and lifespan in Drosophila. Our findings indicate that γH2AX may be a reliable biomarker for assessing muscle aging in Drosophila.
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Affiliation(s)
- Ho-Jun Jeon
- Department of Molecular Biology, Pusan National University, Busan, 609-735, Republic of Korea
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31
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Burgess RC, Burman B, Kruhlak MJ, Misteli T. Activation of DNA damage response signaling by condensed chromatin. Cell Rep 2014; 9:1703-1717. [PMID: 25464843 DOI: 10.1016/j.celrep.2014.10.060] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 09/11/2014] [Accepted: 10/25/2014] [Indexed: 12/20/2022] Open
Abstract
The DNA damage response (DDR) occurs in the context of chromatin, and architectural features of chromatin have been implicated in DNA damage signaling and repair. Whereas a role of chromatin decondensation in the DDR is well established, we show here that chromatin condensation is integral to DDR signaling. We find that, in response to DNA damage chromatin regions transiently expand before undergoing extensive compaction. Using a protein-chromatin-tethering system to create defined chromatin domains, we show that interference with chromatin condensation results in failure to fully activate DDR. Conversely, forced induction of local chromatin condensation promotes ataxia telangiectasia mutated (ATM)- and ATR-dependent activation of upstream DDR signaling in a break-independent manner. Whereas persistent chromatin compaction enhanced upstream DDR signaling from irradiation-induced breaks, it reduced recovery and survival after damage. Our results demonstrate that chromatin condensation is sufficient for activation of DDR signaling and is an integral part of physiological DDR signaling.
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Affiliation(s)
- Rebecca C Burgess
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bharat Burman
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Program in Cell, Molecular and Developmental Biology, Sackler School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Michael J Kruhlak
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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32
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Rodrigues HF, Souza TA, Ghiraldini FG, Mello MLS, Moraes AS. Increased age is associated with epigenetic and structural changes in chromatin from neuronal nuclei. J Cell Biochem 2014; 115:659-65. [PMID: 24166948 DOI: 10.1002/jcb.24705] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/22/2013] [Indexed: 01/06/2023]
Abstract
Chromatin organization has been considered to play a major role on aging, by regulating DNA accessibility to transcription and repair machinery. Such organization can be modulated by epigenetic events, such as DNA methylation and histone post-translational modifications. Since changes on gene expression profiles have been described in aged neurons, our aim was to study the age-dependent relationship between structural and epigenetic alterations on chromatin of cortical neurons from mice. For this purpose, isolated neuronal nuclei from mice of two ages were studied by image analysis after cytochemistry, or assessed for chromatin accessibility by enzymatic digestion. Additionally, two epigenetic marks, for open and for densely packed chromatin fibers were quantified. Results indicate epigenetically driven alterations on chromatin organization of cortical neurons with advancing age, whose fibers seem to undergo redistribution and unpackaging. Since increased transcriptional activity is not characteristic of aged neurons, these loosened chromatin fibers may be associated with impaired genome stability, as well as with increased accessibility of repair machinery to a life span damaged DNA.
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Affiliation(s)
- Henrique F Rodrigues
- Cytology, Histology, and Embryology Section, Institute of Biomedical Sciences, Federal University of Uberlandia (UFU), Uberlandia, Minas Gerais, 38400-902, Brazil
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33
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Shiloh Y. ATM: expanding roles as a chief guardian of genome stability. Exp Cell Res 2014; 329:154-61. [PMID: 25218947 DOI: 10.1016/j.yexcr.2014.09.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/19/2014] [Accepted: 09/01/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Yosef Shiloh
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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34
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Zane L, Sharma V, Misteli T. Common features of chromatin in aging and cancer: cause or coincidence? Trends Cell Biol 2014; 24:686-94. [PMID: 25103681 DOI: 10.1016/j.tcb.2014.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 02/06/2023]
Abstract
Age is a major risk factor for cancer. Alterations in DNA methylation, histone modifications, chromatin structure, and epigenetic regulatory mechanisms are prominent hallmarks of both the aging process and cancer. Intriguingly--or possibly coincidentally--several chromatin features are common between aging and cancer. Here we ask whether, and if so how, aging-associated chromatin modifications contribute to tumor susceptibility and tumorigenesis.
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Affiliation(s)
- Linda Zane
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vivek Sharma
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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35
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deHaro D, Kines KJ, Sokolowski M, Dauchy RT, Streva VA, Hill SM, Hanifin JP, Brainard GC, Blask DE, Belancio VP. Regulation of L1 expression and retrotransposition by melatonin and its receptor: implications for cancer risk associated with light exposure at night. Nucleic Acids Res 2014; 42:7694-707. [PMID: 24914052 PMCID: PMC4081101 DOI: 10.1093/nar/gku503] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 04/30/2014] [Accepted: 05/19/2014] [Indexed: 12/17/2022] Open
Abstract
Expression of long interspersed element-1 (L1) is upregulated in many human malignancies. L1 can introduce genomic instability via insertional mutagenesis and DNA double-strand breaks, both of which may promote cancer. Light exposure at night, a recently recognized carcinogen, is associated with an increased risk of cancer in shift workers. We report that melatonin receptor 1 inhibits mobilization of L1 in cultured cells through downregulation of L1 mRNA and ORF1 protein. The addition of melatonin receptor antagonists abolishes the MT1 effect on retrotransposition in a dose-dependent manner. Furthermore, melatonin-rich, but not melatonin-poor, human blood collected at different times during the circadian cycle suppresses endogenous L1 mRNA during in situ perfusion of tissue-isolated xenografts of human cancer. Supplementation of human blood with exogenous melatonin or melatonin receptor antagonist during the in situ perfusion establishes a receptor-mediated action of melatonin on L1 expression. Combined tissue culture and in vivo data support that environmental light exposure of the host regulates expression of L1 elements in tumors. Our data imply that light-induced suppression of melatonin production in shift workers may increase L1-induced genomic instability in their genomes and suggest a possible connection between L1 activity and increased incidence of cancer associated with circadian disruption.
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Affiliation(s)
- Dawn deHaro
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70115, USA Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Kristine J Kines
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70115, USA Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Mark Sokolowski
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70115, USA Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Robert T Dauchy
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70115, USA
| | - Vincent A Streva
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70115, USA
| | - Steven M Hill
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70115, USA
| | - John P Hanifin
- Department of Neurology, Thomas Jefferson University, Jefferson Medical College, Philadelphia, PA 19107, USA
| | - George C Brainard
- Department of Neurology, Thomas Jefferson University, Jefferson Medical College, Philadelphia, PA 19107, USA
| | - David E Blask
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70115, USA
| | - Victoria P Belancio
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70115, USA Tulane Center for Aging, New Orleans, LA 70112, USA
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36
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McCauley BS, Dang W. Histone methylation and aging: lessons learned from model systems. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1454-62. [PMID: 24859460 DOI: 10.1016/j.bbagrm.2014.05.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 03/16/2014] [Accepted: 05/13/2014] [Indexed: 01/06/2023]
Abstract
Aging induces myriad cellular and, ultimately, physiological changes that cause a decline in an organism's functional capabilities. Although the aging process and the pathways that regulate it have been extensively studied, only in the last decade have we begun to appreciate that dynamic histone methylation may contribute to this process. In this review, we discuss recent work implicating histone methylation in aging. Loss of certain histone methyltransferases and demethylases changes lifespan in invertebrates, and alterations in histone methylation in aged organisms regulate lifespan and aging phenotypes, including oxidative stress-induced hormesis in yeast, insulin signaling in Caenorhabiditis elegans and mammals, and the senescence-associated secretory phenotype in mammals. In all cases where histone methylation has been shown to impact aging and aging phenotypes, it does so by regulating transcription, suggesting that this is a major mechanism of its action in this context. Histone methylation additionally regulates or is regulated by other cellular pathways that contribute to or combat aging. Given the numerous processes that regulate aging and histone methylation, and are in turn regulated by them, the role of histone methylation in aging is almost certainly underappreciated.
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Affiliation(s)
- Brenna S McCauley
- Huffington Center on Aging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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37
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Schierding W, Cutfield WS, O'Sullivan JM. The missing story behind Genome Wide Association Studies: single nucleotide polymorphisms in gene deserts have a story to tell. Front Genet 2014; 5:39. [PMID: 24600475 PMCID: PMC3927098 DOI: 10.3389/fgene.2014.00039] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/31/2014] [Indexed: 11/13/2022] Open
Abstract
Genome wide association studies are central to the evolution of personalized medicine. However, the propensity for single nucleotide polymorphisms (SNPs) to fall outside of genes means that understanding how these polymorphisms alter cellular function requires an expanded view of human genetics. Integrating the study of genome structure (chromosome conformation capture) into its function opens up new avenues of exploration. Changes in the epigenome associated with SNPs in gene deserts will allow us to define complex diseases in a much clearer manner, and usher in a new era of disease pathway exploration.
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Affiliation(s)
| | - Wayne S. Cutfield
- Liggins Institute, University of AucklandAuckland, New Zealand
- Gravida – National Centre for Growth and DevelopmentAuckland, New Zealand
| | - Justin M. O'Sullivan
- Liggins Institute, University of AucklandAuckland, New Zealand
- Gravida – National Centre for Growth and DevelopmentAuckland, New Zealand
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38
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Ganley ARD, Kobayashi T. Ribosomal DNA and cellular senescence: new evidence supporting the connection between rDNA and aging. FEMS Yeast Res 2014; 14:49-59. [DOI: 10.1111/1567-1364.12133] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 12/10/2013] [Accepted: 12/19/2013] [Indexed: 12/19/2022] Open
Affiliation(s)
- Austen R. D. Ganley
- Institute of Natural and Mathematical Sciences; Massey University; Auckland New Zealand
| | - Takehiko Kobayashi
- Division of Cytogenetics; National Institute of Genetics; Mishima Shizuoka Japan
- Department of Genetics; The Graduate University for Advanced Studies; SOKENDAI; Mishima Shizuoka Japan
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39
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Angelé-Martínez C, Goodman C, Brumaghim J. Metal-mediated DNA damage and cell death: mechanisms, detection methods, and cellular consequences. Metallomics 2014; 6:1358-81. [DOI: 10.1039/c4mt00057a] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metal ions cause various types of DNA damage by multiple mechanisms, and this damage is a primary cause of cell death and disease.
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Affiliation(s)
| | - Craig Goodman
- Department of Chemistry
- Clemson University
- Clemson, USA
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40
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Saccharomyces cerevisiae linker histone-Hho1p maintains chromatin loop organization during ageing. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:437146. [PMID: 24023978 PMCID: PMC3760111 DOI: 10.1155/2013/437146] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 01/10/2023]
Abstract
Intricate, dynamic, and absolutely unavoidable ageing affects cells and organisms through their entire lifetime. Driven by diverse mechanisms all leading to compromised cellular functions and finally to death, this process is a challenge for researchers. The molecular mechanisms, the general rules that it follows, and the complex interplay at a molecular and cellular level are yet little understood. Here, we present our results showing a connection between the linker histones, the higher-order chromatin structures, and the process of chronological lifespan of yeast cells. By deleting the gene for the linker histone in Saccharomyces cerevisiae we have created a model for studying the role of chromatin structures mainly at its most elusive and so far barely understood higher-order levels of compaction in the processes of yeast chronological lifespan. The mutant cells demonstrated controversial features showing slower growth than the wild type combined with better survival during the whole process. The analysis of the global chromatin organization during different time points demonstrated certain loss of the upper levels of chromatin compaction in the cells without linker histone. The results underlay the importance of this histone for the maintenance of the chromatin loop structures during ageing.
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41
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Montecucco A, Biamonti G. Pre-mRNA processing factors meet the DNA damage response. Front Genet 2013; 4:102. [PMID: 23761808 PMCID: PMC3674313 DOI: 10.3389/fgene.2013.00102] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 05/20/2013] [Indexed: 12/04/2022] Open
Abstract
It is well-known that DNA-damaging agents induce genome instability, but only recently have we begun to appreciate that chromosomes are fragile per se and frequently subject to DNA breakage. DNA replication further magnifies such fragility, because it leads to accumulation of single-stranded DNA. Recent findings suggest that chromosome fragility is similarly increased during transcription. Transcripts produced by RNA polymerase II (RNAPII) are subject to multiple processing steps, including maturation of 5′ and 3′ ends and splicing, followed by transport to the cytoplasm. RNA maturation starts on nascent transcripts and is mediated by a number of diverse proteins and ribonucleoprotein particles some of which are recruited cotranscriptionally through interactions with the carboxy-terminal domain of RNAPII. This coupling is thought to maximize efficiency of pre-mRNA maturation and directly impacts the choice of alternative splice sites. Mounting evidence suggests that lack of coordination among different RNA maturation steps, by perturbing the interaction of nascent transcripts with the DNA template, has deleterious effects on genome stability. Thus, in the absence of proper surveillance mechanisms, transcription could be a major source of DNA damage in cancer. Recent high-throughput screenings in human cells and budding yeast have identified several factors implicated in RNA metabolism that are targets of DNA damage checkpoint kinases: ATM (ataxia telangiectasia mutated) and ATR (ATM-Rad3 related) (Tel1 and Mec1 in budding yeast, respectively). Moreover, inactivation of various RNA processing factors induces accumulation of γH2AX foci, an early sign of DNA damage. Thus, a complex network is emerging that links DNA repair and RNA metabolism. In this review we provide a comprehensive overview of the role played by pre-mRNA processing factors in the cell response to DNA damage and in the maintenance of genome stability.
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Abstract
Stem cell ageing underlies the ageing of tissues, especially those with a high cellular turnover. There is growing evidence that the ageing of the immune system is initiated at the very top of the haematopoietic hierarchy and that the ageing of haematopoietic stem cells (HSCs) directly contributes to changes in the immune system, referred to as immunosenescence. In this Review, we summarize the phenotypes of ageing HSCs and discuss how the cell-intrinsic and cell-extrinsic mechanisms of HSC ageing might promote immunosenescence. Stem cell ageing has long been considered to be irreversible. However, recent findings indicate that several molecular pathways could be targeted to rejuvenate HSCs and thus to reverse some aspects of immunosenescence.
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43
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Cavalli G, Misteli T. Functional implications of genome topology. Nat Struct Mol Biol 2013; 20:290-9. [PMID: 23463314 PMCID: PMC6320674 DOI: 10.1038/nsmb.2474] [Citation(s) in RCA: 299] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/20/2012] [Indexed: 01/21/2023]
Abstract
Although genomes are defined by their sequence, the linear arrangement of nucleotides is only their most basic feature. A fundamental property of genomes is their topological organization in three-dimensional space in the intact cell nucleus. The application of imaging methods and genome-wide biochemical approaches, combined with functional data, is revealing the precise nature of genome topology and its regulatory functions in gene expression and genome maintenance. The emerging picture is one of extensive self-enforcing feedback between activity and spatial organization of the genome, suggestive of a self-organizing and self-perpetuating system that uses epigenetic dynamics to regulate genome function in response to regulatory cues and to propagate cell-fate memory.
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Affiliation(s)
- Giacomo Cavalli
- Institut de Génétique Humaine, UPR 1142, Centre National de la Recherche Scientifique, Montpellier, France.
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44
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Wolters S, Schumacher B. Genome maintenance and transcription integrity in aging and disease. Front Genet 2013; 4:19. [PMID: 23443494 PMCID: PMC3580961 DOI: 10.3389/fgene.2013.00019] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/03/2013] [Indexed: 12/21/2022] Open
Abstract
DNA damage contributes to cancer development and aging. Congenital syndromes that affect DNA repair processes are characterized by cancer susceptibility, developmental defects, and accelerated aging (Schumacher et al., 2008). DNA damage interferes with DNA metabolism by blocking replication and transcription. DNA polymerase blockage leads to replication arrest and can gives rise to genome instability. Transcription, on the other hand, is an essential process for utilizing the information encoded in the genome. DNA damage that interferes with transcription can lead to apoptosis and cellular senescence. Both processes are powerful tumor suppressors (Bartek and Lukas, 2007). Cellular response mechanisms to stalled RNA polymerase II complexes have only recently started to be uncovered. Transcription-coupled DNA damage responses might thus play important roles for the adjustments to DNA damage accumulation in the aging organism (Garinis et al., 2009). Here we review human disorders that are caused by defects in genome stability to explore the role of DNA damage in aging and disease. We discuss how the nucleotide excision repair system functions at the interface of transcription and repair and conclude with concepts how therapeutic targeting of transcription might be utilized in the treatment of cancer.
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Affiliation(s)
- Stefanie Wolters
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
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