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Wang X, Huang Z, Li L, Yang Y, Zhang J, Wang L, Yuan J, Li Y. The Role of Alternative Splicing Factors, DDB2-Related Ageing and DNA Damage Repair in the Progression and Prognosis of Stomach Adenocarcinoma Patients. Genes (Basel) 2022; 14:genes14010039. [PMID: 36672781 PMCID: PMC9858704 DOI: 10.3390/genes14010039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/08/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
DNA damage response is a key signal transduction pathway in triggering ageing and tumor progression. Abnormal alternative splicing (AS) is associated with tumors and ageing. However, the role of AS factors associated with DNA damage repair and ageing in stomach adenocarcinoma (STAD) remains unclear. We downloaded the percentage of splicing (PSI) values for AS in STAD from the TCGA SpliceSeq database. The PSI values of DNA repair gene AS events were integrated with STAD patient survival data for Cox regression analysis. The prediction model for the overall survival (OS) was constructed by the clinical traits. The tumor immune microenvironment was analyzed by CIBERSORT and ESTIMATE. We detected 824 AS events originating from 166 DNA repair genes. Cox regression analysis provided 21 prognostic AS events connected with OS statistically, and a prognostic prediction model was constructed. The expression of these AS factors was higher in STAD tumors. DDB2 high senescence levels were associated with active immune responses and better survival in STAD patients. We built a novel prognostic model founded on DNA repair genes with AS events and identified that DDB2 may be a potential biomarker to apply in clinics.
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Affiliation(s)
- Xinshu Wang
- Postgraduate Training Base of Jinzhou Medical University, Shanghai East Hospital, Shanghai 200120, China
| | - Zhiyuan Huang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Lei Li
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Yuntong Yang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Jiyuan Zhang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Li Wang
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200120, China
- Correspondence: (J.Y.); (Y.L.); Tel.: +86-138-1823-3596 (J.Y.); +86-188-1730-0177 (Y.L.)
| | - Yunhui Li
- Research Center for Translational Medicine, East Hospital, Tongji University, School of Medicine, Shanghai 200120, China
- Ji’an Hospital, Shanghai East Hospital, Ji’an 343000, China
- Correspondence: (J.Y.); (Y.L.); Tel.: +86-138-1823-3596 (J.Y.); +86-188-1730-0177 (Y.L.)
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2
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Clarke TL, Mostoslavsky R. DNA repair as a shared hallmark in cancer and ageing. Mol Oncol 2022; 16:3352-3379. [PMID: 35834102 PMCID: PMC9490147 DOI: 10.1002/1878-0261.13285] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/23/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
Increasing evidence demonstrates that DNA damage and genome instability play a crucial role in ageing. Mammalian cells have developed a wide range of complex and well‐orchestrated DNA repair pathways to respond to and resolve many different types of DNA lesions that occur from exogenous and endogenous sources. Defects in these repair pathways lead to accelerated or premature ageing syndromes and increase the likelihood of cancer development. Understanding the fundamental mechanisms of DNA repair will help develop novel strategies to treat ageing‐related diseases. Here, we revisit the processes involved in DNA damage repair and how these can contribute to diseases, including ageing and cancer. We also review recent mechanistic insights into DNA repair and discuss how these insights are being used to develop novel therapeutic strategies for treating human disease. We discuss the use of PARP inhibitors in the clinic for the treatment of breast and ovarian cancer and the challenges associated with acquired drug resistance. Finally, we discuss how DNA repair pathway‐targeted therapeutics are moving beyond PARP inhibition in the search for ever more innovative and efficacious cancer therapies.
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Affiliation(s)
- Thomas L Clarke
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
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3
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Centrosomes and Centrosome Equivalents in Other Systems. THE CENTROSOME AND ITS FUNCTIONS AND DYSFUNCTIONS 2022; 235:85-104. [DOI: 10.1007/978-3-031-20848-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Bacon ER, Brinton RD. Epigenetics of the developing and aging brain: Mechanisms that regulate onset and outcomes of brain reorganization. Neurosci Biobehav Rev 2021; 125:503-516. [PMID: 33657435 DOI: 10.1016/j.neubiorev.2021.02.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/11/2022]
Abstract
Brain development is a life-long process that encompasses several critical periods of transition, during which significant cognitive changes occur. Embryonic development, puberty, and reproductive senescence are all periods of transition that are hypersensitive to environmental factors. Rather than isolated episodes, each transition builds upon the last and is influenced by consequential changes that occur in the transition before it. Epigenetic marks, such as DNA methylation and histone modifications, provide mechanisms by which early events can influence development, cognition, and health outcomes. For example, parental environment influences imprinting patterns in gamete cells, which ultimately impacts gene expression in the embryo which may result in hypersensitivity to poor maternal nutrition during pregnancy, raising the risks for cognitive impairment later in life. This review explores how epigenetics induce and regulate critical periods, and also discusses how early environmental interactions prime a system towards a particular health outcome and influence susceptibility to disease or cognitive impairment throughout life.
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Affiliation(s)
- Eliza R Bacon
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; The Center for Precision Medicine, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Roberta Diaz Brinton
- Department of Neuroscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA; Center for Innovation in Brain Science, School of Medicine, University of Arizona, Tucson, AZ, 85721, USA.
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Guarasci F, D'Aquila P, Montesanto A, Corsonello A, Bellizzi D, Passarino G. Individual DNA Methylation Profile is Correlated with Age and can be Targeted to Modulate Healthy Aging and Longevity. Curr Pharm Des 2019; 25:4139-4149. [DOI: 10.2174/1381612825666191112095655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
Abstract
:Patterns of DNA methylation, the best characterized epigenetic modification, are modulated by aging. In humans, different studies at both site-specific and genome-wide levels have reported that modifications of DNA methylation are associated with the chronological aging process but also with the quality of aging (or biological aging), providing new perspectives for establishing powerful biomarkers of aging.:In this article, the role of DNA methylation in aging and longevity has been reviewed by analysing literature data about DNA methylation variations occurring during the lifetime in response to environmental factors and genetic background, and their association with the aging process and, in particular, with the quality of aging. Special attention has been devoted to the relationship between nuclear DNA methylation patterns, mitochondrial DNA epigenetic modifications, and longevity. Mitochondrial DNA has recently been reported to modulate global DNA methylation levels of the nuclear genome during the lifetime, and, in spite of the previous belief, it has been found to be the target of methylation modifications.:Analysis of DNA methylation profiles across lifetime shows that a remodeling of the methylome occurs with age and/or with age-related decline. Thus, it can be an excellent biomarker of aging and of the individual decline and frailty status. The knowledge about the mechanisms underlying these modifications is crucial since it might allow the opportunity for targeted treatment to modulate the rate of aging and longevity.
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Affiliation(s)
- Francesco Guarasci
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Andrea Corsonello
- Unit of Geriatric Pharmacoepidemiology, Scientific Research Institute - Italian National Research Center on Aging (IRCCS INRCA), Cosenza, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
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Tanaka IB, Komura J, Tanaka S. Pathology of Serially Sacrificed Female B6C3F1 Mice Continuously Exposed to Very Low-Dose-Rate Gamma Rays. Radiat Res 2017; 187:346-360. [DOI: 10.1667/rr14617.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- I. B. Tanaka
- Department of Radiobiology, Institute for Environmental Sciences, 1-7, Ienomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
| | - J. Komura
- Department of Radiobiology, Institute for Environmental Sciences, 1-7, Ienomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
| | - S. Tanaka
- Department of Radiobiology, Institute for Environmental Sciences, 1-7, Ienomae, Obuchi, Rokkasho-mura, Kamikita-gun, Aomori 039-3212, Japan
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Zampieri M, Ciccarone F, Calabrese R, Franceschi C, Bürkle A, Caiafa P. Reconfiguration of DNA methylation in aging. Mech Ageing Dev 2015; 151:60-70. [PMID: 25708826 DOI: 10.1016/j.mad.2015.02.002] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/20/2015] [Accepted: 02/19/2015] [Indexed: 12/12/2022]
Abstract
A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as "epigenetic drift" which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5 hmC.
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Affiliation(s)
- Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Fabio Ciccarone
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Roberta Calabrese
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Claudio Franceschi
- Department of Experimental Pathology, Alma Mater Studiorum, University of Bologna, Bologna 40126, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz D-78457, Germany
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy.
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The quiescent cellular state is Arf/p53-dependent and associated with H2AX downregulation and genome stability. Int J Mol Sci 2012; 13:6492-6506. [PMID: 22754379 PMCID: PMC3382772 DOI: 10.3390/ijms13056492] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/21/2012] [Accepted: 05/22/2012] [Indexed: 12/17/2022] Open
Abstract
Cancer is a disease associated with genomic instability and mutations. Excluding some tumors with specific chromosomal translocations, most cancers that develop at an advanced age are characterized by either chromosomal or microsatellite instability. However, it is still unclear how genomic instability and mutations are generated during the process of cellular transformation and how the development of genomic instability contributes to cellular transformation. Recent studies of cellular regulation and tetraploidy development have provided insights into the factors triggering cellular transformation and the regulatory mechanisms that protect chromosomes from genomic instability.
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9
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Chromosomal aneuploidy in the aging brain. Mech Ageing Dev 2011; 132:429-36. [PMID: 21549743 DOI: 10.1016/j.mad.2011.04.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 03/28/2011] [Accepted: 04/14/2011] [Indexed: 12/31/2022]
Abstract
Mechanisms that govern genome integrity and stability are major guarantors of viability and longevity. As people age, memory and the ability to carry out tasks often decline and their risk for neurodegenerative diseases increases. The biological mechanisms underlying this age-related neuronal decline are not well understood. Genome instability has been implicated in neurodegenerative processes in aging and disease. Aneuploidy, a chromosome content that deviates from a diploid genome, is a recognized form of genomic instability. Here, we will review chromosomal aneuploidy in the aging brain, its possible causes, its consequences for cellular homeostasis and its possible link to functional decline and neuropathies.
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11
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Richardson RB. Ionizing radiation and aging: rejuvenating an old idea. Aging (Albany NY) 2009; 1:887-902. [PMID: 20157573 PMCID: PMC2815743 DOI: 10.18632/aging.100081] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 11/16/2009] [Indexed: 12/27/2022]
Abstract
This paper reviews the contemporary evidence that radiation can accelerate aging, degenerative health effects and mortality. Around the 1960s, the idea that ionizing radiation caused premature aging was dismissed as the radiation-induced health effects appeared to be virtually confined to neoplasms. More recently, radiation has become associated with a much wider spectrum of age-related diseases, including cardiovascular disease; although some diseases of old age, such as diabetes, are notably absent as a radiation risk. On the basis of recent research, is there a stronger case today to be made linking radiation and aging? Comparison is made between the now-known biological mechanisms of aging and those of radiation, including oxidative stress, chromosomal damage, apoptosis, stem cell exhaustion and inflammation. The association between radiation effects and the free-radical theory of aging as the causative hypothesis seems to be more compelling than that between radiation and the nutrient-sensing TOR pathway. Premature aging has been assessed by biomarkers in calorie restriction studies; yet, biomarkers such as telomere erosion and p16(INK4a) are ambiguous for radiation-induced aging. Some animal studies suggest low dose radiation may even demonstrate hormesis health benefits. Regardless, there is virtually no support for a life span extending hypothesis for A-bomb survivors and other exposed subjects.
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Affiliation(s)
- Richard B Richardson
- Radiation Protection Research and Instrumentation Branch, Atomic Energy of Canada Limited, Chalk River Laboratories, Chalk River, ON K0J 1J0, Canada.
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12
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Sinclair DA, Oberdoerffer P. The ageing epigenome: damaged beyond repair? Ageing Res Rev 2009; 8:189-98. [PMID: 19439199 DOI: 10.1016/j.arr.2009.04.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 04/30/2009] [Accepted: 04/30/2009] [Indexed: 12/28/2022]
Abstract
Of all the proposed causes of ageing, DNA damage remains a leading, though still debated theory. Unlike most other types of age-related cellular damage, which can hypothetically be reversed, mutations in DNA are permanent. Such errors result in the accumulation of changes to RNA and protein sequences with age, and are tightly linked to cellular senescence and overall organ dysfunction. Over the past few years, an additional, more global role has emerged for the contribution of DNA damage and genomic instability to the ageing process. We, and others have found that DNA damage and the concomitant repair process can induce genome-wide epigenetic changes, which may promote a variety of age-related transcriptional and functional changes. Here, we discuss the link between DNA damage, chromatin alterations and ageing, an interplay that explains how seemingly random DNA damage could manifest in predictable phenotypic changes that define ageing, changes that may ultimately be reversible.
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14
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Maslov AY, Vijg J. Genome instability, cancer and aging. Biochim Biophys Acta Gen Subj 2009; 1790:963-9. [PMID: 19344750 DOI: 10.1016/j.bbagen.2009.03.020] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 03/16/2009] [Accepted: 03/24/2009] [Indexed: 10/20/2022]
Abstract
DNA damage-driven genome instability underlies the diversity of life forms generated by the evolutionary process but is detrimental to the somatic cells of individual organisms. The cellular response to DNA damage can be roughly divided in two parts. First, when damage is severe, programmed cell death may occur or, alternatively, temporary or permanent cell cycle arrest. This protects against cancer but can have negative effects on the long term, e.g., by depleting stem cell reservoirs. Second, damage can be repaired through one or more of the many sophisticated genome maintenance pathways. However, erroneous DNA repair and incomplete restoration of chromatin after damage is resolved, produce mutations and epimutations, respectively, both of which have been shown to accumulate with age. An increased burden of mutations and/or epimutations in aged tissues increases cancer risk and adversely affects gene transcriptional regulation, leading to progressive decline in organ function. Cellular degeneration and uncontrolled cell proliferation are both major hallmarks of aging. Despite the fact that one seems to exclude the other, they both may be driven by a common mechanism. Here, we review age-related changes in the mammalian genome and their possible functional consequences, with special emphasis on genome instability in stem/progenitor cells.
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Affiliation(s)
- Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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Song LL, Alimirah F, Panchanathan R, Xin H, Choubey D. Expression of an IFN-Inducible Cellular Senescence Gene, IFI16, Is Up-Regulated by p53. Mol Cancer Res 2008; 6:1732-41. [DOI: 10.1158/1541-7786.mcr-08-0208] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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