51
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Schwender K, Holländer O, Klopfleisch S, Eveslage M, Danzer MF, Pfeiffer H, Vennemann M. Development of two age estimation models for buccal swab samples based on 3 CpG sites analyzed with pyrosequencing and minisequencing. Forensic Sci Int Genet 2021; 53:102521. [PMID: 33933877 DOI: 10.1016/j.fsigen.2021.102521] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/07/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
The analysis of DNA methylation levels of specific CpG sites is one of the most promising molecular techniques to estimate an individual's age. Numerous studies were published recently presenting age estimation models based on DNA methylation patterns from blood samples, with only a few using saliva or buccal swabs. The aim of this study was to identify age-dependent methylation of 88 CpG sites in eight different marker regions (PDE4C, ELOVL2, ITGA2B, ASPA, EDARADD, SST, KLF14 and SLC12A5) in buccal swab samples. A total of 141 buccal swabs from individuals with age ranging from 21 to 69 years were split into a training set (n = 95) and a validation set (n = 46). Samples of the training set were analyzed by pyrosequencing and markers with best age correlation were identified. Stepwise linear regression analysis was performed resulting in an age estimation model including three of the examined CpG sites and showing a mean absolute deviation of estimated from chronological age of 5.11 years. To allow easy implementation into forensic laboratories without the need for pyrosequencing equipment, a multiplex minisequencing reaction was developed, including the same CpG sites previously identified by pyrosequencing. An adjusted age estimation model was evaluated with a mean absolute deviation of estimated from chronological age of 5.16 years. The independent validation set of 46 buccal swab samples was used to test model performances. Mean absolute deviation of estimated from chronological age was 5.33 years and 6.44 years for the pyrosequencing model and the minisequencing model, respectively. Comparison of the two methods showed a high concordance of results, both, qualitatively and quantitatively. In conclusion, buccal swabs offer a suitable alternative to blood samples for molecular age estimation with the additional advantage of being collected non-invasively. Furthermore we showed that minisequencing offers a cost-effective and easy-to-integrate alternative to pyrosequencing for the analysis of methylation status of individual CpG sites.
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Affiliation(s)
- Kristina Schwender
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149 Münster, Germany; Institute of Legal Medicine, University of Munich, Nußbaumstraße 26, 80336 Munich, Germany
| | - Olivia Holländer
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149 Münster, Germany
| | | | - Maria Eveslage
- Institute of Biostatistics and Clinical Research, University of Münster, Schmeddingstraße 56, 48149 Münster, Germany
| | - Moritz Fabian Danzer
- Institute of Biostatistics and Clinical Research, University of Münster, Schmeddingstraße 56, 48149 Münster, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149 Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstraße 23, 48149 Münster, Germany.
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Zhang Z, Wang H, Wang Y, Xi F, Wang H, Kohnen MV, Gao P, Wei W, Chen K, Liu X, Gao Y, Han X, Hu K, Zhang H, Zhu Q, Zheng Y, Liu B, Ahmad A, Hsu YH, Jacobsen SE, Gu L. Whole-genome characterization of chronological age-associated changes in methylome and circular RNAs in moso bamboo (Phyllostachys edulis) from vegetative to floral growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:435-453. [PMID: 33506534 DOI: 10.1111/tpj.15174] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
In mammals, DNA methylation is associated with aging. However, age-related DNA methylation changes during phase transitions largely remain unstudied in plants. Moso bamboo (Phyllostachys edulis) requires a very long time to transition from the vegetative to the floral phase. To comprehensively investigate the association of DNA methylation with aging, we present here single-base-resolution DNA methylation profiles using both high-throughput bisulfite sequencing and single-molecule nanopore-based DNA sequencing, covering the long period of vegetative growth and transition to flowering in moso bamboo. We discovered that CHH methylation gradually accumulates from vegetative to reproductive growth in a time-dependent fashion. Differentially methylated regions, correlating with chronological aging, occurred preferentially at both transcription start sites and transcription termination sites. Genes with CG methylation changes showed an enrichment of Gene Ontology (GO) categories in 'vegetative to reproductive phase transition of meristem'. Combining methylation data with mRNA sequencing revealed that DNA methylation in promoters, introns and exons may have different roles in regulating gene expression. Finally, circular RNA (circRNA) sequencing revealed that the flanking introns of circRNAs are hypermethylated and enriched in long terminal repeat (LTR) retrotransposons. Together, the observations in this study provide insights into the dynamic DNA methylation and circRNA landscapes, correlating with chronological age, which paves the way to study further the impact of epigenetic factors on flowering in moso bamboo.
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Affiliation(s)
- Zeyu Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Markus V Kohnen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pengfei Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kai Chen
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Ximei Han
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kaiqiang Hu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yushan Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ayaz Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Steven E Jacobsen
- Department of Molecular, Cell & Developmental Biology, Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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53
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Pignolo RJ, Law SF, Chandra A. Bone Aging, Cellular Senescence, and Osteoporosis. JBMR Plus 2021; 5:e10488. [PMID: 33869998 PMCID: PMC8046105 DOI: 10.1002/jbm4.10488] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/17/2021] [Indexed: 12/15/2022] Open
Abstract
Changes in aging bone that lead to osteoporosis are mediated at multiple levels, including hormonal alterations, skeletal unloading, and accumulation of senescent cells. This pathological interplay is superimposed upon medical conditions, potentially bone-wasting medications, modifiable and unmodifiable personal risk factors, and genetic predisposition that accelerate bone loss with aging. In this study, the focus is on bone hemostasis and its dysregulation with aging. The major physiological changes with aging in bone and the role of cellular senescence in contributing to age-related osteoporosis are summarized. The aspects of bone aging are reviewed including remodeling deficits, uncoupling phenomena, inducers of cellular senescence related to bone aging, roles of the senescence-associated secretory phenotype, radiation-induced bone loss as a model for bone aging, and the accumulation of senescent cells in the bone microenvironment as a predominant mechanism for age-related osteoporosis. The study also addresses the rationale and potential for therapeutic interventions based on the clearance of senescent cells or suppression of the senescence-associated secretory phenotype. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Robert J Pignolo
- Department of MedicineMayo ClinicRochesterMNUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMNUSA
| | - Susan F Law
- Department of MedicineMayo ClinicRochesterMNUSA
| | - Abhishek Chandra
- Department of MedicineMayo ClinicRochesterMNUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMNUSA
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54
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Berben L, Floris G, Wildiers H, Hatse S. Cancer and Aging: Two Tightly Interconnected Biological Processes. Cancers (Basel) 2021; 13:1400. [PMID: 33808654 PMCID: PMC8003441 DOI: 10.3390/cancers13061400] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
Age is one of the main risk factors of cancer; several biological changes linked with the aging process can explain this. As our population is progressively aging, the proportion of older patients with cancer is increasing significantly. Due to the heterogeneity of general health and functional status amongst older persons, treatment of cancer is a major challenge in this vulnerable population. Older patients often experience more side effects of anticancer treatments. Over-treatment should be avoided to ensure an optimal quality of life. On the other hand, under-treatment due to fear of toxicity is a frequent problem and can lead to an increased risk of relapse and worse survival. There is a delicate balance between benefits of therapy and risk of toxicity. Robust biomarkers that reflect the body's biological age may aid in outlining optimal individual treatment regimens for older patients with cancer. In particular, the impact of age on systemic immunity and the tumor immune infiltrate should be considered, given the expanding role of immunotherapy in cancer treatment. In this review, we summarize current knowledge concerning the mechanistic connections between aging and cancer, as well as aging biomarkers that could be helpful in the field of geriatric oncology.
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Affiliation(s)
- Lieze Berben
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium;
| | - Giuseppe Floris
- Department of Pathology, University Hospitals Leuven, 3000 Leuven, Belgium;
- Laboratory of Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, 3000 Leuven, Belgium
| | - Hans Wildiers
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium;
- Department of General Medical Oncology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Sigrid Hatse
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium;
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55
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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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56
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Lahtinen A, Häkkinen A, Puttonen S, Vanttola P, Viitasalo K, Porkka-Heiskanen T, Härmä M, Paunio T. Differential DNA methylation in recovery from shift work disorder. Sci Rep 2021; 11:2895. [PMID: 33536559 PMCID: PMC7858604 DOI: 10.1038/s41598-021-82627-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/22/2021] [Indexed: 01/07/2023] Open
Abstract
The human DNA methylome is responsive to our environment, but its dynamics remain underexplored. We investigated the temporal changes to DNA methylation (DNAme) in relation to recovery from a shift work disorder (SWD) by performing a paired epigenome-wide analysis in an occupational cohort of 32 shift workers (25 men, age = 43.8 ± 8.8 years, 21 SWD cases). We found that the effect of vacation on DNAme was more prominent in the SWD-group as compared to controls, with respect to the amount of significantly differentially methylated positions (DMPs; Punadj < 0.05) 6.5 vs 3.7%, respectively. The vast majority (78%) of these DMPs were hypomethylated in SWD but not in controls (27%) during the work period. The Gene Ontology Cellular component "NMDA glutamate receptor" (PFDR < 0.05) was identified in a pathway analysis of the top 30 genes in SWD. In-depth pathway analyses revealed that the Reactome pathway "CREB phosphorylation through the activation of CaMKII" might underlie the recovery. Furthermore, three DMPs from this pathway, corresponding to GRIN2C, CREB1, and CAMK2B, correlated with the degree of recovery (Punadj < 0.05). Our findings provide evidence for the dynamic nature of DNAme in relation to the recovery process from a circadian disorder, with biological relevance of the emerging pathways.
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Affiliation(s)
- Alexandra Lahtinen
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland. .,Genomics and Biobank UnitDepartment of Public Health Solutions, Finnish Institute for Health and Welfare (THL), PO Box 30, 00271, Helsinki, Finland.
| | - Antti Häkkinen
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sampsa Puttonen
- Work Ability and Working Careersareers, Finnish Institute of Occupational Health, PO Box 40, 00032, Helsinki, Finland
| | - Päivi Vanttola
- Work Ability and Working Careersareers, Finnish Institute of Occupational Health, PO Box 40, 00032, Helsinki, Finland
| | | | - Tarja Porkka-Heiskanen
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland
| | - Mikko Härmä
- Work Ability and Working Careersareers, Finnish Institute of Occupational Health, PO Box 40, 00032, Helsinki, Finland
| | - Tiina Paunio
- Department of Psychiatry and SleepWell Research Program, Faculty of Medicine, University of Helsinki and Helsinki University Central Hospital, Biomedicum 1, Haartmaninkatu 8, 00290, Helsinki, Finland. .,Genomics and Biobank UnitDepartment of Public Health Solutions, Finnish Institute for Health and Welfare (THL), PO Box 30, 00271, Helsinki, Finland.
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57
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Siametis A, Niotis G, Garinis GA. DNA Damage and the Aging Epigenome. J Invest Dermatol 2021; 141:961-967. [PMID: 33494932 DOI: 10.1016/j.jid.2020.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/29/2022]
Abstract
In mammals, genome instability and aging are intimately linked as illustrated by the growing list of patients with progeroid and animal models with inborn DNA repair defects. Until recently, DNA damage was thought to drive aging by compromising transcription or DNA replication, thereby leading to age-related cellular malfunction and somatic mutations triggering cancer. However, recent evidence suggests that DNA lesions also elicit widespread epigenetic alterations that threaten cell homeostasis as a function of age. In this review, we discuss the functional links of persistent DNA damage with the epigenome in the context of aging and age-related diseases.
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Affiliation(s)
- Athanasios Siametis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece
| | - George Niotis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece; Department of Biology, University of Crete, Heraklion, Greece.
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58
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Kuzmina NS, Luong TM, Rubanovich AV. Changes in DNA Methylation Induced by Dioxins and Dioxin-Like Compounds as Potential Predictor of Disease Risk. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420100063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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59
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Xie K, Kapetanou M, Sidiropoulou K, Bano D, Gonos ES, Djordjevic AM, Ehninger D. Signaling pathways of dietary energy restriction and metabolism on brain physiology and in age-related neurodegenerative diseases. Mech Ageing Dev 2020; 192:111364. [PMID: 32991920 DOI: 10.1016/j.mad.2020.111364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/17/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
Several laboratory animal models have shown that dietary energy restriction (ER) can promote longevity and improve various health aspects in old age. However, whether the entire spectrum of ER-induced short- and long-term physiological and metabolic adaptions is translatable to humans remains to be determined. In this review article, we present recent evidence towards the elucidation of the impact of ER on brain physiology and in age-related neurodegenerative diseases. We also discuss modulatory influences of ER on metabolism and overall on human health, limitations of current experimental designs as well as future perspectives for ER trials in humans. Finally, we summarize signaling pathways and processes known to be affected by both aging and ER with a special emphasis on the link between ER and cellular proteostasis.
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Affiliation(s)
- Kan Xie
- Molecular and Cellular Cognition Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, 53127 Bonn, Germany
| | - Marianna Kapetanou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece
| | | | - Daniele Bano
- Aging and Neurodegeneration Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, 53127 Bonn, Germany
| | - Efstathios S Gonos
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece
| | - Aleksandra Mladenovic Djordjevic
- Department of Neurobiology, Institute for Biological Research 'Sinisa Stankovic', University of Belgrade, National Institute of Republic of Serbia, Boulevard Despota Stefana 142, 11000 Belgrade, Serbia
| | - Dan Ehninger
- Molecular and Cellular Cognition Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1, 53127 Bonn, Germany.
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60
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Lee JH, Kim EW, Croteau DL, Bohr VA. Heterochromatin: an epigenetic point of view in aging. Exp Mol Med 2020; 52:1466-1474. [PMID: 32887933 PMCID: PMC8080806 DOI: 10.1038/s12276-020-00497-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
Aging is an inevitable process of life. Defined by progressive physiological and functional loss of tissues and organs, aging increases the risk of mortality for the organism. The aging process is affected by various factors, including genetic and epigenetic ones. Here, we review the chromatin-specific epigenetic changes that occur during normal (chronological) aging and in premature aging diseases. Taking advantage of the reversible nature of epigenetic modifications, we will also discuss possible lifespan expansion strategies through epigenetic modulation, which was considered irreversible until recently.
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Affiliation(s)
- Jong-Hyuk Lee
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Edward W Kim
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA. .,Danish Center for Healthy Aging, University of Copenhagen, 2200, Copenhagen, Denmark.
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61
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Fusion Potential of Human Osteoclasts In Vitro Reflects Age, Menopause, and In Vivo Bone Resorption Levels of Their Donors-A Possible Involvement of DC-STAMP. Int J Mol Sci 2020; 21:ijms21176368. [PMID: 32887359 PMCID: PMC7504560 DOI: 10.3390/ijms21176368] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/28/2022] Open
Abstract
It is well established that multinucleation is central for osteoclastic bone resorption. However, our knowledge on the mechanisms regulating how many nuclei an osteoclast will have is limited. The objective of this study was to investigate donor-related variations in the fusion potential of in vitro-generated osteoclasts. Therefore, CD14+ monocytes were isolated from 49 healthy female donors. Donor demographics were compared to the in vivo bone biomarker levels and their monocytes’ ability to differentiate into osteoclasts, showing that: (1) C-terminal telopeptide of type I collagen (CTX) and procollagen type I N-terminal propeptide (PINP) levels increase with age, (2) the number of nuclei per osteoclast in vitro increases with age, and (3) there is a positive correlation between the number of nuclei per osteoclast in vitro and CTX levels in vivo. Furthermore, the expression levels of the gene encoding dendritic cell-specific transmembrane protein (DCSTAMP) of osteoclasts in vitro correlated positively with the number of nuclei per osteoclast, CTX levels in vivo, and donor age. Our results furthermore suggest that these changes in gene expression may be mediated through age-related changes in DNA methylation levels. We conclude that both intrinsic factors and age-induced increase in fusion potential of osteoclasts could be contributing factors for the enhanced bone resorption in vivo, possibly caused by increased expression levels of DCSTAMP.
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Abstract
PURPOSE OF REVIEW This review aims to explore how circadian rhythms influence disease susceptibility and potentially modify the effect of environmental exposures. We aimed to identify biomarkers commonly used in environmental health research that have also been the subject of chronobiology studies, in order to review circadian rhythms of relevance to environmental health and determine if time-of-day is an important factor to consider in environmental health studies. Moreover, we discuss opportunities for studying how environmental exposures may interact with circadian rhythms to structure disease pathology and etiology. RECENT FINDINGS In recent years, the study of circadian rhythms in mammals has flourished. Animal models revealed that all body tissues have circadian rhythms. In humans, circadian rhythms were also shown to exist at multiple levels of organization: molecular, cellular, and physiological processes, including responding to oxidative stress, cell trafficking, and sex hormone production, respectively. Together, these rhythms are an essential component of human physiology and can shape an individual's susceptibility and response to disease. Circadian rhythms are relatively unexplored in environmental health research. However, circadian clocks control many physiological and behavioral processes that impact exposure pathways and disease systems. We believe this review will motivate new studies of (i) the impact of exposures on circadian rhythms, (ii) how circadian rhythms modify the effect of environmental exposures, and (iii) how time-of-day impacts our ability to observe the body's response to exposure.
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Affiliation(s)
- Jacqueline M Leung
- Department of Environmental Health Sciences, Columbia University, 630 West 168th Street, Room 16-421C, New York, NY, USA
| | - Micaela E Martinez
- Department of Environmental Health Sciences, Columbia University, 630 West 168th Street, Room 16-421C, New York, NY, USA.
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63
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Dahan L, Rampon C, Florian C. Age-related memory decline, dysfunction of the hippocampus and therapeutic opportunities. Prog Neuropsychopharmacol Biol Psychiatry 2020; 102:109943. [PMID: 32298784 DOI: 10.1016/j.pnpbp.2020.109943] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 12/13/2022]
Abstract
While the aging of the population is a sign of progress for societies, it also carries its load of negative aspects. Among them, cognitive decline and in particular memory loss is a common feature of non-pathological aging. Autobiographical memories, which rely on the hippocampus, are a primary target of age-related cognitive decline. Here, focusing on the neurobiological mechanisms of memory formation and storage, we describe how hippocampal functions are altered across time in non-pathological mammalian brains. Several hallmarks of aging have been well described over the last decades; among them, we consider altered synaptic communication and plasticity, reduction of adult neurogenesis and epigenetic alterations. Building on the neurobiological processes of cognitive aging that have been identified to date, we review some of the strategies based on lifestyle manupulation allowing to address age-related cognitive deficits.
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Affiliation(s)
- Lionel Dahan
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse; CNRS, UPS, Toulouse Cedex 9, France
| | - Claire Rampon
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse; CNRS, UPS, Toulouse Cedex 9, France
| | - Cédrick Florian
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université de Toulouse; CNRS, UPS, Toulouse Cedex 9, France.
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64
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Comparative genome-wide DNA methylation analysis in myocardial tissue from donors with and without Down syndrome. Gene 2020; 764:145099. [PMID: 32861879 DOI: 10.1016/j.gene.2020.145099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/27/2020] [Accepted: 08/24/2020] [Indexed: 01/09/2023]
Abstract
Down syndrome (DS, trisomy 21) is the most common major chromosomal aneuploidy compatible with life. The additional whole or partial copy of chromosome 21 results in genome-wide imbalances that drive the complex pathobiology of DS. Differential DNA methylation in the context of trisomy 21 may contribute to the variable architecture of the DS phenotype. The goal of this study was to examine the genomic DNA methylation landscape in myocardial tissue from non-fetal individuals with DS. >480,000 unique CpG sites were interrogated in myocardial DNA samples from individuals with (n = 12) and without DS (n = 12) using DNA methylation arrays. A total of 93 highly differentially methylated CpG sites and 16 differentially methylated regions were identified in myocardial DNA from subjects with DS. There were 18 differentially methylated CpG sites in chromosome 21, including 5 highly differentially methylated sites. A CpG site in the RUNX1 locus was differentially methylated in DS myocardium, and linear regression suggests that donors' age, gender, DS status, and RUNX1 methylation may contribute up to ~51% of the variability in RUNX1 mRNA expression. In DS myocardium, only 58% of the genes overlapping with differentially methylated regions codify for proteins with known functions and 24% are non-coding RNAs. This study provides an initial snapshot on the extent of genome-wide differential methylation in myocardial tissue from persons with DS.
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Hahn A, Pensold D, Bayer C, Tittelmeier J, González-Bermúdez L, Marx-Blümel L, Linde J, Groß J, Salinas-Riester G, Lingner T, von Maltzahn J, Spehr M, Pieler T, Urbach A, Zimmer-Bensch G. DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons. Front Cell Dev Biol 2020; 8:639. [PMID: 32793592 PMCID: PMC7387673 DOI: 10.3389/fcell.2020.00639] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/25/2020] [Indexed: 01/19/2023] Open
Abstract
Increased life expectancy in modern society comes at the cost of age-associated disabilities and diseases. Aged brains not only show reduced excitability and plasticity, but also a decline in inhibition. Age-associated defects in inhibitory circuits likely contribute to cognitive decline and age-related disorders. Molecular mechanisms that exert epigenetic control of gene expression contribute to age-associated neuronal impairments. Both DNA methylation, mediated by DNA methyltransferases (DNMTs), and histone modifications maintain neuronal function throughout lifespan. Here we provide evidence that DNMT1 function is implicated in the age-related loss of cortical inhibitory interneurons. Dnmt1 deletion in parvalbumin-positive interneurons attenuates their age-related decline in the cerebral cortex. Moreover, conditional Dnmt1-deficient mice show improved somatomotor performance and reduced aging-associated transcriptional changes. A decline in the proteostasis network, responsible for the proper degradation and removal of defective proteins, is implicated in age- and disease-related neurodegeneration. Our data suggest that DNMT1 acts indirectly on interneuron survival in aged mice by modulating the proteostasis network during life-time.
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Affiliation(s)
- Anne Hahn
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Daniel Pensold
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany.,Department of Functional Epigenetics in the Animal Model, Institute of Biology II, RWTH Aachen University, Aachen, Germany
| | - Cathrin Bayer
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany.,Department of Functional Epigenetics in the Animal Model, Institute of Biology II, RWTH Aachen University, Aachen, Germany
| | - Jessica Tittelmeier
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Lourdes González-Bermúdez
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Lisa Marx-Blümel
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Jenice Linde
- Department of Functional Epigenetics in the Animal Model, Institute of Biology II, RWTH Aachen University, Aachen, Germany.,Research Training Group 2416 MultiSenses - MultiScales, RWTH Aachen University, Aachen, Germany
| | - Jonas Groß
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Gabriela Salinas-Riester
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Göttingen, Göttingen, Germany
| | - Thomas Lingner
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Göttingen, Göttingen, Germany
| | - Julia von Maltzahn
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Marc Spehr
- Research Training Group 2416 MultiSenses - MultiScales, RWTH Aachen University, Aachen, Germany.,Department of Chemosensation, Institute of Biology II, RWTH Aachen University, Aachen, Germany
| | - Tomas Pieler
- Centre for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Department of Developmental Biochemistry, University of Göttingen, Göttingen, Germany
| | - Anja Urbach
- Institute of Neurology, University Hospital Jena, Jena, Germany
| | - Geraldine Zimmer-Bensch
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany.,Department of Functional Epigenetics in the Animal Model, Institute of Biology II, RWTH Aachen University, Aachen, Germany.,Research Training Group 2416 MultiSenses - MultiScales, RWTH Aachen University, Aachen, Germany
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66
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Kader F, Ghai M, Zhou M. Ethnicity, age and disease-associated variation in body fluid-specific CpG sites in a diverse South African cohort. Forensic Sci Int 2020; 314:110372. [PMID: 32623090 DOI: 10.1016/j.forsciint.2020.110372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 12/11/2022]
Abstract
Tissue-specific differential DNA methylation has been an attractive target for the development of markers for discrimination of body fluids found at crime scenes. Though mostly stable, DNA methylation patterns have been shown to vary between different ethnic groups, in different age groups as well as between healthy and diseased individuals. To the best of our knowledge, none of the markers for body fluid identification have been applied to different ethnic groups to ascertain if variability exists. In the present study, saliva and blood were collected to determine the effects of ethnicity (Blacks, Whites, Coloureds and Indians), age (20-30 years, 40-50years and above 60 years) and diabetes on methylation profiles of potential saliva- and blood-specific DMSs. Both DMSs were previously shown to exhibit hypermethylation in their target body fluids at single CpG sites, however in the present study, additional CpG sites flanking the reported sites were also screened. Bisulfite sequencing revealed that Coloureds showed highest methylation levels for both body fluids, and blacks displayed significant differences between other ethnic groups in the blood-specific CpG sites. A decline in methylation for both potential DMRs was observed with increasing age. Heavily methylated CpG sites in different ethnic groups and previously reported DMSs displayed hypomethylation with increasing age and disease status. Diabetic status did not show any significant difference in methylation when compared to healthy counterparts. Thus, the use of methylation markers for forensics needs thorough investigation of influence of external factors and ideally, several CpG sites should be co-analysed instead of a single DMS.
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Affiliation(s)
- Farzeen Kader
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa.
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa.
| | - Marvellous Zhou
- South African Sugarcane Research Institute, Mount Edgecombe, Durban, South Africa; University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa.
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Saccà SC, Vernazza S, Iorio EL, Tirendi S, Bassi AM, Gandolfi S, Izzotti A. Molecular changes in glaucomatous trabecular meshwork. Correlations with retinal ganglion cell death and novel strategies for neuroprotection. PROGRESS IN BRAIN RESEARCH 2020; 256:151-188. [PMID: 32958211 DOI: 10.1016/bs.pbr.2020.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Glaucoma is a chronic neurodegenerative disease characterized by retinal ganglion cell loss. Although significant advances in ophthalmologic knowledge and practice have been made, some glaucoma mechanisms are not yet understood, therefore, up to now there is no effective treatment able to ensure healing. Indeed, either pharmacological or surgical approaches to this disease aim in lowering intraocular pressure, which is considered the only modifiable risk factor. However, it is well known that several factors and metabolites are equally (if not more) involved in glaucoma. Oxidative stress, for instance, plays a pivotal role in both glaucoma onset and progression because it is responsible for the trabecular meshwork cell damage and, consequently, for intraocular pressure increase as well as for glaucomatous damage cascade. This review at first shows accurately the molecular-derived dysfunctions in antioxidant system and in mitochondria homeostasis which due to both oxidative stress and aging, lead to a chronic inflammation state, the trabecular meshwork damage as well as the glaucoma neurodegeneration. Therefore, the main molecular events triggered by oxidative stress up to the proapoptotic signals that promote the ganglion cell death have been highlighted. The second part of this review, instead, describes some of neuroprotective agents such as polyphenols or polyunsaturated fatty acids as possible therapeutic source against the propagation of glaucomatous damage.
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Affiliation(s)
- Sergio C Saccà
- Policlinico San Martino University Hospital, Department of Neuroscience and sense organs, Ophthalmology Unit, Genoa, Italy.
| | | | | | - Sara Tirendi
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Pisa, Italy
| | - Anna Maria Bassi
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Inter-University Center for the Promotion of the 3Rs Principles in Teaching & Research (Centro 3R), Pisa, Italy
| | - Stefano Gandolfi
- Ophthalmology Unit, Department of Biological, Biotechnological and Translational Sciences, University of Parma, Parma, Italy
| | - Alberto Izzotti
- Department of Experimental Medicine (DIMES), University of Genoa, Genoa, Italy; Mutagenesis Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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Møller AMJ, Delaissé JM, Olesen JB, Madsen JS, Canto LM, Bechmann T, Rogatto SR, Søe K. Aging and menopause reprogram osteoclast precursors for aggressive bone resorption. Bone Res 2020; 8:27. [PMID: 32637185 PMCID: PMC7329827 DOI: 10.1038/s41413-020-0102-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/06/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022] Open
Abstract
Women gradually lose bone from the age of ~35 years, but around menopause, the rate of bone loss escalates due to increasing bone resorption and decreasing bone formation levels, rendering these individuals more prone to developing osteoporosis. The increased osteoclast activity has been linked to a reduced estrogen level and other hormonal changes. However, it is unclear whether intrinsic changes in osteoclast precursors around menopause can also explain the increased osteoclast activity. Therefore, we set up a protocol in which CD14+ blood monocytes were isolated from 49 female donors (40-66 years old). Cells were differentiated into osteoclasts, and data on differentiation and resorption activity were collected. Using multiple linear regression analyses combining in vitro and in vivo data, we found the following: (1) age and menopausal status correlate with aggressive osteoclastic bone resorption in vitro; (2) the type I procollagen N-terminal propeptide level in vivo inversely correlates with osteoclast resorption activity in vitro; (3) the protein level of mature cathepsin K in osteoclasts in vitro increases with age and menopause; and (4) the promoter of the gene encoding the dendritic cell-specific transmembrane protein is less methylated with age. We conclude that monocytes are "reprogrammed" in vivo, allowing them to "remember" age, the menopausal status, and the bone formation status in vitro, resulting in more aggressive osteoclasts. Our discovery suggests that this may be mediated through DNA methylation. We suggest that this may have clinical implications and could contribute to understanding individual differences in age- and menopause-induced bone loss.
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Affiliation(s)
- Anaïs Marie Julie Møller
- Clinical Cell Biology, Lillebaelt Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Clinical Biochemistry and Immunology, Lillebaelt Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Jean-Marie Delaissé
- Clinical Cell Biology, Lillebaelt Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5230 Odense M, Denmark
- Clinical Cell Biology, Department of Pathology, Odense University Hospital, 5000 Odense C, Denmark
- Department of Clinical Research, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Molecular Medicine, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jacob Bastholm Olesen
- Clinical Cell Biology, Lillebaelt Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Clinical Cell Biology, Department of Pathology, Odense University Hospital, 5000 Odense C, Denmark
| | - Jonna Skov Madsen
- Department of Regional Health Research, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Clinical Biochemistry and Immunology, Lillebaelt Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Luisa Matos Canto
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Troels Bechmann
- Department of Regional Health Research, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Oncology, Lillebaelt Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Silvia Regina Rogatto
- Department of Regional Health Research, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Kent Søe
- Clinical Cell Biology, Lillebaelt Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5230 Odense M, Denmark
- Clinical Cell Biology, Department of Pathology, Odense University Hospital, 5000 Odense C, Denmark
- Department of Clinical Research, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Molecular Medicine, University of Southern Denmark, 5230 Odense M, Denmark
- OPEN, Odense Patient data Explorative Network, Odense University Hospital, 5000 Odense C, Denmark
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69
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Han Y, Franzen J, Stiehl T, Gobs M, Kuo CC, Nikolić M, Hapala J, Koop BE, Strathmann K, Ritz-Timme S, Wagner W. New targeted approaches for epigenetic age predictions. BMC Biol 2020; 18:71. [PMID: 32580727 PMCID: PMC7315536 DOI: 10.1186/s12915-020-00807-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/08/2020] [Indexed: 12/16/2022] Open
Abstract
Background Age-associated DNA methylation changes provide a promising biomarker for the aging process. While genome-wide DNA methylation profiles enable robust age-predictors by integration of many age-associated CG dinucleotides (CpGs), there are various alternative approaches for targeted measurements at specific CpGs that better support standardized and cost-effective high-throughput analysis. Results In this study, we utilized 4647 Illumina BeadChip profiles of blood to select CpG sites that facilitate reliable age-predictions based on pyrosequencing. We demonstrate that the precision of DNA methylation measurements can be further increased with droplet digital PCR (ddPCR). In comparison, bisulfite barcoded amplicon sequencing (BBA-seq) gave slightly lower correlation between chronological age and DNA methylation at individual CpGs, while the age-predictions were overall relatively accurate. Furthermore, BBA-seq data revealed that the correlation of methylation levels with age at neighboring CpG sites follows a bell-shaped curve, often associated with a CTCF binding site. We demonstrate that within individual BBA-seq reads the DNA methylation at neighboring CpGs is not coherently modified, but reveals a stochastic pattern. Based on this, we have developed a new approach for epigenetic age predictions based on the binary sequel of methylated and non-methylated sites in individual reads, which reflects heterogeneity in epigenetic aging within a sample. Conclusion Targeted DNA methylation analysis at few age-associated CpGs by pyrosequencing, BBA-seq, and particularly ddPCR enables high precision of epigenetic age-predictions. Furthermore, we demonstrate that the stochastic evolution of age-associated DNA methylation patterns in BBA-seq data enables epigenetic clocks for individual DNA strands.
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Affiliation(s)
- Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Stiehl
- Interdisciplinary Center for Scientific Computing (IWR), Institute of Applied Mathematics, University of Heidelberg, Heidelberg, Germany
| | - Michael Gobs
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Chao-Chung Kuo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Jan Hapala
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | | | - Klaus Strathmann
- Institute for Transfusion Medicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Stefanie Ritz-Timme
- Institute for Legal Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany.
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70
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Abstract
Background Epigenetic processes control timing and level of gene expression throughout life, during development, differentiation, and aging, and are the link to adapting gene expression profiles to environmental cues. To qualify for the definition of ‘epigenetic’, a change to a gene's activity must be inherited through at least one mitotic division. Epigenetic mechanisms link changes in the environment to adaptions of the genome that do not rely on changes in the DNA sequence. In the past two decades, multiple studies have aimed to identify epigenetic mechanisms, and to define their role in development, differentiation and disease. Scope of review In this review, we will focus on the current knowledge of the epigenetic control of pancreatic beta cell maturation and dysfunction and its relationship to the development of islet cell failure in diabetes. Most of the data currently available have been obtained in mice, but we will summarize studies of human data as well. We will focus here on DNA methylation, as this is the most stable epigenetic mark, and least impacted by the variables inherent in islet procurement, isolation, and culture. Major conclusions DNA methylation patterns of beta cell are dynamic during maturation and during the diabetic process. In both cases, the changes occur at cell specific regulatory regions such as enhancers, where the methylation profile is cell type specific. Frequently, the differentially methylated regulatory elements are associated with key function genes such as PDX1, NKX6-1 and TCF7L2. During maturation, enhancers tend to become demethylated in association with increased activation of beta cell function genes and increased functionality, as indicated by glucose stimulated insulin secretion. Likewise, the changes to the DNA methylome that are present in pancreatic islets from diabetic donors are enriched in regulatory regions as well.
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Affiliation(s)
- Dana Avrahami
- Endocrinology and Metabolism Department, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Klaus H Kaestner
- University of Pennsylvania, Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA, USA.
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71
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The relationship between DNA methylation in neurotrophic genes and age as evidenced from three independent cohorts: differences by delirium status. Neurobiol Aging 2020; 94:227-235. [PMID: 32650186 DOI: 10.1016/j.neurobiolaging.2020.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/07/2020] [Accepted: 06/06/2020] [Indexed: 12/19/2022]
Abstract
We previously reported the association between DNA methylation (DNAm) of pro-inflammatory cytokine genes and age. In addition, neurotrophic factors are known to be associated with age and neurocognitive disorders. Therefore, we hypothesized that DNAm of neurotrophic genes change with age, especially in delirium patients. DNAm was analyzed using the Illumina HumanMethylation450 or HumanMethylationEPIC BeadChip Kit in 3 independent cohorts: blood from 383 Grady Trauma Project subjects, brain from 21 neurosurgery patients, and blood from 87 inpatients with and without delirium. Both blood and brain samples showed that most of the DNAm of neurotrophic genes were positively correlated with age. Furthermore, DNAm of neurotrophic genes was more positively correlated with age in delirium cases than in non-delirium controls. These findings support our hypothesis that the neurotrophic genes may be epigenetically modulated with age, and this process may be contributing to the pathophysiology of delirium.
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72
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Wei Y, Fu J, Wu W, Wu J. Comparative profiles of DNA methylation and differential gene expression in osteocytic areas from aged and young mice. Cell Biochem Funct 2020; 38:721-732. [PMID: 32526817 DOI: 10.1002/cbf.3539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/09/2020] [Accepted: 03/29/2020] [Indexed: 12/19/2022]
Abstract
Altered DNA methylation upon ageing may result in many age-related diseases such as osteoporosis. However, the changes in DNA methylation that occur in cortical bones, the major osteocytic areas, remain unknown. In our study, we extracted total DNA and RNA from the cortical bones of 6-month-old and 24-month-old mice and systematically analysed the differentially methylated regions (DMRs), differentially methylated promoters (DMPs) and differentially expressed genes (DEGs) between the mouse groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DMR-related genes revealed that they were mainly associated with metabolic signalling pathways, including glycolysis, fatty acid and amino acid metabolism. Other genes with DMRs were related to signalling pathways that regulate the growth and development of cells, including the PI3K-AKT, Ras and Rap1 signalling pathways. The gene expression profiles indicated that the DEGs were mainly involved in metabolic pathways and the PI3K-AKT signalling pathway, and the profiles were verified through real-time quantitative PCR (RT-qPCR). Due to the pivotal roles of the affected genes in maintaining bone homeostasis, we suspect that these changes may be key factors in age-related bone loss, either together or individually. Our study may provide a novel perspective for understanding the osteocyte and its relationship with osteoporosis during ageing. SIGNIFICANCE OF THE STUDY: Our study identified age-related changes in gene expressions in osteocytic areas through whole-genome bisulfite sequencing (WGBS) and RNA-seq, providing new theoretical foundations for the targeted treatment of senile osteoporosis.
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Affiliation(s)
- Yu Wei
- Department of Prosthodontics, School and Hospital of Stomatology, Tongji University and Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Jiayao Fu
- Department of Prosthodontics, School and Hospital of Stomatology, Tongji University and Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Wenjing Wu
- Department of Prosthodontics, School and Hospital of Stomatology, Tongji University and Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Junhua Wu
- Department of Prosthodontics, School and Hospital of Stomatology, Tongji University and Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
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73
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The Role of Nutri(epi)genomics in Achieving the Body's Full Potential in Physical Activity. Antioxidants (Basel) 2020; 9:antiox9060498. [PMID: 32517297 PMCID: PMC7346155 DOI: 10.3390/antiox9060498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Physical activity represents a powerful tool to achieve optimal health. The overall activation of several molecular pathways is associated with many beneficial effects, mainly converging towards a reduced systemic inflammation. Not surprisingly, regular activity can contribute to lowering the “epigenetic age”, acting as a modulator of risk toward several diseases and enhancing longevity. Behind this, there are complex molecular mechanisms induced by exercise, which modulate gene expression, also through epigenetic modifications. The exercise-induced epigenetic imprint can be transient or permanent and contributes to the muscle memory, which allows the skeletal muscle adaptation to environmental stimuli previously encountered. Nutrition, through key macro- and micronutrients with antioxidant properties, can play an important role in supporting skeletal muscle trophism and those molecular pathways triggering the beneficial effects of physical activity. Nutrients and antioxidant food components, reversibly altering the epigenetic imprint, have a big impact on the phenotype. This assigns a role of primary importance to nutri(epi)genomics, not only in optimizing physical performance, but also in promoting long term health. The crosstalk between physical activity and nutrition represents a major environmental pressure able to shape human genotypes and phenotypes, thus, choosing the right combination of lifestyle factors ensures health and longevity.
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74
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García-Guede Á, Vera O, Ibáñez-de-Caceres I. When Oxidative Stress Meets Epigenetics: Implications in Cancer Development. Antioxidants (Basel) 2020; 9:antiox9060468. [PMID: 32492865 PMCID: PMC7346131 DOI: 10.3390/antiox9060468] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide and it can affect any part of the organism. It arises as a consequence of the genetic and epigenetic changes that lead to the uncontrolled growth of the cells. The epigenetic machinery can regulate gene expression without altering the DNA sequence, and it comprises methylation of the DNA, histones modifications, and non-coding RNAs. Alterations of these gene-expression regulatory elements can be produced by an imbalance of the intracellular environment, such as the one derived by oxidative stress, to promote cancer development, progression, and resistance to chemotherapeutic treatments. Here we review the current literature on the effect of oxidative stress in the epigenetic machinery, especially over the largely unknown ncRNAs and its consequences toward cancer development and progression.
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Affiliation(s)
- Álvaro García-Guede
- Epigenetics Laboratory, INGEMM, Hospital La PAZ. 28046 Madrid, Spain; (Á.G.-G.); (I.I.-d.-C.)
- Experimental Therapies and Novel Biomarkers in Cancer, Instituto de Investigación Sanitaria del Hospital La Paz. IdiPAZ, 28046 Madrid, Spain
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
- Correspondence:
| | - Inmaculada Ibáñez-de-Caceres
- Epigenetics Laboratory, INGEMM, Hospital La PAZ. 28046 Madrid, Spain; (Á.G.-G.); (I.I.-d.-C.)
- Experimental Therapies and Novel Biomarkers in Cancer, Instituto de Investigación Sanitaria del Hospital La Paz. IdiPAZ, 28046 Madrid, Spain
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75
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Köhler F, Bormann F, Raddatz G, Gutekunst J, Corless S, Musch T, Lonsdorf AS, Erhardt S, Lyko F, Rodríguez-Paredes M. Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome. Genome Med 2020; 12:46. [PMID: 32450911 PMCID: PMC7249329 DOI: 10.1186/s13073-020-00749-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Hutchinson-Gilford progeria syndrome (HGPS) is a progeroid disease characterized by the early onset of age-related phenotypes including arthritis, loss of body fat and hair, and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein lamin A (termed progerin) and have previously been shown to exhibit prominent histone modification changes. METHODS Here, we analyze the possibility that epigenetic deregulation of lamina-associated domains (LADs) is involved in the molecular pathology of HGPS. To do so, we studied chromatin accessibility (Assay for Transposase-accessible Chromatin (ATAC)-see/-seq), DNA methylation profiles (Infinium MethylationEPIC BeadChips), and transcriptomes (RNA-seq) of nine primary HGPS fibroblast cell lines and six additional controls, two parental and four age-matched healthy fibroblast cell lines. RESULTS Our ATAC-see/-seq data demonstrate that primary dermal fibroblasts from HGPS patients exhibit chromatin accessibility changes that are enriched in LADs. Infinium MethylationEPIC BeadChip profiling further reveals that DNA methylation alterations observed in HGPS fibroblasts are similarly enriched in LADs and different from those occurring during healthy aging and Werner syndrome (WS), another premature aging disease. Moreover, HGPS patients can be stratified into two different subgroups according to their DNA methylation profiles. Finally, we show that the epigenetic deregulation of LADs is associated with HGPS-specific gene expression changes. CONCLUSIONS Taken together, our results strongly implicate epigenetic deregulation of LADs as an important and previously unrecognized feature of HGPS, which contributes to disease-specific gene expression. Therefore, they not only add a new layer to the study of epigenetic changes in the progeroid syndrome, but also advance our understanding of the disease's pathology at the cellular level.
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Affiliation(s)
- Florian Köhler
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Felix Bormann
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Samuel Corless
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
- DKFZ-ZMBH-Alliance, 69120, Heidelberg, Germany
- CellNetworks Excellence Cluster, Heidelberg University, 69120, Heidelberg, Germany
| | - Tanja Musch
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Anke S Lonsdorf
- Department of Dermatology, University Hospital, Ruprecht-Karls University of Heidelberg, Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
- DKFZ-ZMBH-Alliance, 69120, Heidelberg, Germany
- CellNetworks Excellence Cluster, Heidelberg University, 69120, Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
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76
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Braga DL, Mousovich-Neto F, Tonon-da-Silva G, Salgueiro WG, Mori MA. Epigenetic changes during ageing and their underlying mechanisms. Biogerontology 2020; 21:423-443. [PMID: 32356238 DOI: 10.1007/s10522-020-09874-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022]
Abstract
As life expectancy increases worldwide, ageing and age-related diseases arise as a major issue for societies around the globe. Understanding the biological mechanisms underlying the ageing process is thus instrumental for the development of efficient interventions aimed to prevent and treat age-related conditions. Current knowledge in the biogerontology field points to epigenetics as a critical component of the ageing process, not only by serving as a bona-fide marker of biological age but also by controlling and conferring inheritability to cellular and organismal ageing. This is reflected by a myriad of evidences demonstrating the relationship between DNA methylation, histone modifications, chromatin remodeling and small non-coding RNAs and several age-related phenotypes. Given the reversibility of epigenetic alterations, epigenetic reprogramming may also be envisioned as a potential approach to treat age-related disorders. Here we review how different types of epigenetic mechanisms are involved in the ageing process. In addition, we highlight how interventions modulate epigenetics and thus promote health- and lifespan.
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Affiliation(s)
- Deisi L Braga
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Felippe Mousovich-Neto
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
| | - Guilherme Tonon-da-Silva
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Willian G Salgueiro
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil.
- Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, São Paulo, 13083-862, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, São Paulo, 13083-862, Brazil.
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77
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Newman JA, Aitkenhead H, Gavard AE, Rota IA, Handel AE, Hollander GA, Gileadi O. The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity. J Biol Chem 2020; 295:2948-2958. [PMID: 31914405 PMCID: PMC7062188 DOI: 10.1074/jbc.ra119.010365] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
Forkhead box N1 (FOXN1) is a member of the forkhead box family of transcription factors and plays an important role in thymic epithelial cell differentiation and development. FOXN1 mutations in humans and mice give rise to the "nude" phenotype, which is marked by athymia. FOXN1 belongs to a subset of the FOX family that recognizes an alternative forkhead-like (FHL) consensus sequence (GACGC) that is different from the more widely recognized forkhead (FKH) sequence RYAAAYA (where R is purine, and Y is pyrimidine). Here, we present the FOXN1 structure in complex with DNA containing an FHL motif at 1.6 Å resolution, in which the DNA sequence is recognized by a mixture of direct and water-mediated contacts provided by residues in an α-helix inserted in the DNA major groove (the recognition helix). Comparisons with the structure of other FOX family members revealed that the FKH and FHL DNA sequences are bound in two distinct modes, with partially different registers for the protein DNA contacts. We identified a single alternative rotamer within the recognition helix itself as an important determinant of DNA specificity and found protein sequence features in the recognition helix that could be used to predict the specificity of other FOX family members. Finally, we demonstrate that the C-terminal region of FOXN1 is required for high-affinity DNA binding and that FOXN1 has a significantly reduced affinity for DNA that contains 5'-methylcytosine, which may have implications for the role of FOXN1 in thymic involution.
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Affiliation(s)
- Joseph A Newman
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Hazel Aitkenhead
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Angeline E Gavard
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ioanna A Rota
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Adam E Handel
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Georg A Hollander
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom; Paediatric Immunology, Department of Biomedicine, University of Basel and University Children's Hospital Basel, 4056 Basel, Switzerland
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.
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78
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Inter-laboratory adaption of age estimation models by DNA methylation analysis—problems and solutions. Int J Legal Med 2020; 134:953-961. [DOI: 10.1007/s00414-020-02263-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/31/2020] [Indexed: 12/24/2022]
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79
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Zhao X, Fan Y, Vann PH, Wong JM, Sumien N, He JJ. Long-term HIV-1 Tat Expression in the Brain Led to Neurobehavioral, Pathological, and Epigenetic Changes Reminiscent of Accelerated Aging. Aging Dis 2020; 11:93-107. [PMID: 32010484 PMCID: PMC6961778 DOI: 10.14336/ad.2019.0323] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/23/2019] [Indexed: 12/19/2022] Open
Abstract
HIV infects the central nervous system and causes HIV/neuroAIDS, which is predominantly manifested in the form of mild cognitive and motor disorder in the era of combination antiretroviral therapy. HIV Tat protein is known to be a major pathogenic factor for HIV/neuroAIDS through a myriad of direct and indirect mechanisms. However, most, if not all of studies involve short-time exposure of recombinant Tat protein in vitro or short-term Tat expression in vivo. In this study, we took advantage of the doxycycline-inducible brain-specific HIV-1 Tat transgenic mouse model, fed the animals for 12 months, and assessed behavioral, pathological, and epigenetic changes in these mice. Long-term Tat expression led to poorer short-and long-term memory, lower locomotor activity and impaired coordination and balance ability, increased astrocyte activation and compromised neuronal integrity, and decreased global genomic DNA methylation. There were sex- and brain region-dependent differences in behaviors, pathologies, and epigenetic changes resulting from long-term Tat expression. All these changes are reminiscent of accelerated aging, raising the possibility that HIV Tat contributes, at least in part, to HIV infection-associated accelerated aging in HIV-infected individuals. These findings also suggest another utility of this model for HIV infection-associated accelerated aging studies.
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Affiliation(s)
- Xiaojie Zhao
- 1Department of Microbiology, Immunology & Genetics and
| | - Yan Fan
- 2Department of Pharmacology & Neuroscience, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Philip H Vann
- 2Department of Pharmacology & Neuroscience, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Jessica M Wong
- 2Department of Pharmacology & Neuroscience, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Nathalie Sumien
- 2Department of Pharmacology & Neuroscience, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas 76107, USA
| | - Johnny J He
- 1Department of Microbiology, Immunology & Genetics and
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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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81
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El Khoury LY, Gorrie-Stone T, Smart M, Hughes A, Bao Y, Andrayas A, Burrage J, Hannon E, Kumari M, Mill J, Schalkwyk LC. Systematic underestimation of the epigenetic clock and age acceleration in older subjects. Genome Biol 2019; 20:283. [PMID: 31847916 PMCID: PMC6915902 DOI: 10.1186/s13059-019-1810-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/03/2019] [Indexed: 11/18/2022] Open
Abstract
Background The Horvath epigenetic clock is widely used. It predicts age quite well from 353 CpG sites in the DNA methylation profile in unknown samples and has been used to calculate “age acceleration” in various tissues and environments. Results The model systematically underestimates age in tissues from older people. This is seen in all examined tissues but most strongly in the cerebellum and is consistently observed in multiple datasets. Age acceleration is thus age-dependent, and this can lead to spurious associations. The current literature includes examples of association tests with age acceleration calculated in a wide variety of ways. Conclusions The concept of an epigenetic clock is compelling, but caution should be taken in interpreting associations with age acceleration. Association tests of age acceleration should include age as a covariate.
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Affiliation(s)
- Louis Y El Khoury
- School of Life Sciences, University of Essex, Colchester, UK.,Present Address: Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | - Melissa Smart
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - Amanda Hughes
- MRC Integrative Epidemiology Unit - University of Bristol, Bristol, UK
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | - Joe Burrage
- Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- Medical School, University of Exeter, Exeter, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
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Effect of imbalance in folate and vitamin B12 in maternal/parental diet on global methylation and regulatory miRNAs. Sci Rep 2019; 9:17602. [PMID: 31772242 PMCID: PMC6879517 DOI: 10.1038/s41598-019-54070-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/08/2019] [Indexed: 12/24/2022] Open
Abstract
DNA methylation, a central component of the epigenetic network is altered in response to nutritional influences. In one-carbon cycle, folate acts as a one-carbon carrier and vitamin B12 acts as co-factor for the enzyme methionine synthase. Both folate and vitamin B12 are the important regulators of DNA methylation which play an important role in development in early life. Previous studies carried out in this regard have shown the individual effects of these vitamins but recently the focus has been to study the combined effects of both the vitamins during pregnancy. Therefore, this study was planned to elucidate the effect of the altered dietary ratio of folate and B12 on the expression of transporters, related miRNAs and DNA methylation in C57BL/6 mice. Female mice were fed diets with 9 combinations of folate and B12 for 4 weeks. They were mated and off-springs born (F1) were continued on the same diet for 6 weeks post-weaning. Maternal and fetal (F2) tissues were collected at day 20 of gestation. Deficient state of folate led to an increase in the expression of folate transporters in both F1 and F2 generations, however, B12 deficiency (BDFN) also led to an increase in the expression in both the generations. B12 transporters/proteins were found to be increased with B12 deficiency in F1 and F2 generations except for TC-II in the kidney which was found to be decreased in the F1 generation. miR-483 was found to be increased with all conditions of folate and B12 in both F1 and F2 generations, however, deficient conditions of B12 led to an increase in the expression of miR-221 in both F1 and F2 generations. The level of miR-133 was found to be increased in BDFN group in F1 generation however; in F2 generation the change in expression was tissue and sex-specific. Global DNA methylation was decreased with deficiency of both folate and B12 in maternal tissues (F1) but increased with folate deficiency in placenta (F1) and under all conditions in fetal tissues (F2). DNA methyltransferases were overall found to be increased with deficiency of folate and B12 in both F1 and F2 generations. Results suggest that the dietary ratio of folate and B12 resulted in altered expression of transporters, miRNAs, and genomic DNA methylation in association with DNMTs.
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83
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The Metabolic Interplay between Cancer and Other Diseases. Trends Cancer 2019; 5:809-821. [PMID: 31813458 DOI: 10.1016/j.trecan.2019.10.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 02/06/2023]
Abstract
Over the past decade, knowledge of cancer metabolism has expanded exponentially and has provided several clinically relevant targets for cancer therapy. Although these current approaches have shown promise, there are very few studies showing how seemingly unrelated metabolic processes in other diseases can readily occur in cancer. Moreover, the striking metabolic overlap between cancer and other diseases such as diabetes, cardiovascular, neurological, obesity, and aging has provided key therapeutic strategies that have even begun to be translated into clinical trials. These promising results necessitate consideration of the interconnected metabolic network while studying the metabolism of cancer. This review article discusses how cancer metabolism is intertwined with systemic metabolism and how knowledge from other diseases can help to broaden therapeutic opportunities for cancer.
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84
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Jansen RJ, Tong L, Argos M, Jasmine F, Rakibuz-Zaman M, Sarwar G, Islam MT, Shahriar H, Islam T, Rahman M, Yunus M, Kibriya MG, Baron JA, Ahsan H, Pierce BL. The effect of age on DNA methylation in whole blood among Bangladeshi men and women. BMC Genomics 2019; 20:704. [PMID: 31506065 PMCID: PMC6734473 DOI: 10.1186/s12864-019-6039-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/16/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND It is well-known that methylation changes occur as humans age, however, understanding how age-related changes in DNA methylation vary by sex is lacking. In this study, we characterize the effect of age on DNA methylation in a sex-specific manner and determine if these effects vary by genomic context. We used the Illumina HumanMethylation 450 K array and DNA derived from whole blood for 400 adult participants (189 males and 211 females) from Bangladesh to identify age-associated CpG sites and regions and characterize the location of these age-associated sites with respect to CpG islands (vs. shore, shelf, or open sea) and gene regions (vs. intergenic). We conducted a genome-wide search for age-associated CpG sites (among 423,604 sites) using a reference-free approach to adjust for cell type composition (the R package RefFreeEWAS) and performed an independent replication analysis of age-associated CpGs. RESULTS The number of age-associated CpGs (p < 5 x 10- 8) were 986 among men and 3479 among women of which 2027(63.8%) and 572 (64.1%) replicated (using Bonferroni adjusted p < 1.2 × 10- 5). For both sexes, age-associated CpG sites were more likely to be hyper-methylated with increasing age (compared to hypo-methylated) and were enriched in CpG islands and promoter regions compared with other locations and all CpGs on the array. Although we observed strong correlation between chronological age and previously-developed epigenetic age models (r ≈ 0.8), among our top (based on lowest p-value) age-associated CpG sites only 12 for males and 44 for females are included in these prediction models, and the median chronological age compared to predicted age was 44 vs. 51.7 in males and 45 vs. 52.1 in females. CONCLUSIONS Our results describe genome-wide features of age-related changes in DNA methylation. The observed associations between age and methylation were generally consistent for both sexes, although the associations tended to be stronger among women. Our population may have unique age-related methylation changes that are not captured in the established methylation-based age prediction model we used, which was developed to be non-tissue-specific.
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Affiliation(s)
- Rick J Jansen
- Department of Public Health, North Dakota State University, Fargo, ND, USA
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
- Biostatistics Core Facility, North Dakota State University, Fargo, ND, USA
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA
| | - Maria Argos
- Divison of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA
| | | | - Golam Sarwar
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
| | | | - Hasan Shahriar
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
| | - Tariqul Islam
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
| | - Mahfuzar Rahman
- UChicago Research Bangladesh Mohakhali, Dhaka, 1230, Bangladesh
- Research and Evaluation Division BRAC, Mohakhali, Dhaka, 1212, Bangladesh
| | - Md Yunus
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, 1000, Bangladesh
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA
| | - John A Baron
- Department of Epidemiology, Gillings School of Global Public Health, University of North Caroline, Chapel Hill, NC, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA.
- Department of Medicine, The University of Chicago, Chicago, IL, USA.
- Department of Human Genetics and Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA.
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Ave., W264, MC2000, Chicago, IL, 60637, USA.
- Department of Human Genetics and Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA.
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85
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Bosticardo M, Yamazaki Y, Cowan J, Giardino G, Corsino C, Scalia G, Prencipe R, Ruffner M, Hill DA, Sakovich I, Yemialyanava I, Tam JS, Padem N, Elder ME, Sleasman JW, Perez E, Niebur H, Seroogy CM, Sharapova S, Gebbia J, Kleiner GI, Peake J, Abbott JK, Gelfand EW, Crestani E, Biggs C, Butte MJ, Hartog N, Hayward A, Chen K, Heimall J, Seeborg F, Bartnikas LM, Cooper MA, Pignata C, Bhandoola A, Notarangelo LD. Heterozygous FOXN1 Variants Cause Low TRECs and Severe T Cell Lymphopenia, Revealing a Crucial Role of FOXN1 in Supporting Early Thymopoiesis. Am J Hum Genet 2019; 105:549-561. [PMID: 31447097 PMCID: PMC6731368 DOI: 10.1016/j.ajhg.2019.07.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022] Open
Abstract
FOXN1 is the master regulatory gene of thymic epithelium development. FOXN1 deficiency leads to thymic aplasia, alopecia, and nail dystrophy, accounting for the nude/severe combined immunodeficiency (nu/SCID) phenotype in humans and mice. We identified several newborns with low levels of T cell receptor excision circles (TRECs) and T cell lymphopenia at birth, who carried heterozygous loss-of-function FOXN1 variants. Longitudinal analysis showed persistent T cell lymphopenia during infancy, often associated with nail dystrophy. Adult individuals with heterozygous FOXN1 variants had in most cases normal CD4+ but lower than normal CD8+ cell counts. We hypothesized a FOXN1 gene dosage effect on the function of thymic epithelial cells (TECs) and thymopoiesis and postulated that these effects would be more prominent early in life. To test this hypothesis, we analyzed TEC subset frequency and phenotype, early thymic progenitor (ETP) cell count, and expression of FOXN1 target genes (Ccl25, Cxcl12, Dll4, Scf, Psmb11, Prss16, and Cd83) in Foxn1nu/+ (nu/+) mice and age-matched wild-type (+/+) littermate controls. Both the frequency and the absolute count of ETP were significantly reduced in nu/+ mice up to 3 weeks of age. Analysis of the TEC compartment showed reduced expression of FOXN1 target genes and delayed maturation of the medullary TEC compartment in nu/+ mice. These observations establish a FOXN1 gene dosage effect on thymic function and identify FOXN1 haploinsufficiency as an important genetic determinant of T cell lymphopenia at birth.
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Affiliation(s)
- Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD 20892, USA
| | - Yasuhiro Yamazaki
- Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD 20892, USA
| | - Jennifer Cowan
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Giuliana Giardino
- Department of Translational Medical Sciences Federico II University, Naples 80138, Italy
| | - Cristina Corsino
- Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD 20892, USA
| | - Giulia Scalia
- Laboratory of Clinical research and Advanced Diagnostics, CEINGE Biotecnologie Avanzate, Naples 80131, Italy
| | - Rosaria Prencipe
- Department of Translational Medical Sciences Federico II University, Naples 80138, Italy
| | - Melanie Ruffner
- Division of Allergy and Immunology, Department of Pediatrics, Children's Hospital Philadelphia, Philadelphia, PA 19104, USA
| | - David A Hill
- Division of Allergy and Immunology, Department of Pediatrics, Children's Hospital Philadelphia, Philadelphia, PA 19104, USA
| | - Inga Sakovich
- Immunology Lab, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk 223053, Belarus
| | - Irma Yemialyanava
- Immunology Lab, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk 223053, Belarus
| | - Jonathan S Tam
- Division of Clinical Immunology and Allergy, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Nurcicek Padem
- Division of Allergy and Immunology, Lurie Children's Hospital, Chicago, IL 60611, USA
| | - Melissa E Elder
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - John W Sleasman
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27705, USA
| | - Elena Perez
- Allergy Associates of the Palm Beaches, North Palm Beach, FL 33408, USA
| | - Hana Niebur
- Division of Pediatric Allergy and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Christine M Seroogy
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Svetlana Sharapova
- Immunology Lab, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk 223053, Belarus
| | - Jennifer Gebbia
- Department of Pediatric Allergy and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Gary Ira Kleiner
- Department of Pediatric Allergy and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jane Peake
- Division of Paediatric Immunology and Allergy, Lady Cilento Children's Hospital, University of Queensland School of Medicine, South Brisbane, QLD 4101, Australia
| | - Jordan K Abbott
- Immunodeficiency Diagnosis and Treatment Program, Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Erwin W Gelfand
- Immunodeficiency Diagnosis and Treatment Program, Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA
| | - Elena Crestani
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Catherine Biggs
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, British Columbia Children's Hospital, University of British Columbia, Vancouver, BC V6H 0B3, Canada
| | - Manish J Butte
- Division of Allergy, Immunology and Rheumatology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Nicholas Hartog
- Spectrum Health Allergy and Immunology, Grand Rapids, MI 49525, USA
| | - Anthony Hayward
- Division of Allergy and Immunology, Department of Pediatrics, Brown University and Rhode Island Hospital, Providence, RI 02905, USA
| | - Karin Chen
- Division of Allergy and Immunology, Department of Pediatrics, University of Utah, Salt Lake City, UT 84112, USA
| | - Jennifer Heimall
- Division of Allergy and Immunology, Department of Pediatrics, Children's Hospital Philadelphia, Philadelphia, PA 19104, USA
| | - Filiz Seeborg
- Section of Allergy, Immunology and Rheumatology & Center for Human Immunobiology, Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA
| | - Lisa M Bartnikas
- Division of Immunology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Megan A Cooper
- Department of Pediatrics, Division of Rheumatology, Washington University in St. Louis, MO 63110, USA
| | - Claudio Pignata
- Department of Translational Medical Sciences Federico II University, Naples 80138, Italy
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, IDGS, DIR, NIAID, NIH, Bethesda, MD 20892, USA.
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87
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Köhler F, Rodríguez-Paredes M. DNA Methylation in Epidermal Differentiation, Aging, and Cancer. J Invest Dermatol 2019; 140:38-47. [PMID: 31427190 DOI: 10.1016/j.jid.2019.05.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/24/2019] [Accepted: 05/17/2019] [Indexed: 12/22/2022]
Abstract
The formation and maintenance of the epidermis depend on epidermal stem cell differentiation and must be tightly regulated. Epigenetic mechanisms such as DNA methylation allow the precise gene expression cascade needed during cellular differentiation. However, these mechanisms become deregulated during aging and tumorigenesis, where cellular function and identity become compromised. Here we provide a review of this rapidly developing field. We discuss recent discoveries related to epidermal homeostasis, aging, and cancer, including the functional role of DNA methyltransferases, the methylation clock, and the determination of tumor cells-of-origin. Finally, we focus on future advances, greatly influenced by single-cell sequencing technologies.
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Affiliation(s)
- Florian Köhler
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
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88
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Writers and Readers of DNA Methylation/Hydroxymethylation in Physiological Aging and Its Impact on Cognitive Function. Neural Plast 2019; 2019:5982625. [PMID: 31396272 PMCID: PMC6664507 DOI: 10.1155/2019/5982625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/25/2019] [Accepted: 05/26/2019] [Indexed: 12/31/2022] Open
Abstract
The chromatin landscape has acquired deep attention from several fields ranging from cell biology to neurological and psychiatric diseases. The role that DNA modifications have on gene expression regulation has become apparent in several physiological processes, and numerous efforts have been performed to establish a relationship between DNA modifications and physiological conditions, such as cognitive performance and aging. DNA modifications are incorporated by specific sets of enzymes-the writers-and the modified DNA-interacting partners-the readers-are ultimately responsible for maintaining a functional epigenetic landscape. Therefore, understanding how these epigenetic mediators-writers and readers-are modulated in physiological aging will contribute to unraveling how aging-associated neuronal disturbances arise and contribute to the cognitive decline associated with this period of life. In this review, we focused on DNA modifications, writers and readers, highlighting that despite some methodological disparities, the evidence suggests a critical role for epigenetic mediators in the aging-associated neuronal dysfunction.
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89
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Terao H, Wada‐Hiraike O, Nagumo A, Kunitomi C, Azhary JMK, Harada M, Hirata T, Hirota Y, Koga K, Fujii T, Osuga Y. Role of oxidative stress in follicular fluid on embryos of patients undergoing assisted reproductive technology treatment. J Obstet Gynaecol Res 2019; 45:1884-1891. [DOI: 10.1111/jog.14040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 05/29/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Hiromi Terao
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Osamu Wada‐Hiraike
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Aiko Nagumo
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Chisato Kunitomi
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Jerilee M. K. Azhary
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Miyuki Harada
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Tetsuya Hirata
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Yasushi Hirota
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Kaori Koga
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Tomoyuki Fujii
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, Graduate School of MedicineThe University of Tokyo Tokyo Japan
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90
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Methylation Marks of Blood Leukocytes of Native Hucul Mares Differentiated in Age. Int J Genomics 2019; 2019:2839614. [PMID: 31281827 PMCID: PMC6589255 DOI: 10.1155/2019/2839614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/16/2019] [Indexed: 11/17/2022] Open
Abstract
Horses are one of the longest-living species of farm animals. Advanced age is often associated with a decrease in body condition, dysfunction of immune system, and late-onset disorders. Due to this, the search for new solutions in the prevention and treatment of pathological conditions of the advanced age of horses is desirable. That is why the identification of aging-related changes in the horse genome is interesting in this respect. In the recent years, the research on aging includes studies of age-related epigenetic effects observed on the DNA methylation level. We applied reduced representation bisulfite sequencing (RRBS) to uncover a range of age DMR sites in genomes of blood leukocytes derived from juvenile and aged horses of native Hucul breed. Genes colocated with age-related differentially methylated regions (age DMRs) are the members of pathways involved in cellular signal transduction, immune response, neurogenesis, differentiation, development, and cancer progression. A positive correlation was found between methylation states and gene expression in particular loci from our data set. Some of described age DMR-linked genes were also reported elsewhere. Obtained results contribute to the knowledge about the molecular basis of aging of equine blood cells.
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91
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Csiszar A, Balasubramanian P, Tarantini S, Yabluchanskiy A, Zhang XA, Springo Z, Benbrook D, Sonntag WE, Ungvari Z. Chemically induced carcinogenesis in rodent models of aging: assessing organismal resilience to genotoxic stressors in geroscience research. GeroScience 2019; 41:209-227. [PMID: 31037472 DOI: 10.1007/s11357-019-00064-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/04/2019] [Indexed: 02/07/2023] Open
Abstract
There is significant overlap between the cellular and molecular mechanisms of aging and pathways contributing to carcinogenesis, including the role of genome maintenance pathways. In the field of geroscience analysis of novel genetic mouse models with either a shortened, or an extended, lifespan provides a unique opportunity to evaluate the synergistic roles of longevity assurance pathways in cancer resistance and regulation of lifespan and to develop novel targets for interventions that both delay aging and prevent carcinogenesis. There is a growing need for robust assays to assess the susceptibility of cancer in these models. The present review focuses on a well-characterized method frequently used in cancer research, which can be adapted to study resilience to genotoxic stress and susceptibility to genotoxic stress-induced carcinogenesis in geroscience research namely, chemical carcinogenesis induced by treatment with 7,12-dimethylbenz(a)anthracene (DMBA). Recent progress in understanding how longer-living mice may achieve resistance to chemical carcinogenesis and how these pathways are modulated by anti-aging interventions is reviewed. Strain-specific differences in sensitivity to DMBA-induced carcinogenesis are also explored and contrasted with mouse lifespan. The clinical relevance of inhibition of DMBA-induced carcinogenesis for the pathogenesis of mammary adenocarcinomas in older human subjects is discussed. Finally, the potential role of insulin-like growth factor-1 (IGF-1) in the regulation of pathways responsible for cellular resilience to DMBA-induced mutagenesis is discussed.
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Affiliation(s)
- Anna Csiszar
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Priya Balasubramanian
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA
| | - Stefano Tarantini
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA
| | - Andriy Yabluchanskiy
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Xin A Zhang
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Zsolt Springo
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA.,Theoretical Medicine Doctoral School, University of Szeged, Szeged, Hungary
| | - Doris Benbrook
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - William E Sonntag
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA.,Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Zoltan Ungvari
- Department of Geriatric Medicine Vascular Cognitive Impairment and Neurodegeneration Program, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, 975 NE 10th Street, BRC 1311, Oklahoma City, OK, 73104, USA. .,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Theoretical Medicine Doctoral School, University of Szeged, Szeged, Hungary. .,Department of Medical Physics and Informatics, University of Szeged, Szeged, Hungary. .,Department of Public Health, Semmelweis University, Budapest, Hungary.
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92
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The Impact of Caloric Restriction on the Epigenetic Signatures of Aging. Int J Mol Sci 2019; 20:ijms20082022. [PMID: 31022953 PMCID: PMC6515465 DOI: 10.3390/ijms20082022] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
Aging is characterized by an extensive remodeling of epigenetic patterns, which has been implicated in the physiopathology of age-related diseases. Nutrition plays a significant role in modulating the epigenome, and a growing amount of data indicate that dietary changes can modify the epigenetic marks associated with aging. In this review, we will assess the current advances in the relationship between caloric restriction, a proven anti-aging intervention, and epigenetic signatures of aging. We will specifically discuss the impact of caloric restriction on epigenetic regulation and how some of the favorable effects of caloric restriction on lifespan and healthspan could be mediated by epigenetic modifications.
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93
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Chronic Chlamydia infection in human organoids increases stemness and promotes age-dependent CpG methylation. Nat Commun 2019; 10:1194. [PMID: 30886143 PMCID: PMC6423033 DOI: 10.1038/s41467-019-09144-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/22/2019] [Indexed: 01/12/2023] Open
Abstract
Chronic infections of the fallopian tubes with Chlamydia trachomatis (Ctr) cause scarring and can lead to infertility. Here we use human fallopian tube organoids and genital Ctr serovars D, K and E for long-term in vitro analysis. The epithelial monolayer responds with active expulsion of the bacteria into the lumen and with compensatory cellular proliferation—demonstrating a role of epithelial homeostasis in the defense against this pathogen. In addition, Ctr infection activates LIF signaling, which we find to be an essential regulator of stemness in the organoids. Infected organoids exhibit a less differentiated phenotype with higher stemness potential, as confirmed by increased organoid forming efficiency. Moreover, Ctr increases hypermethylation of DNA, which is an indicator of accelerated molecular aging. Thus, the chronic organoid infection model suggests that Ctr has a long-term impact on the epithelium. These heritable changes might be a contributing factor in the development of tubal pathologies, including the initiation of high grade serous ovarian cancer. Chronic infections of the fallopian tubes with Chlamydia trachomatis can cause scarring and infertility. Here, the authors show that the pathogen alters stem cell differentiation and DNA methylation in human fallopian tube organoids, suggesting a potential link to cellular ageing and malignant transformation.
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94
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Lu S, Xu F, Hu W, Niu Z, Cai H, Chen Y, Tu Q, Zhang Y, Chen W, Liu W, Tang S, Zhang Z. SCD1 methylation in subcutaneous adipose tissue associated with menopausal age. Climacteric 2019; 22:395-402. [PMID: 30777456 DOI: 10.1080/13697137.2019.1571028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- S. Lu
- Department of Obstetrics and Gynecology, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - F. Xu
- Department of Gastroenterology, Hangzhou Third People's Hospital, Hangzhou, China
| | - W. Hu
- Department of Obstetrics and Gynecology, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Z. Niu
- Department of Obstetrics and Gynecology, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, China
| | - H. Cai
- Department of Obstetrics and Gynecology, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, China
| | - Y. Chen
- Laboratory of Gene Diagnosis, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, China
| | - Q. Tu
- Laboratory of Gene Diagnosis, The Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou, China
| | - Y. Zhang
- Department of Obstetrics and Gynecology, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - W. Chen
- Department of Obstetrics and Gynecology, The Second People's Hospital of Tonglu, Hangzhou, China
| | - W. Liu
- Department of Obstetrics and Gynecology, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - S. Tang
- Department of Obstetrics and Gynecology, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Z. Zhang
- Department of Obstetrics and Gynecology, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
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95
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Kane AE, Sinclair DA. Epigenetic changes during aging and their reprogramming potential. Crit Rev Biochem Mol Biol 2019; 54:61-83. [PMID: 30822165 PMCID: PMC6424622 DOI: 10.1080/10409238.2019.1570075] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 02/07/2023]
Abstract
The aging process results in significant epigenetic changes at all levels of chromatin and DNA organization. These include reduced global heterochromatin, nucleosome remodeling and loss, changes in histone marks, global DNA hypomethylation with CpG island hypermethylation, and the relocalization of chromatin modifying factors. Exactly how and why these changes occur is not fully understood, but evidence that these epigenetic changes affect longevity and may cause aging, is growing. Excitingly, new studies show that age-related epigenetic changes can be reversed with interventions such as cyclic expression of the Yamanaka reprogramming factors. This review presents a summary of epigenetic changes that occur in aging, highlights studies indicating that epigenetic changes may contribute to the aging process and outlines the current state of research into interventions to reprogram age-related epigenetic changes.
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Affiliation(s)
- Alice E. Kane
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - David A. Sinclair
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pharmacology, The University of New South Wales, Sydney, Australia
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96
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Aliaga B, Bulla I, Mouahid G, Duval D, Grunau C. Universality of the DNA methylation codes in Eucaryotes. Sci Rep 2019; 9:173. [PMID: 30655579 PMCID: PMC6336885 DOI: 10.1038/s41598-018-37407-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 10/24/2018] [Indexed: 12/26/2022] Open
Abstract
Genetics and epigenetics are tightly linked heritable information classes. Question arises if epigenetics provides just a set of environment dependent instructions, or whether it is integral part of an inheritance system. We argued that in the latter case the epigenetic code should share the universality quality of the genetic code. We focused on DNA methylation. Since availability of DNA methylation data is biased towards model organisms we developed a method that uses kernel density estimations of CpG observed/expected ratios to infer DNA methylation types in any genome. We show here that our method allows for robust prediction of mosaic and full gene body methylation with a PPV of 1 and 0.87, respectively. We used this prediction to complement experimental data, and applied hierarchical clustering to identify methylation types in ~150 eucaryotic species covering different body plans, reproduction types and living conditions. Our analysis indicates that there are only four gene body methylation types. These types do not follow phylogeny (i.e. phylogenetically distant clades can have identical methylation types) but they are consistent within clades. We conclude that the gene body DNA methylation codes have universality similar to the universality of the genetic code and should consequently be considered as part of the inheritance system.
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Affiliation(s)
- Benoît Aliaga
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
| | - Ingo Bulla
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
- Institute for Mathematics and Informatics, University of Greifswald, Greifswald, Germany
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Gabriel Mouahid
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
| | - David Duval
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
| | - Christoph Grunau
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France.
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97
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Rustad SR, Papale LA, Alisch RS. DNA Methylation and Hydroxymethylation and Behavior. Curr Top Behav Neurosci 2019; 42:51-82. [PMID: 31392630 DOI: 10.1007/7854_2019_104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Environmentally sensitive molecular mechanisms in the brain, such as DNA methylation, have become a significant focus of neuroscience research because of mounting evidence indicating that they are critical in response to social situations, stress, threats, and behavior. The recent identification of 5-hydroxymethylcytosine (5hmC), which is enriched in the brain (tenfold over peripheral tissues), raises new questions as to the role of this base in mediating epigenetic effects in the brain. The development of genome-wide methods capable of distinguishing 5-methylcytosine (5mC) from 5hmC has revealed that a growing number of behaviors are linked to independent disruptions of 5mC and 5hmC levels, further emphasizing the unique importance of both of these modifications in the brain. Here, we review the recent links that indicate DNA methylation (both 5mC and 5hmC) is highly dynamic and that perturbations in this modification may contribute to behaviors related to psychiatric disorders and hold clinical relevance.
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Affiliation(s)
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA. .,Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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98
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Liou CJ, Tong M, Vonsattel JP, de la Monte SM. Altered Brain Expression of Insulin and Insulin-Like Growth Factors in Frontotemporal Lobar Degeneration: Another Degenerative Disease Linked to Dysregulation of Insulin Metabolic Pathways. ASN Neuro 2019; 11:1759091419839515. [PMID: 31081340 PMCID: PMC6535914 DOI: 10.1177/1759091419839515] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/21/2019] [Accepted: 02/06/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Frontotemporal lobar degeneration (FTLD) is the third most common dementing neurodegenerative disease with nearly 80% having no known etiology. OBJECTIVE Growing evidence that neurodegeneration can be linked to dysregulated metabolism prompted us to measure a panel of trophic factors, receptors, and molecules that modulate brain metabolic function in FTLD. METHODS Postmortem frontal (Brodmann's area [BA]8/9 and BA24) and temporal (BA38) lobe homogenates were used to measure immunoreactivity to Tau, phosphorylated tau (pTau), ubiquitin, 4-hydroxynonenal (HNE), transforming growth factor-beta 1 (TGF-β1) and its receptor (TGF-β1R), brain-derived neurotrophic factor (BDNF), nerve growth factor, neurotrophin-3, neurotrophin-4, tropomyosin receptor kinase, and insulin and insulin-like growth factor-1 (IGF-1) and insulin-like growth factor-2 (IGF-2) and their receptors by direct-binding enzyme-linked immunosorbent assay. RESULTS FTLD brains had significantly elevated pTau, ubiquitin, TGF-β1, and HNE immunoreactivity relative to control. In addition, BDNF and neurotrophin-4 were respectively reduced in BA8/9 and BA38, while neurotrophin-3 and nerve growth factor were upregulated in BA38, and tropomyosin receptor kinase was elevated in BA24. Lastly, insulin and insulin receptor expressions were elevated in the frontal lobe, IGF-1 was increased in BA24, IGF-1R was upregulated in all three brain regions, and IGF-2 receptor was reduced in BA24 and BA38. CONCLUSIONS Aberrantly increased levels of pTau, ubiquitin, HNE, and TGF-β1, marking neurodegeneration, oxidative stress, and neuroinflammation, overlap with altered expression of insulin/IGF signaling ligand and receptors in frontal and temporal lobe regions targeted by FTLD. Dysregulation of insulin-IGF signaling networks could account for brain hypometabolism and several characteristic neuropathologic features that characterize FTLD but overlap with Alzheimer's disease, Parkinson's disease, and Dementia with Lewy Body Disease.
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Affiliation(s)
- Connie J. Liou
- Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Ming Tong
- Warren Alpert Medical School of Brown University, Providence, RI, USA
- Division of Neuropathology, Departments of Pathology, Medicine, Neurology, and Neurosurgery, Rhode Island Hospital, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, the Providence VA Medical Center, Providence, RI, USA
| | - Jean P. Vonsattel
- New York Brain Bank, Taub Institute, Columbia University, New York, NY, USA
| | - Suzanne M. de la Monte
- Warren Alpert Medical School of Brown University, Providence, RI, USA
- Division of Neuropathology, Departments of Pathology, Medicine, Neurology, and Neurosurgery, Rhode Island Hospital, Providence, RI, USA
- Department of Pathology and Laboratory Medicine, the Providence VA Medical Center, Providence, RI, USA
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Epigenetic Regulation of Skin Cells in Natural Aging and Premature Aging Diseases. Cells 2018; 7:cells7120268. [PMID: 30545089 PMCID: PMC6315602 DOI: 10.3390/cells7120268] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 02/06/2023] Open
Abstract
Skin undergoes continuous renewal throughout an individual’s lifetime relying on stem cell functionality. However, a decline of the skin regenerative potential occurs with age. The accumulation of senescent cells over time probably reduces tissue regeneration and contributes to skin aging. Keratinocytes and dermal fibroblasts undergo senescence in response to several intrinsic or extrinsic stresses, including telomere shortening, overproduction of reactive oxygen species, diet, and sunlight exposure. Epigenetic mechanisms directly regulate skin homeostasis and regeneration, but they also mark cell senescence and the natural and pathological aging processes. Progeroid syndromes represent a group of clinical and genetically heterogeneous pathologies characterized by the accelerated aging of various tissues and organs, including skin. Skin cells from progeroid patients display molecular hallmarks that mimic those associated with naturally occurring aging. Thus, investigations on progeroid syndromes strongly contribute to disclose the causal mechanisms that underlie the aging process. In the present review, we discuss the role of epigenetic pathways in skin cell regulation during physiologic and premature aging.
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Nevalainen T, Autio A, Mishra BH, Marttila S, Jylhä M, Hurme M. Aging-associated patterns in the expression of human endogenous retroviruses. PLoS One 2018; 13:e0207407. [PMID: 30513106 PMCID: PMC6279030 DOI: 10.1371/journal.pone.0207407] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/30/2018] [Indexed: 11/18/2022] Open
Abstract
Human endogenous retroviruses (HERV) are relics of ancient retroviral infections in our genome. Most of them have lost their coding capacity, but proviral RNA or protein have been observed in several disease states (e.g. in inflammatory and autoimmune diseases and malignancies). However, their clinical significance as well as their mechanisms of action have still remained elusive. As human aging is associated with several biological characteristics of these diseases, we now analyzed the aging-associated expression of the individual proviruses of two HERV families, HERV-K (91 proviruses) and HERV-W (213 proviruses) using genome-wide RNA-sequencing (RNA-seq). RNA was purified from blood cells derived from healthy young individuals (n = 7) and from nonagenarians (n = 7). The data indicated that in the case of HERV-K (HML-2) 33 proviruses had a detectable expression but in only 3 of those the expression levels were significantly different between the young and old individuals. In the HERV-W family expression was observed in 45 loci and only in one case the young/old difference was significant. However, applying hierarchical clustering on the HERV expression data resulted in the formation of two distinct clusters, one containing the young individuals and another the nonagenarians. This suggests, that even though the aging-associated differences in the expression levels of individual proviruses are minor, there seems to be some underlying aging-related pattern. These data indicate that aging does not have a strong effect on the expression of individual HERV proviruses, but instead several proviruses are affected moderately, leading to age-dependent expression profiles.
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Affiliation(s)
- Tapio Nevalainen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- Gerontology Research Center (GEREC), University of Tampere, Tampere, Finland
- * E-mail:
| | - Arttu Autio
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | | | - Saara Marttila
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- Gerontology Research Center (GEREC), University of Tampere, Tampere, Finland
| | - Marja Jylhä
- Gerontology Research Center (GEREC), University of Tampere, Tampere, Finland
- Faculty of Social Sciences, University of Tampere, Tampere, Finland
| | - Mikko Hurme
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
- Gerontology Research Center (GEREC), University of Tampere, Tampere, Finland
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