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Luciano C, Fernando DD, Lucia Z, Elvira I, Romano D, Rebecca C, Alberto B, Francesco R, Maria DBA, Luca P, Irene C, Sara DM, Antonella F, Veronica B, Michela GZ, Nicole BG, Carlo G, Gianfranco P, Davide G. Epigenetic patterns, accelerated biological aging, and enhanced epigenetic drift detected 6 months following COVID-19 infection: insights from a genome-wide DNA methylation study. Clin Epigenetics 2024; 16:112. [PMID: 39164752 PMCID: PMC11337605 DOI: 10.1186/s13148-024-01724-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 08/08/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND The epigenetic status of patients 6-month post-COVID-19 infection remains largely unexplored. The existence of long-COVID, or post-acute sequelae of SARS-CoV-2 infection (PASC), suggests potential long-term changes. Long-COVID includes symptoms like fatigue, neurological issues, and organ-related problems, regardless of initial infection severity. The mechanisms behind long-COVID are unclear, but virus-induced epigenetic changes could play a role. METHODS AND RESULTS Our study explores the lasting epigenetic impacts of SARS-CoV-2 infection. We analyzed genome-wide DNA methylation patterns in an Italian cohort of 96 patients 6 months after COVID-19 exposure, comparing them to 191 healthy controls. We identified 42 CpG sites with significant methylation differences (FDR < 0.05), primarily within CpG islands and gene promoters. Dysregulated genes highlighted potential links to glutamate/glutamine metabolism, which may be relevant to PASC symptoms. Key genes with potential significance to COVID-19 infection and long-term effects include GLUD1, ATP1A3, and ARRB2. Furthermore, Horvath's epigenetic clock showed a slight but significant age acceleration in post-COVID-19 patients. We also observed a substantial increase in stochastic epigenetic mutations (SEMs) in the post-COVID-19 group, implying potential epigenetic drift. SEM analysis identified 790 affected genes, indicating dysregulation in pathways related to insulin resistance, VEGF signaling, apoptosis, hypoxia response, T-cell activation, and endothelin signaling. CONCLUSIONS Our study provides valuable insights into the epigenetic consequences of COVID-19. Results suggest possible associations with accelerated aging, epigenetic drift, and the disruption of critical biological pathways linked to insulin resistance, immune response, and vascular health. Understanding these epigenetic changes could be crucial for elucidating the complex mechanisms behind long-COVID and developing targeted therapeutic interventions.
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Affiliation(s)
- Calzari Luciano
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy
| | - Dragani Davide Fernando
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy
| | - Zanotti Lucia
- Department of Cardiology, S. Luca Hospital, IRCCS, Istituto Auxologico Italiano, Milan, Italy
| | - Inglese Elvira
- Clinical Chemistry Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy
| | - Danesi Romano
- Clinical Chemistry Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milano, Milan, Italy
| | - Cavagnola Rebecca
- Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy
| | - Brusati Alberto
- Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy
| | - Ranucci Francesco
- Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy
| | - Di Blasio Anna Maria
- Molecular Biology Laboratory, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy
| | - Persani Luca
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
- Department of Endocrine and Metabolic Diseases, Lab of Endocrine and Metabolic Research, San Luca Hospital, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Campi Irene
- Department of Endocrine and Metabolic Diseases, Lab of Endocrine and Metabolic Research, San Luca Hospital, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - De Martino Sara
- Consiglio Nazionale delle Ricerche (CNR) - IASI, Rome, Italy
| | | | - Barbi Veronica
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100, Pavia, Italy
| | - Gottardi Zamperla Michela
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100, Pavia, Italy
| | - Baldrighi Giulia Nicole
- Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy
| | - Gaetano Carlo
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100, Pavia, Italy
| | - Parati Gianfranco
- Department of Cardiology, S. Luca Hospital, IRCCS, Istituto Auxologico Italiano, Milan, Italy
- Department of Medicine and Surgery, University of Milan-Bicocca, Milan, Italy
| | - Gentilini Davide
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Cusano Milanino, Milan, Italy.
- Department of Brain and Behavioral Sciences, University of Pavia, Via Bassi 21, Pavia, Italy.
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Kushwah AS, Masood S, Mishra R, Banerjee M. Genetic and epigenetic alterations in DNA repair genes and treatment outcome of chemoradiotherapy in cervical cancer. Crit Rev Oncol Hematol 2024; 194:104240. [PMID: 38122918 DOI: 10.1016/j.critrevonc.2023.104240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Cervical cancer (CaCx) is the deadliest malignancy among women which is caused by human papillomavirus (HPV) and anthro-demographical/clinicopathological factors. HPV oncoproteins E6 and E7 target p53 and RB (retinoblastoma) protein degradation, Ataxia telangiectasia mutated (ATM), ATM-RAD3-related (ATR) inactivation and subsequent impairment of non-homologous end joining (NHEJ), homologous recombination, and base excision repair pathways. There is also an accumulation of genetic and epigenetic alterations in Tumor Growth Suppressors (TGS), oncogenes, and DNA repair genes leading to increased genome instability and CaCx development. These alterations might be responsible for differential clinical response to Cisplatin-based chemoradiotherapy (CRT) in patients. This review explores HPV-mediated DNA damage as a risk factor in CaCx development, the mechanistic role of genetic and epigenetic alterations in DNA repair genes and their association with CRT and outcome, It also explores new possibilities for the development of genetic and epigenetic-based biomarkers for diagnostic, prognostic, and molecular therapeutic interventions.
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Affiliation(s)
- Atar Singh Kushwah
- Department of Urology and Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York 10029, NY, USA; Molecular & Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India; Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Shireen Masood
- Molecular & Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Rajnikant Mishra
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Monisha Banerjee
- Molecular & Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow 226007, Uttar Pradesh, India.
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3
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Pan J, Wang Y, Li C, Zhang S, Ye Z, Ni J, Li H, Li Y, Yue H, Ruan C, Zhao D, Jiang Y, Wu X, Shen X, Zufall RA, Zhang Y, Li W, Lynch M, Long H. Molecular basis of phenotypic plasticity in a marine ciliate. THE ISME JOURNAL 2024; 18:wrae136. [PMID: 39018220 PMCID: PMC11308186 DOI: 10.1093/ismejo/wrae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/06/2024] [Accepted: 07/16/2024] [Indexed: 07/19/2024]
Abstract
Phenotypic plasticity, which involves phenotypic transformation in the absence of genetic change, may serve as a strategy for organisms to survive in complex and highly fluctuating environments. However, its reaction norm, molecular basis, and evolution remain unclear in most organisms, especially microbial eukaryotes. In this study, we explored these questions by investigating the reaction norm, regulation, and evolution of phenotypic plasticity in the cosmopolitan marine free-living ciliates Glauconema spp., which undergo significant phenotypic changes in response to food shortages. This study led to the de novo assembly of macronuclear genomes using long-read sequencing, identified hundreds of differentially expressed genes associated with phenotypic plasticity in different life stages, validated the function of two of these genes, and revealed that the reaction norm of body shape in response to food density follows a power-law distribution. Purifying selection may be the dominant evolutionary force acting on the genes associated with phenotypic plasticity, and the overall data support the hypothesis that phenotypic plasticity is a trait maintained by natural selection. This study provides novel insight into the developmental genetics of phenotypic plasticity in non-model unicellular eukaryotes and sheds light on the complexity and long evolutionary history of this important survival strategy.
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Affiliation(s)
- Jiao Pan
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, China
| | - Yaohai Wang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Chao Li
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Simo Zhang
- Department of Biology, Indiana University, Bloomington, IN 47405, United States
| | - Zhiqiang Ye
- School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China
| | - Jiahao Ni
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Haichao Li
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yichen Li
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Hongwei Yue
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Chenchen Ruan
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Dange Zhao
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Yujian Jiang
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Xiaolin Wu
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
| | - Xiaopeng Shen
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, United States
| | - Yu Zhang
- School of Mathematics Science, Ocean University of China, Qingdao, Shandong Province 266000, China
| | - Weiyi Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, United States
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, United States
| | - Hongan Long
- Key Laboratory of Evolution and Marine Biodiversity (Ministry of Education), Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, China
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Abudahab S, Slattum PW, Price ET, McClay JL. Epigenetic regulation of drug metabolism in aging: utilizing epigenetics to optimize geriatric pharmacotherapy. Pharmacogenomics 2024; 25:41-54. [PMID: 38126340 PMCID: PMC10794944 DOI: 10.2217/pgs-2023-0199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
We explore the relationship between epigenetic aging and drug metabolism. We review current evidence for changes in drug metabolism in normal aging, followed by a description of how epigenetic modifications associated with age can regulate the expression and functionality of genes. In particular, we focus on the role of epigenome-wide studies of human and mouse liver in understanding these age-related processes with respect to xenobiotic processing. We highlight genes encoding drug metabolizing enzymes and transporters revealed to be affected by epigenetic aging in these studies. We conclude that substantial evidence exists for epigenetic aging impacting drug metabolism and transport genes, but more work is needed. We further highlight the promise of pharmacoepigenetics applied to enhancing drug safety in older adults.
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Affiliation(s)
- Sara Abudahab
- Department of Pharmacotherapy & Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Patricia W Slattum
- Department of Pharmacotherapy & Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
- Virginia Center on Aging, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Elvin T Price
- Department of Pharmacotherapy & Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Joseph L McClay
- Department of Pharmacotherapy & Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA
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5
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Mir FA, Amanullah A, Jain BP, Hyderi Z, Gautam A. Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review. Ageing Res Rev 2023; 91:102067. [PMID: 37689143 DOI: 10.1016/j.arr.2023.102067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Gene expression is tremendously altered in the brain during memory acquisition, recall, and forgetfulness. However, non-genetic factors, including environmental elements, epigenetic changes, and lifestyle, have grabbed significant attention in recent years regarding the etiology of neurodegenerative diseases (NDD) and age-associated dementia. Epigenetic modifications are essential in regulating gene expression in all living organisms in a DNA sequence-independent manner. The genes implicated in ageing and NDD-related memory disorders are epigenetically regulated by processes such as DNA methylation, histone acetylation as well as messenger RNA editing machinery. The physiological and optimal state of the epigenome, especially within the CNS of humans, plays an intricate role in helping us adjust to the changing environment, and alterations in it cause many brain disorders, but the mechanisms behind it still need to be well understood. When fully understood, these epigenetic landscapes could act as vital targets for pharmacogenetic rescue strategies for treating several diseases, including neurodegeneration- and age-induced dementia. Keeping this objective in mind, this updated review summarises the epigenetic changes associated with age and neurodegeneration-associated dementia.
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Affiliation(s)
- Fayaz Ahmad Mir
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Zeeshan Hyderi
- Department of Biotechnology, Alagappa University, Karaikudi, India
| | - Akash Gautam
- Centre for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India.
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6
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Traxler L, Lucciola R, Herdy JR, Jones JR, Mertens J, Gage FH. Neural cell state shifts and fate loss in ageing and age-related diseases. Nat Rev Neurol 2023; 19:434-443. [PMID: 37268723 PMCID: PMC10478103 DOI: 10.1038/s41582-023-00815-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2023] [Indexed: 06/04/2023]
Abstract
Most age-related neurodegenerative diseases remain incurable owing to an incomplete understanding of the disease mechanisms. Several environmental and genetic factors contribute to disease onset, with human biological ageing being the primary risk factor. In response to acute cellular damage and external stimuli, somatic cells undergo state shifts characterized by temporal changes in their structure and function that increase their resilience, repair cellular damage, and lead to their mobilization to counteract the pathology. This basic cell biological principle also applies to human brain cells, including mature neurons that upregulate developmental features such as cell cycle markers or glycolytic reprogramming in response to stress. Although such temporary state shifts are required to sustain the function and resilience of the young human brain, excessive state shifts in the aged brain might result in terminal fate loss of neurons and glia, characterized by a permanent change in cell identity. Here, we offer a new perspective on the roles of cell states in sustaining health and counteracting disease, and we examine how cellular ageing might set the stage for pathological fate loss and neurodegeneration. A better understanding of neuronal state and fate shifts might provide the means for a controlled manipulation of cell fate to promote brain resilience and repair.
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Affiliation(s)
- Larissa Traxler
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Raffaella Lucciola
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Joseph R Herdy
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jeffrey R Jones
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jerome Mertens
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
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7
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Hao J, Liu T, Xiu Y, Yuan H, Xu D. High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma. Front Immunol 2023; 14:1208223. [PMID: 37388735 PMCID: PMC10303802 DOI: 10.3389/fimmu.2023.1208223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
Like telomere shortening, global DNA hypomethylation occurs progressively with cellular divisions or in vivo aging and functions as a mitotic clock to restrain malignant transformation/progression. Several DNA-methylation (DNAm) age clocks have been established to precisely predict chronological age using normal tissues, but show DNAm age drift in tumors, which suggests disruption of this mitotic clock during carcinogenesis. Little is known about DNAm age alterations and biological/clinical implications in endometrial cancer (EC). Here we address these issues by analyzing TCGA and GSE67116 cohorts of ECs. Horvath clock analysis of these tumors unexpectedly revealed that almost 90% of them exhibited DNAm age deceleration (DNAmad) compared to patient chronological age. Combined with an additional clock named Phenoage, we identified a subset of tumors (82/429) with high DNAmad (hDNAmad+) as assessed by both clocks. Clinically, hDNAmad+ tumors were associated with advanced diseases and shorter patient survival, compared to hDNAmad- ones. Genetically, hDNAmad+ tumors were characterized by higher copy number alterations (CNAs) whereas lower tumor mutation burden. Functionally, hDNAmad+ tumors were enriched with cell cycle and DNA mismatch repair pathways. Increased PIK3CA alterations and downregulation of SCGB2A1, the inhibitor of PI3K kinase, in hDNAmad+ tumors, might promote tumor growth/proliferation and stemness. In addition, the inactivation of aging drivers/tumor suppressors (TP53, RB1, and CDKN2A) while enhanced telomere maintenance occurred more frequently in hDNAmad+ tumors, which supports sustained tumor growth. Prominently, hDNAmad+ tumors were featured with immunoexclusion microenvironments, accompanied by significantly higher levels of VTCN1 expression while lower PD-L1 and CTLA4 expression, which indicates their poor response to immune checkpoint inhibitor (ICI)-based immunotherapy. We further showed significantly higher levels of DNMT3A and 3B expression in hDNAmad+ than in hDNAmad- tumors. Thus, the tumor suppressive function of aging-like DNA hypomethylation is severely impaired in hDNAmad+ tumors, likely due to enhanced expression of DNMT3A/3B and dysregulated aging regulators. Our findings not only enrich biological knowledge of EC pathogenesis but also help improve EC risk stratification and precision ICI immunotherapy.
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Affiliation(s)
- Jing Hao
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan, China
| | - Tiantian Liu
- Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuchen Xiu
- Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Huiyang Yuan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Dawei Xu
- Department of Medicine, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
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Kühlwein JK, Ruf WP, Kandler K, Witzel S, Lang C, Mulaw MA, Ekici AB, Weishaupt JH, Ludolph AC, Grozdanov V, Danzer KM. ALS is imprinted in the chromatin accessibility of blood cells. Cell Mol Life Sci 2023; 80:131. [PMID: 37095391 PMCID: PMC10126052 DOI: 10.1007/s00018-023-04769-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/20/2023] [Accepted: 03/27/2023] [Indexed: 04/26/2023]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a complex and incurable neurodegenerative disorder in which genetic and epigenetic factors contribute to the pathogenesis of all forms of ALS. The interplay of genetic predisposition and environmental footprints generates epigenetic signatures in the cells of affected tissues, which then alter transcriptional programs. Epigenetic modifications that arise from genetic predisposition and systemic environmental footprints should in theory be detectable not only in affected CNS tissue but also in the periphery. Here, we identify an ALS-associated epigenetic signature ('epiChromALS') by chromatin accessibility analysis of blood cells of ALS patients. In contrast to the blood transcriptome signature, epiChromALS includes also genes that are not expressed in blood cells; it is enriched in CNS neuronal pathways and it is present in the ALS motor cortex. By combining simultaneous ATAC-seq and RNA-seq with single-cell sequencing in PBMCs and motor cortex from ALS patients, we demonstrate that epigenetic changes associated with the neurodegenerative disease can be found in the periphery, thus strongly suggesting a mechanistic link between the epigenetic regulation and disease pathogenesis.
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Affiliation(s)
- Julia K Kühlwein
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Wolfgang P Ruf
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Katharina Kandler
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Simon Witzel
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Christina Lang
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Medhanie A Mulaw
- Medical Faculty, University of Ulm, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Clinic Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, 91054, Erlangen, Bayern, Germany
| | - Jochen H Weishaupt
- Division for Neurodegenerative Diseases, Neurology Department, University Medicine Mannheim, Heidelberg University, 68167, Mannheim, Baden-Wuerttemberg, Germany
| | - Albert C Ludolph
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
- German Center for Neurodegenerative Diseases (DZNE), 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Veselin Grozdanov
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany
| | - Karin M Danzer
- Department of Neurology, University Clinic, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Baden-Wuerttemberg, Germany.
- German Center for Neurodegenerative Diseases (DZNE), 89081, Ulm, Baden-Wuerttemberg, Germany.
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Michki NS, Ndeh R, Helmin KA, Singer BD, McGrath-Morrow SA. DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4 + T cells of neonatal mice with E. coli pneumonia. Sci Rep 2023; 13:4283. [PMID: 36922640 PMCID: PMC10017701 DOI: 10.1038/s41598-023-31285-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial pulmonary infections are a major cause of morbidity and mortality in neonates, with less severity in older children. Previous studies demonstrated that the DNA of CD4+ T cells in the mouse lung, whose primary responsibility is to coordinate the immune response to foreign pathogens, is differentially methylated in neonates compared with juveniles. Nevertheless, the effect of this differential DNA methylation on CD4+ T cell gene expression and response to infection remains unclear. Here we treated E. coli-infected neonatal (4-day-old) and juvenile (13-day-old) mice with decitabine (DAC), a DNA methyltransferase inhibitor with broad-spectrum DNA demethylating activity, and performed simultaneous genome-wide DNA methylation and transcriptional profiling on lung CD4+ T cells. We show that juvenile and neonatal mice experienced differential demethylation in response to DAC treatment, with larger methylation differences observed in neonates. By cross-filtering differentially expressed genes between juveniles and neonates with those sites that were demethylated in neonates, we find that interferon-responsive genes such as Ifit1 are the most down-regulated methylation-sensitive genes in neonatal mice. DAC treatment shifted neonatal lung CD4+ T cells toward a gene expression program similar to that of juveniles. Following lung infection with E. coli, lung CD4+ T cells in neonatal mice exhibit epigenetic repression of important host defense pathways, which are activated by inhibition of DNA methyltransferase activity to resemble a more mature profile.
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Affiliation(s)
- Nigel S Michki
- Children's Hospital of Philadelphia Division of Pulmonary and Sleep Medicine, Philadelphia, PA, 19104, USA.
- Children's Hospital of Philadelphia Division of Cardiology, Philadelphia, PA, 19104, USA.
| | - Roland Ndeh
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Kathryn A Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine Chicago, Chicago, IL, 60611, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine Chicago, Chicago, IL, 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sharon A McGrath-Morrow
- Children's Hospital of Philadelphia Division of Pulmonary and Sleep Medicine, Philadelphia, PA, 19104, USA
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University, Baltimore, MD, 21287, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
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Dye CK, Wu H, Monk C, Belsky DW, Alschuler D, Lee S, O’Donnell K, Scorza P. Mother's childhood adversity is associated with accelerated epigenetic aging in pregnancy and in male newborns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530806. [PMID: 36945654 PMCID: PMC10028804 DOI: 10.1101/2023.03.02.530806] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Background Adverse childhood experiences (ACEs) are correlated with accelerated epigenetic aging, but it is not clear whether altered epigenetic aging from childhood adversities persists into adulthood and can be transmitted to the next generation. Thus, we tested whether mothers' childhood adversity is associated with accelerated epigenetic aging during pregnancy and in their newborn offspring. Methods Data were from the Avon Longitudinal Study of Parents and Children (ALSPAC) sub-study, Accessible Resource for Integrated Epigenomic Studies (ARIES). Women provided retrospective self-reports during pregnancy of ACE exposure. DNA methylation was measured in mothers during pregnancy and cord blood at birth. Estimates of epigenetic age acceleration were calculated using Principal Components of Horvath, Hannum skin & blood, GrimAge, PhenoAge, and DunedinPACE epigenetic clocks for mothers; and the Knight and Bohlin cord blood clocks for newborns. Associations between a cumulative maternal ACE score and epigenetic age acceleration were estimated using linear regression models, adjusting for maternal age at pregnancy, smoking during pregnancy, education, and pre-pregnancy BMI. Models for offspring were stratified by sex and additionally adjusted for gestation age. Results Mothers' total ACE score was positively associated with accelerated maternal PhenoAge and GrimAge. In newborn offspring, mothers' total ACE score was positively associated with accelerated epigenetic aging in males using the Bohlin clock, but not in females using either epigenetic clock. We found male offsprings' epigenetic age was accelerated in those born to mothers exposed to neglect using the Knight clock; and parental substance abuse using the Bohlin clock. Conclusion Our results show that mothers' ACE exposure is associated with DNAm age acceleration in male offspring, supporting the notion that DNAm age could be a marker of intergenerational biological embedding of mothers' childhood adversity. This is consistent with findings on vulnerability of male fetuses to environmental insults.
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Affiliation(s)
- Christian K. Dye
- Department of Environmental Health Sciences, Columbia University, New York, New York, USA
| | - Haotian Wu
- Department of Environmental Health Sciences, Columbia University, New York, New York, USA
| | - Catherine Monk
- Department of Psychiatry, Columbia University, Columbia University, New York, New York, USA
- Division of Behavioral Medicine, New York State Psychiatric Institute, New York, New York, USA
- Department of Obstetrics and Gynecology, Columbia University, New York, New York, USA
| | - Daniel W. Belsky
- Department of Epidemiology & Butler Columbia Aging Center, Columbia University, New York, New York, USA
| | - Daniel Alschuler
- Division of Behavioral Medicine, New York State Psychiatric Institute, New York, New York, USA
| | - Seonjoo Lee
- Division of Behavioral Medicine, New York State Psychiatric Institute, New York, New York, USA
- Department of Biostatistics, Columbia University, New York, New York, USA
| | - Kieran O’Donnell
- Yale Child Study Center, Yale School of Medicine, New Haven, Connecticut, USA
| | - Pamela Scorza
- Department of Psychiatry, Columbia University, Columbia University, New York, New York, USA
- Department of Obstetrics and Gynecology, Columbia University, New York, New York, USA
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Gentilini D, Muzza M, de Filippis T, Vigone MC, Weber G, Calzari L, Cassio A, Di Frenna M, Bartolucci M, Grassi ES, Carbone E, Olivieri A, Persani L. Stochastic epigenetic mutations as possible explanation for phenotypical discordance among twins with congenital hypothyroidism. J Endocrinol Invest 2023; 46:393-404. [PMID: 36071330 PMCID: PMC9859866 DOI: 10.1007/s40618-022-01915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
PURPOSE The elevated frequency of discordance for congenital hypothyroidism (CH) phenotype between monozygotic twins suggests the involvement of non-mendelian mechanisms. The aim of the study was to investigate the role of epigenetics in CH pathogenesis. METHODS A genome-wide DNA methylation analysis was performed on the peripheral blood of 23 twin pairs (10 monozygotic and 13 dizygotic), 4 concordant and 19 discordant pairs for CH at birth. RESULTS Differential methylation analysis did not show significant differences in methylation levels between CH cases and controls, but a different methylation status of several genes may explain the CH discordance of a monozygotic twin couple carrying a monoallelic nonsense mutation of DUOX2. In addition, the median number of hypo-methylated Stochastic Epigenetic Mutations (SEMs) resulted significantly increased in cases compared to controls. The prioritization analysis for CH performed on the genes epimutated exclusively in the cases identified SLC26A4, FOXI1, NKX2-5 and TSHB as the genes with the highest score. The analysis of significantly SEMs-enriched regions led to the identification of two genes (FAM50B and MEG8) that resulted epigenetically dysregulated in cases. CONCLUSION Epigenetic modifications may potentially account for CH pathogenesis and explain discordance among monozygotic twins.
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Affiliation(s)
- D Gentilini
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095, Milan, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - M Muzza
- Laboratory of Endocrine and Metabolic Research, Department of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Piazzale Brescia 20, 20149, Milan, Italy
| | - T de Filippis
- Laboratory of Endocrine and Metabolic Research, Department of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Piazzale Brescia 20, 20149, Milan, Italy
| | - M C Vigone
- Department of Pediatrics, Endocrine Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - G Weber
- Department of Pediatrics, Endocrine Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - L Calzari
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS, Cusano Milanino, 20095, Milan, Italy
| | - A Cassio
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - M Di Frenna
- Department of Pediatrics, Endocrine Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - M Bartolucci
- Department of Maternal and Child Sciences and Urology, University "La Sapienza", Rome, Italy
| | - E S Grassi
- Department of Medical Biotechnology and Experimental Medicine, University of Milan, 20122, Milan, Italy
| | - E Carbone
- Laboratory of Endocrine and Metabolic Research, Department of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Piazzale Brescia 20, 20149, Milan, Italy
| | - A Olivieri
- Department of Cardiovascular and Endocrine-Metabolic Diseases and Aging, Italian National Institute of Health, 00161, Rome, Italy
| | - L Persani
- Laboratory of Endocrine and Metabolic Research, Department of Endocrine and Metabolic Diseases, Istituto Auxologico Italiano IRCCS, Piazzale Brescia 20, 20149, Milan, Italy.
- Department of Medical Biotechnology and Experimental Medicine, University of Milan, 20122, Milan, Italy.
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12
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Davide G, Rebecca C, Irene P, Luciano C, Francesco R, Marta N, Miriam O, Natascia B, Pierluigi P. Epigenetics of Autism Spectrum Disorders: A Multi-level Analysis Combining Epi-signature, Age Acceleration, Epigenetic Drift and Rare Epivariations Using Public Datasets. Curr Neuropharmacol 2023; 21:2362-2373. [PMID: 37489793 PMCID: PMC10556384 DOI: 10.2174/1570159x21666230725142338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Epigenetics of Autism Spectrum Disorders (ASD) is still an understudied field. The majority of the studies on the topic used an approach based on mere classification of cases and controls. OBJECTIVE The present study aimed at providing a multi-level approach in which different types of epigenetic analysis (epigenetic drift, age acceleration) are combined. METHODS We used publicly available datasets from blood (n = 3) and brain tissues (n = 3), separately. Firstly, we evaluated for each dataset and meta-analyzed the differential methylation profile between cases and controls. Secondly, we analyzed age acceleration, epigenetic drift and rare epigenetic variations. RESULTS We observed a significant epi-signature of ASD in blood but not in brain specimens. We did not observe significant age acceleration in ASD, while epigenetic drift was significantly higher compared to controls. We reported the presence of significant rare epigenetic variations in 41 genes, 35 of which were never associated with ASD. Almost all genes were involved in pathways linked to ASD etiopathogenesis (i.e., neuronal development, mitochondrial metabolism, lipid biosynthesis and antigen presentation). CONCLUSION Our data support the hypothesis of the use of blood epi-signature as a potential tool for diagnosis and prognosis of ASD. The presence of an enhanced epigenetic drift, especially in brain, which is linked to cellular replication, may suggest that alteration in epigenetics may occur at a very early developmental stage (i.e., fetal) when neuronal replication is still high.
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Affiliation(s)
- Gentilini Davide
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milan, 20090, Italy
| | - Cavagnola Rebecca
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Possenti Irene
- Department of Statistical Sciences Paolo Fortunati, University of Bologna, Bologna, Italy
| | - Calzari Luciano
- Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milan, 20090, Italy
| | - Ranucci Francesco
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Nola Marta
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Olivola Miriam
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Brondino Natascia
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
| | - Politi Pierluigi
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, 27100, Italy
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Population Epigenetics: The Extent of DNA Methylation Variation in Wild Animal Populations. EPIGENOMES 2022; 6:epigenomes6040031. [PMID: 36278677 PMCID: PMC9589984 DOI: 10.3390/epigenomes6040031] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Population epigenetics explores the extent of epigenetic variation and its dynamics in natural populations encountering changing environmental conditions. In contrast to population genetics, the basic concepts of this field are still in their early stages, especially in animal populations. Epigenetic variation may play a crucial role in phenotypic plasticity and local adaptation as it can be affected by the environment, it is likely to have higher spontaneous mutation rate than nucleotide sequences do, and it may be inherited via non-mendelian processes. In this review, we aim to bring together natural animal population epigenetic studies to generate new insights into ecological epigenetics and its evolutionary implications. We first provide an overview of the extent of DNA methylation variation and its autonomy from genetic variation in wild animal population. Second, we discuss DNA methylation dynamics which create observed epigenetic population structures by including basic population genetics processes. Then, we highlight the relevance of DNA methylation variation as an evolutionary mechanism in the extended evolutionary synthesis. Finally, we suggest new research directions by highlighting gaps in the knowledge of the population epigenetics field. As for our results, DNA methylation diversity was found to reveal parameters that can be used to characterize natural animal populations. Some concepts of population genetics dynamics can be applied to explain the observed epigenetic structure in natural animal populations. The set of recent advancements in ecological epigenetics, especially in transgenerational epigenetic inheritance in wild animal population, might reshape the way ecologists generate predictive models of the capacity of organisms to adapt to changing environments.
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14
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Reale A, Tagliatesta S, Zardo G, Zampieri M. Counteracting aged DNA methylation states to combat ageing and age-related diseases. Mech Ageing Dev 2022; 206:111695. [PMID: 35760211 DOI: 10.1016/j.mad.2022.111695] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/09/2022] [Accepted: 06/22/2022] [Indexed: 12/18/2022]
Abstract
DNA methylation (DNAm) overwrites information about multiple extrinsic factors on the genome. Age is one of these factors. Age causes characteristic DNAm changes that are thought to be not only major drivers of normal ageing but also precursors to diseases, cancer being one of these. Although there is still much to learn about the relationship between ageing, age-related diseases and DNAm, we now know how to interpret some of the effects caused by age in the form of changes in methylation marks at specific loci. In fact, these changes form the basis of the so called "epigenetic clocks", which translate the genomic methylation profile into an "epigenetic age". Epigenetic age does not only estimate chronological age but can also predict the risk of chronic diseases and mortality. Epigenetic age is believed to be one of the most accurate metrics of biological age. Initial evidence has recently been gathered pointing to the possibility that the rate of epigenetic ageing can be slowed down or even reversed. In this review, we discuss some of the most relevant advances in this field. Expected outcome is that this approach can provide insights into how to preserve health and reduce the impact of ageing diseases in humans.
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Affiliation(s)
- Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Stefano Tagliatesta
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00161 Rome, Italy.
| | - Giuseppe Zardo
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
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Ryznar RJ, Phibbs L, Onat E, Van Winkle LJ. Epigenetic Regulation of Development, Cellular Differentiation, and Disease Progression/Protection in Adults. Cells 2022; 11:cells11121907. [PMID: 35741035 PMCID: PMC9221476 DOI: 10.3390/cells11121907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Rebecca J. Ryznar
- Department of Biomedical Sciences, Rocky Vista University, Parker, CO 80134, USA
- Correspondence:
| | - Lacie Phibbs
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80134, USA; (L.P.); (E.O.)
| | - Erin Onat
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80134, USA; (L.P.); (E.O.)
| | - Lon J. Van Winkle
- Department of Medical Humanities, Rocky Vista University, 8401 S. Chambers Road, Parker, CO 80112, USA;
- Department of Biochemistry, Midwestern University, Downers Grove, IL 60515, USA
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Prenatal ethanol exposure induces dynamic changes of expression and activity of hepatic cytochrome P450 isoforms in male rat offspring. Reprod Toxicol 2022; 109:101-108. [PMID: 35301062 DOI: 10.1016/j.reprotox.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 02/07/2023]
Abstract
This study aimed at determining the effect of prenatal ethanol exposure (PEE) on the expression and activity of cytochrome P450 (CYP) isozymes at different life stages of male rat offspring. Pregnant Wistar rats were administered with ethanol (4 g/kg/d) intragastrically from gestational day (GD) 9-20. Male offspring's gene and activity of CYP isozymes were analyzed on GD 20 (only expression), postnatal day (PD) 84 and 196. Using aniline as probe, we compared the enzyme kinetics of hepatic CYP2E1 between two groups. Expression of CYP isozymes was examined in rat primary hepatocytes and human hepatic cell lines treated with ethanol or/and glucocorticoid. Gene level of Cyp1a2, 2b1, 2d1, 2e1, 3a1 and aryl hydrocarbon receptor were increased in PEE group on GD 20 and PD 84 and Cyp2e1 still exhibited an increasing trend on PD 196 compared with the control. PEE inhibited CYP2D1 and 2E1 activities in male offspring on PD 84. CYP activities in two groups became the same level on PD 196. PEE induced an opposite change in gene and protein level of hepatic CYP2E1 before and after birth. In consistent with lower protein level, aniline metabolism in PEE was weaker in liver microsome. Both single and combined use of ethanol or/and glucocorticoid increased CYPs expression in vitro. In conclusion, PEE programmed a higher gene and lower protein level of CYPs in male offspring, which dwindled with age. Impairment of protein levels and enzyme activities of CYPs may affect individual metabolism of endogenous and exogenous substances in early adulthood.
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17
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Liu Y, Song F, Yang Y, Yang S, Jiang M, Zhang W, Ma Z, Gu X. Mitochondrial DNA methylation drift and postoperative delirium in mice. Eur J Anaesthesiol 2022; 39:133-144. [PMID: 34726198 DOI: 10.1097/eja.0000000000001620] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Mitochondrial dysfunction is linked to the etiopathogenesis of postoperative delirium (POD), which severely affects the prognosis of elderly patients undergoing surgery. The methylation of mitochondrial DNA (mtDNA), a new and incompletely described phenomenon that regulates the structure and function of mitochondria, is associated with ageing. However, the relationship between mtDNA methylation and POD has not been established. OBJECTIVE To explore the potential roles of mitochondrial epigenetic regulation in POD. DESIGN A randomised animal study. PARTICIPANTS Eighty-eight 6-month-old and one hundred seventy-six 18-month-old male C57BL/6N mice. INTERVENTIONS POD was induced by abdominal surgery under 1.4% isoflurane for 2 h. Behavioural tests were performed at 24 h before surgery and at 6, 9 and 24 h after surgery. MAIN OUTCOME MEASURES 5-methylcytosine (5-mC) at five CpG sites of the displacement loop (D-loop) and at 60 CpG sites of coding gene loci in the mitochondrial genome after surgery of the hippocampus, prefrontal cortex, amygdala and anterior cingulate cortex in 6 and 18-month-old mice were detected using bisulfite pyrosequencing. Mitochondrial structure, mitochondrial gene expression and mtDNA copy number were also examined using Electron microscopy and real time PCR to find the association with mtDNA methylation. RESULTS The mtDNA methylation drift manifested as a decrease in the methylation levels at the D-loop and an increase or decrease in the methylation levels at several coding gene loci, ultimately resulting in reduced mtDNA copy numbers, altered mitochondrial gene expression and damaged mitochondrial structures in the hippocampus and prefrontal cortex after surgery. The activation of Silent information regulator-1 (SIRT1) ameliorated anaesthesia-induced and surgery-induced mitochondrial dysfunction and delirium-like behaviours by regulating mtDNA methyltransferase-mediated mtDNA methylation. CONCLUSION These data support the existence of epigenetic mtDNA regulation in POD; however, further studies are required to explore the specific mechanisms. TRIAL REGISTRATION No 20181204 Drum tower hospital.
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Affiliation(s)
- Yue Liu
- From the Department of Anesthesiology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, Jiangsu Province, China
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Liu T, Wang J, Xiu Y, Wu Y, Xu D. DNA Methylation Age Drift Is Associated with Poor Outcomes and De-Differentiation in Papillary and Follicular Thyroid Carcinomas. Cancers (Basel) 2021; 13:cancers13194827. [PMID: 34638311 PMCID: PMC8508076 DOI: 10.3390/cancers13194827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/19/2021] [Accepted: 09/23/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Normal human tissues contain an epigenetic clock resulting from the age-dependent DNA methylation signature, which is the so-called DNA methylation (DNAm) age and can be used to precisely predict chronological age of healthy individuals. Abnormal DNAm age drift has been implicated in cancer risk and pathogenesis. Here, we observed that highly drifted DNAm age (HDDA) occurred in approximately 1/3 tumors derived from patients with papillary and follicular thyroid carcinomas. HDDA is significantly associated with dedifferentiation of tumor cells and poor patient outcomes. Thus, HDDA may serve as a new prognostic factor for thyroid carcinoma. Abstract Alterations in global DNA methylation play a critical role in both aging and cancer, and DNA methylation (DNAm) age drift has been implicated in cancer risk and pathogenesis. In the present study, we analyzed the TCGA cohort of papillary and follicular thyroid carcinoma (PTC and FTC) for their DNAm age and association with clinic-pathological features. In 54 noncancerous thyroid (NT) samples, DNAm age was highly correlated with patient chronological age (R2 = 0.928, p = 2.6 × 10−31), but drifted to younger than chronological age in most specimens, especially those from patients >50 years old. DNAm age in 502 tumors was also correlated with patient chronological age, but to a much lesser extent (R2 = 0.403). Highly drifted DNAm age (HDDA) was identified in 161 tumors, among which were 101 with DNAm age acceleration while 60 with DNAm age deceleration. Tumors with HDDA were characterized by the robust aberrations in metabolic activities, extracellular microenvironment components and inflammation/immunology responses, and dedifferentiation. Importantly, HDDA in tumors independently predicted shorter disease-free survival of patients. Collectively, NT thyroids from TC patients have younger DNAm age, while HDDA frequently occurs in TCs, and contributes to the TC progression and poor patient outcomes. HDDA may serve as a new prognostic factor for TCs.
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Affiliation(s)
- Tiantian Liu
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
- Correspondence:
| | - Jiansheng Wang
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
| | - Yuchen Xiu
- Pathology Department, School of Basic Medical Science, Shandong University, Jinan 250012, China; (J.W.); (Y.X.)
| | - Yujiao Wu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska University Hospital Solna, Karolinsk Institutet, SE-171 76 Stockholm, Sweden; (Y.W.); (D.X.)
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine (CMM), Karolinska University Hospital Solna, Karolinsk Institutet, SE-171 76 Stockholm, Sweden; (Y.W.); (D.X.)
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Seo MK, Lee JG, Park SW. Early life stress induces age-dependent epigenetic changes in p11 gene expression in male mice. Sci Rep 2021; 11:10663. [PMID: 34471143 PMCID: PMC8410943 DOI: 10.1038/s41598-021-89593-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
Early life stress (ELS) causes long-lasting changes in gene expression through epigenetic mechanisms. However, little is known about the effects of ELS in adulthood, specifically across different age groups. In this study, the epigenetic modifications of p11 expression in adult mice subjected to ELS were investigated in different stages of adulthood. Pups experienced maternal separation (MS) for 3 h daily from postnatal day 1 to 21. At young and middle adulthood, behavioral test, hippocampal p11 expression levels, and levels of histone acetylation and methylation and DNA methylation at the hippocampal p11 promoter were measured. Middle-aged, but not young adult, MS mice exhibited increased immobility time in the forced swimming test. Concurrent with reduced hippocampal p11 levels, mice in both age groups showed a decrease in histone acetylation (AcH3) and permissive histone methylation (H3K4me3) at the p11 promoter, as well as an increase in repressive histone methylation (H3K27me3). Moreover, our results showed that the expression, AcH3 and H3Kme3 levels of p11 gene in response to MS were reduced with age. DNA methylation analysis of the p11 promoter revealed increased CpG methylation in middle-aged MS mice only. The results highlight the age-dependent deleterious effects of ELS on the epigenetic modifications of p11 transcription.
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Affiliation(s)
- Mi Kyoung Seo
- Paik Institute for Clinical Research, Inje University, Busan, 47392, Republic of Korea
| | - Jung Goo Lee
- Paik Institute for Clinical Research, Inje University, Busan, 47392, Republic of Korea. .,Department of Psychiatry, College of Medicine, Haeundae Paik Hospital, Inje University, Busan, 48108, Republic of Korea.
| | - Sung Woo Park
- Paik Institute for Clinical Research, Inje University, Busan, 47392, Republic of Korea. .,Department of Convergence Biomedical Science, College of Medicine, Inje University, Busan, 47392, Republic of Korea.
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Boughey H, Jurga M, El-Khamisy SF. DNA Homeostasis and Senescence: Lessons from the Naked Mole Rat. Int J Mol Sci 2021; 22:ijms22116011. [PMID: 34199458 PMCID: PMC8199619 DOI: 10.3390/ijms22116011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/13/2022] Open
Abstract
As we age, our bodies accrue damage in the form of DNA mutations. These mutations lead to the generation of sub-optimal proteins, resulting in inadequate cellular homeostasis and senescence. The build-up of senescent cells negatively affects the local cellular micro-environment and drives ageing associated disease, including neurodegeneration. Therefore, limiting the accumulation of DNA damage is essential for healthy neuronal populations. The naked mole rats (NMR) are from eastern Africa and can live for over three decades in chronically hypoxic environments. Despite their long lifespan, NMRs show little to no biological decline, neurodegeneration, or senescence. Here, we discuss molecular pathways and adaptations that NMRs employ to maintain genome integrity and combat the physiological and pathological decline in organismal function.
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Affiliation(s)
- Harvey Boughey
- The Healthy Lifespan Institute and the Institute of Neuroscience, University of Sheffield, Sheffield S10 2TN, UK;
| | - Mateusz Jurga
- The Institute of Cancer Therapeutics, University of Bradford, Bradford BD7 1DP, UK;
| | - Sherif F. El-Khamisy
- The Healthy Lifespan Institute and the Institute of Neuroscience, University of Sheffield, Sheffield S10 2TN, UK;
- The Institute of Cancer Therapeutics, University of Bradford, Bradford BD7 1DP, UK;
- Correspondence: ; Tel.: +44-(0)-114-2222-791; Fax: +44-(0)-114-222-2850
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21
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Da Silva MLR, De Albuquerque BHDR, Allyrio TADMF, De Almeida VD, Cobucci RNDO, Bezerra FL, Andrade VS, Lanza DCF, De Azevedo JCV, De Araújo JMG, Fernandes JV. The role of HPV-induced epigenetic changes in cervical carcinogenesis (Review). Biomed Rep 2021; 15:60. [PMID: 34094536 PMCID: PMC8165754 DOI: 10.3892/br.2021.1436] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Cervical cancer is associated with infection by certain types of human papillomaviruses (HPVs), and this affects women worldwide. Despite the improvements in prevention and cure of HPV-induced cervical cancer, it remains the second most common type of cancer in women in the least developed regions of the world. Epigenetic modifications are stable long-term changes that occur in the DNA, and are part of a natural evolutionary process of necessary adaptations to the environment. They do not result in changes in the DNA sequence, but do affect gene expression and genomic stability. Epigenetic changes are important in several biological processes. The effects of the environment on gene expression can contribute to the development of numerous diseases. Epigenetic modifications may serve a critical role in cancer cells, by silencing tumor suppressor genes, activating oncogenes, and exacerbating defects in DNA repair mechanisms. Although cervical cancer is directly related to a persistent high-risk HPV infection, several epigenetic changes have been identified in both the viral DNA and the genome of the infected cells: DNA methylation, histone modification and gene silencing by non-coding RNAs, which initiate and sustain epigenetic changes. In the present review, recent advances in the role of epigenetic changes in cervical cancer are summarized.
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Affiliation(s)
- Martha Laysla Ramos Da Silva
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil.,Post-Graduate Program in Parasite Biology, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| | | | | | - Valéria Duarte De Almeida
- Department of Biomedical Sciences, State University of Rio Grande do Norte, Mossoro 59607-360, Brazil
| | | | - Fabiana Lima Bezerra
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| | - Vania Sousa Andrade
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil.,Post-Graduate Program in Parasite Biology, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| | - Daniel Carlos Ferreira Lanza
- Laboratory of Applied Molecular Biology, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| | | | - Josélio Maria Galvão De Araújo
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil.,Post-Graduate Program in Parasite Biology, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| | - José Veríssimo Fernandes
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil.,Post-Graduate Program in Parasite Biology, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
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22
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DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift. Commun Biol 2021; 4:598. [PMID: 34011964 PMCID: PMC8134454 DOI: 10.1038/s42003-021-02116-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 04/14/2021] [Indexed: 12/27/2022] Open
Abstract
Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated during long-term culture of mesenchymal stem cells (MSCs) and other cell types. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpopulations. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no enriched interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results support the notion that DNAm changes during culture-expansion are not directly regulated by a targeted mechanism but rather resemble epigenetic drift. Julia Franzen et al. investigate if changes in DNA methylation at specific genetic loci during cell culture expansion are due to a specific mechanism or gradual deregulation of an epigenetic state. Their results suggest that changes in CpG methylation are due to indirect epigenetic drift, rather than a consequence of targeting by DNA methyltransferases.
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23
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Huibregtse BM, Newell-Stamper BL, Domingue BW, Boardman JD. Genes Related to Education Predict Frailty Among Older Adults in the United States. J Gerontol B Psychol Sci Soc Sci 2021; 76:173-183. [PMID: 31362310 DOI: 10.1093/geronb/gbz092] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE This article expands on research that links education and frailty among older adults by considering the role of genes associated with education. METHOD Data come from a sample of 7,064 non-Hispanic, white adults participating in the 2004-2012 waves of the Health and Retirement Study. Frailty was measured with two indices: (a) The Frailty Index which corresponds to a deficit accumulation model; and (b) The Paulson-Lichtenberg Frailty Index which corresponds to the biological syndrome/phenotype model. Genes associated with education were quantified using an additive polygenic score. Associations between the polygenic score and frailty indices were tested using a series of multilevel models, controlling for multiple observations for participants across waves. RESULTS Results showed a strong and negative association between genes for education and frailty symptoms in later life. This association exists above and beyond years of completed education and we demonstrate that this association becomes weaker as older adults approach their 80s. DISCUSSION The results contribute to the education-health literature by highlighting new and important pathways through which education might be linked to successful aging.
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Affiliation(s)
- Brooke M Huibregtse
- Institute of Behavioral Science, University of Colorado Boulder.,Institute for Behavioral Genetics, University of Colorado Boulder
| | - Breanne L Newell-Stamper
- Institute of Behavioral Science, University of Colorado Boulder.,Institute for Behavioral Genetics, University of Colorado Boulder.,Department of Integrative Physiology, University of Colorado Boulder
| | - Benjamin W Domingue
- Institute of Behavioral Science, University of Colorado Boulder.,Graduate School of Education, Stanford University, California
| | - Jason D Boardman
- Institute of Behavioral Science, University of Colorado Boulder.,Institute for Behavioral Genetics, University of Colorado Boulder.,Department of Sociology, University of Colorado Boulder
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24
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Baker SA, Kwok S, Berry GJ, Montine TJ. Angiotensin-converting enzyme 2 (ACE2) expression increases with age in patients requiring mechanical ventilation. PLoS One 2021; 16:e0247060. [PMID: 33592054 PMCID: PMC7886150 DOI: 10.1371/journal.pone.0247060] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/30/2021] [Indexed: 01/08/2023] Open
Abstract
Mortality due to Covid-19 is highly associated with advanced age, owing in large part to severe lower respiratory tract infection. SARS-CoV-2 utilizes the host ACE2 receptor for infection. Whether ACE2 abundance in the lung contributes to age-associated vulnerability is currently unknown. We set out to characterize the RNA and protein expression profiles of ACE2 in aging human lung in the context of phenotypic parameters likely to affect lung physiology. Examining publicly available RNA sequencing data, we discovered that mechanical ventilation is a critical variable affecting lung ACE2 levels. Therefore, we investigated ACE2 protein abundance in patients either requiring mechanical ventilation or spontaneously breathing. ACE2 distribution and expression were determined in archival lung samples by immunohistochemistry (IHC). Tissues were selected from the specimen inventory at a large teaching hospital collected between 2010-2020. Twelve samples were chosen from patients receiving mechanical ventilation for acute hypoxic respiratory failure (AHRF). Twenty samples were selected from patients not requiring ventilation. We compared samples across age, ranging from 40-83 years old in the ventilated cohort and 14-80 years old in the non-ventilated cohort. Within the alveolated parenchyma, ACE2 expression is predominantly observed in type II pneumocytes (or alveolar type II / AT2 cells) and alveolar macrophages. All 12 samples from our ventilated cohort showed histologic features of diffuse alveolar damage including reactive, proliferating AT2 cells. In these cases, ACE2 was strongly upregulated with age when normalized to lung area (p = 0.004) or cellularity (p = 0.003), associated with prominent expression in AT2 cells. In non-ventilated individuals, AT2 cell reactive changes were not observed and ACE2 expression did not change with age when normalized to lung area (p = 0.231) or cellularity (p = 0.349). In summary, ACE2 expression increases with age in the setting of alveolar damage observed in patients on mechanical ventilation, providing a potential mechanism for higher Covid-19 mortality in the elderly.
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Affiliation(s)
- Steven Andrew Baker
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shirley Kwok
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Gerald J. Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Thomas J. Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
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25
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Kachroo P, Morrow JD, Vyhlidal CA, Gaedigk R, Silverman EK, Weiss ST, Tantisira KG, DeMeo DL. DNA methylation perturbations may link altered development and aging in the lung. Aging (Albany NY) 2021; 13:1742-1764. [PMID: 33468710 PMCID: PMC7880367 DOI: 10.18632/aging.202544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
Fetal perturbations in DNA methylation during lung development may reveal insights into the enduring impacts on adult lung health and disease during aging that have not been explored altogether before. We studied the association between genome-wide DNA-methylation and post-conception age in fetal-lung (n=78, 42 exposed to in-utero-smoke (IUS)) tissue and chronological age in adult-lung tissue (n=160, 114 with Chronic Obstructive Pulmonary Disease) using multi-variate linear regression models with covariate adjustment and tested for effect modification by phenotypes. Overlapping age-associations were evaluated for functional and tissue-specific enrichment using the Genotype-Tissue-Expression (GTEx) project. We identified 244 age-associated differentially methylated positions and 878 regions overlapping between fetal and adult-lung tissues. Hyper-methylated CpGs (96%) were enriched in transcription factor activity (FDR adjusted P=2x10-33) and implicated in developmental processes including embryonic organ morphogenesis, neurogenesis and growth delay. Hypo-methylated CpGs (2%) were enriched in oxido-reductase activity and VEGFA-VEGFR2 Signaling. Twenty-one age-by-sex and eleven age-by-pack-years interactions were statistically significant (FDR<0.05) in adult-lung tissue. DNA methylation in transcription factors during development in fetal lung recapitulates in adult-lung tissue with aging. These findings reveal molecular mechanisms and pathways that may link disrupted development in early-life and age-associated lung diseases.
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Affiliation(s)
- Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jarrett D. Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Roger Gaedigk
- Children's Mercy Hospital and Clinics, Kansas City, MO 64108, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
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26
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Beacon TH, Su RC, Lakowski TM, Delcuve GP, Davie JR. SARS-CoV-2 multifaceted interaction with the human host. Part II: Innate immunity response, immunopathology, and epigenetics. IUBMB Life 2020; 72:2331-2354. [PMID: 32936531 DOI: 10.1002/iub.2379] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 makes its way into the cell via the ACE2 receptor and the proteolytic action of TMPRSS2. In response to the SARS-CoV-2 infection, the innate immune response is the first line of defense, triggering multiple signaling pathways to produce interferons, pro-inflammatory cytokines and chemokines, and initiating the adaptive immune response against the virus. Unsurprisingly, the virus has developed strategies to evade detection, which can result in delayed, excessive activation of the innate immune system. The response elicited by the host depends on multiple factors, including health status, age, and sex. An overactive innate immune response can lead to a cytokine storm, inflammation, and vascular disruption, leading to the vast array of symptoms exhibited by COVID-19 patients. What is known about the expression and epigenetic regulation of the ACE2 gene and the various players in the host response are explored in this review.
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Affiliation(s)
- Tasnim H Beacon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ruey-Chyi Su
- National HIV and Retrovirology Laboratory, JC Wilt Infectious Disease Research Centre, Winnipeg, Manitoba, Canada
| | - Ted M Lakowski
- College of Pharmacy, Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Geneviève P Delcuve
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
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27
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Leite ML, Oliveira KBS, Cunha VA, Dias SC, da Cunha NB, Costa FF. Epigenetic Therapies in the Precision Medicine Era. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Michel Lopes Leite
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
| | | | - Victor Albuquerque Cunha
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
| | - Simoni Campos Dias
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
- Animal Biology DepartmentUniversidade de Brasília UnB, Campus Darcy Ribeiro. Brasilia DF 70910‐900 Brazil
| | - Nicolau Brito da Cunha
- Genomic Sciences and Biotechnology Program UCB ‐ Brasilia, SgAN 916, Modulo B, Bloco C, 70790‐160 Brasília DF Brazil
| | - Fabricio F. Costa
- Cancer Biology and Epigenomics ProgramAnn & Robert H Lurie Children's Hospital of Chicago Research Center, Northwestern University's Feinberg School of Medicine 2430 N. Halsted St., Box 220 Chicago IL 60611 USA
- Northwestern University's Feinberg School of Medicine 2430 N. Halsted St., Box 220 Chicago IL 60611 USA
- MATTER Chicago 222 W. Merchandise Mart Plaza, Suite 12th Floor Chicago IL 60654 USA
- Genomic Enterprise (www.genomicenterprise.com) San Diego, CA 92008 and New York NY 11581 USA
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28
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Cakouros D, Gronthos S. The changing epigenetic landscape of Mesenchymal Stem/Stromal Cells during aging. Bone 2020; 137:115440. [PMID: 32445894 DOI: 10.1016/j.bone.2020.115440] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/17/2020] [Accepted: 05/17/2020] [Indexed: 12/17/2022]
Abstract
There is mounting evidence in the literature that mesenchymal stromal/stem cell (MSC) like populations derived from different tissues, undergo epigenetic changes during aging, leading to compromised connective tissue integrity and function. This body of work has linked the biological aging of MSC to changes in their epigenetic signatures affecting growth, lifespan, self-renewal and multi-potential, due to deregulation of processes such as cellular senescence, oxidative stress, DNA damage, telomere shortening and DNA damage. This review addresses recent findings examining DNA methylation, histone modifications and miRNA changes in aging MSC populations. Moreover, we explore how epigenetic factors alter cellular pathways and associated biological networks, contributing to the MSC aging phenotype. Finally we discuss the crucial areas requiring a greater understanding of these processes, in order to piece together a global picture of the changing epigenetic landscape in MSC during aging.
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Affiliation(s)
- Dimitrios Cakouros
- Mesenchymal Stem Cell Laboratory, School of Medical Sciences, Faculty of Health Sciences, The University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Stan Gronthos
- Mesenchymal Stem Cell Laboratory, School of Medical Sciences, Faculty of Health Sciences, The University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
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29
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Topart C, Werner E, Arimondo PB. Wandering along the epigenetic timeline. Clin Epigenetics 2020; 12:97. [PMID: 32616071 PMCID: PMC7330981 DOI: 10.1186/s13148-020-00893-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Increasing life expectancy but also healthspan seems inaccessible as of yet but it may become a reality in the foreseeable future. To extend lifespan, it is essential to unveil molecular mechanisms involved in ageing. As for healthspan, a better understanding of the mechanisms involved in age-related pathologies is crucial. MAIN BODY We focus on the epigenetic side of ageing as ageing is traced by specific epigenetic patterns and can be measured by epigenetic clocks. We discuss to what extent exposure to environmental factor, such as alcohol use, unhealthy diet, tobacco and stress, promotes age-related conditions. We focused on inflammation, cancer and Alzheimer's disease. Finally, we discuss strategies to reverse time based on epigenetic reprogramming. CONCLUSIONS Reversibility of the epigenetic marks makes them promising targets for rejuvenation. For this purpose, a better understanding of the epigenetic mechanisms underlying ageing is essential. Epigenetic clocks were successfully designed to monitor these mechanisms and the influence of environmental factors. Further studies on age-related diseases should be conducted to determine their epigenetic signature, but also to pinpoint the defect in the epigenetic machinery and thereby identify potential therapeutic targets. As for rejuvenation, epigenetic reprogramming is still at an early stage.
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Affiliation(s)
- Clémence Topart
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond, 75005, Paris, France
- PSL Research University, 60 Rue Mazarine, 75006, Paris, France
| | - Emilie Werner
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond, 75005, Paris, France
- PSL Research University, 60 Rue Mazarine, 75006, Paris, France
| | - Paola B Arimondo
- EpiCBio, Epigenetic Chemical Biology, Department Structural Biology and Chemistry, Institut Pasteur, CNRS UMR n°3523, 28 rue du Dr Roux, 75015, Paris, France.
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30
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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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31
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Mio C, Bulotta S, Russo D, Damante G. Reading Cancer: Chromatin Readers as Druggable Targets for Cancer Treatment. Cancers (Basel) 2019; 11:cancers11010061. [PMID: 30634442 PMCID: PMC6356452 DOI: 10.3390/cancers11010061] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/30/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023] Open
Abstract
The epigenetic machinery deputed to control histone post-translational modifications is frequently dysregulated in cancer cells. With epigenetics being naturally reversible, it represents a good target for therapies directed to restore normal gene expression. Since the discovery of Bromodomain and Extra Terminal (BET) inhibitors, a great effort has been spent investigating the effects of chromatin readers’ inhibition, specifically the class of proteins assigned to bind acetylated and methylated residues. So far, focused studies have been produced on epigenetic regulation, dissecting a specific class of epigenetic-related proteins or investigating epigenetic therapy in a specific tumor type. In this review, recent steps toward drug discovery on the different classes of chromatin readers have been outlined, highlighting the pros and cons of current therapeutic approaches.
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Affiliation(s)
- Catia Mio
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
| | - Stefania Bulotta
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Diego Russo
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Giuseppe Damante
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
- Medical Genetics Institute, University Hospital of Udine, 33100 Udine, Italy.
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Montesanto A, D'Aquila P, Rossano V, Passarino G, Bellizzi D. Mini Nutritional Assessment Scores Indicate Higher Risk for Prospective Mortality and Contrasting Correlation With Age-Related Epigenetic Biomarkers. Front Endocrinol (Lausanne) 2019; 10:672. [PMID: 31632350 PMCID: PMC6779723 DOI: 10.3389/fendo.2019.00672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 09/16/2019] [Indexed: 02/03/2023] Open
Abstract
The plasticity of the individual epigenetic landscape that goes to countless rearrangements throughout life is closely the reflection of environmental factors such as chemical exposure, socio-economic status and nutrient intakes both early and late in life. The Mini Nutritional Assessment (MNA) is a well-validated tool for assessing malnutrition in old people. It includes 6 (MNA-SF) or 18 (MNA-LF) self-reported questions derived from general, anthropometric, dietary, and self- assessment. We evaluated the association between the nutritional status, as measured by MNA, and methylation biomarkers we previously demonstrated to be associated with chronological and biological age in human. We found that malnutrition is positively correlated with DNA methylation status at the global level, in line with our previous reports. On the contrary, most of the sites located within specific genes, which were previously reported to be correlated with chronological and biological aging, showed to be not affected by malnutrition, or even to have correlations with malnutrition opposite to those previously reported with frailty. These results may suggest that malnutrition is among the first effects of disability and other age- related problems and a generalized non-specific epigenetic remodeling may be the initial response of the organism. By contrast, the fine remodeling of specific genomic sites is scarcely affected by malnutrition and may respond to a more complex interaction of different factors. Therefore, although malnutrition in the elderly is certainly a risk factor for survival, this is partially independent of the aging process of the organism which leads to the methylation remodeling previously described to measure chronological and biological aging.
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Abstract
Research in the field of gerontology has traditionally focused on later life stages. There is increasing evidence, however, that both the rate of age-related functional decline and the later-life health status can be programmed during early development. The central role of epigenetic mechanisms (methylation of DNA, histone modifications and regulation by non-coding RNAs) in mediating these long-term effects has been elucidated. Both rate and direction of age-associated change of epigenetic patterns (“epigenetic drift”) were shown to be largely dependent on early-life environmental conditions. Inter-individual divergences in epigenetic profiles may arise following the stochastic errors in maintaining epigenetic marks, but they may also be adaptively mediated by specific environmental cues. Recent cohort studies indicate that ticking rate of epigenetic clock, estimated by a DNA methylation-based methods, may be developmentally adjusted, and that individual’s discrepancies among epigenetic and chronological age would be likely programmed early in development. In this Perspective article, recent findings suggesting the importance of early-life determinants for life-course dynamics of epigenetic drift are summarized and discussed.
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Vaiserman A, Koliada A, Lushchak O. Developmental programming of aging trajectory. Ageing Res Rev 2018; 47:105-122. [PMID: 30059788 DOI: 10.1016/j.arr.2018.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 12/12/2022]
Abstract
There is accumulating evidence that aging phenotype and longevity may be developmentally programmed. Main mechanisms linking developmental conditions to later-life health outcomes include persistent changes in epigenetic regulation, (re)programming of major endocrine axes such as growth hormone/insulin-like growth factor axis and hypothalamic-pituitary-adrenal axis and also early-life immune maturation. Recently, evidence has also been generated on the role of telomere biology in developmental programming of aging trajectory. In addition, persisting changes of intestinal microbiota appears to be crucially involved in these processes. In this review, experimental and epidemiological evidence on the role of early-life conditions in programming of aging phenotypes are presented and mechanisms potentially underlying these associations are discussed.
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35
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Coppedè F, Stoccoro A, Lazzarotti A, Spisni R, Migliore L. Investigation of GHSR and GHRL methylation in colorectal cancer. Epigenomics 2018; 10:1525-1539. [PMID: 29963901 DOI: 10.2217/epi-2018-0030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM To investigate GHSR and GHRL methylation in 73 pairs of colorectal cancer (CRC) tissues and healthy adjacent mucosa. METHODS Methylation was assessed with methylation-sensitive high-resolution melting. RESULTS GHSR was significantly hypermethylated in CRC tissues than in healthy mucosa (p < 1 × 10-5), but no significant changes of GHRL methylation were observed. GHSR hypermethylation was already detectable at the adenoma stage and maintained in later stages independently of age, gender, anatomical location, histological grading, MLH1 deficiency, as well as of major polymorphisms in folate-pathway genes, yielding an area under the curve of 0.824 for discriminating cancers from respective non-neoplastic mucosa specimens. CONCLUSION GHSR hypermethylation occurs early in CRC, but is not paralleled by significant changes of GHRL methylation.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
| | - Andrea Stoccoro
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
| | - Alessandro Lazzarotti
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
| | - Roberto Spisni
- Department of Surgery, Medical, Molecular, & Critical Area Pathology, University of Pisa, Pisa, Italy
| | - Lucia Migliore
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
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Ray D, Yung R. Immune senescence, epigenetics and autoimmunity. Clin Immunol 2018; 196:59-63. [PMID: 29654845 DOI: 10.1016/j.clim.2018.04.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022]
Abstract
Aging of the immune system in humans and animals is characterized by a decline in both adaptive and innate immune responses. Paradoxically, aging is also associated with a state of chronic inflammation ("inflammaging") and an increased likelihood of developing autoimmune diseases. Epigenetic changes in non-dividing and dividing cells, including immune cells, due to environmental factors contribute to the inflammation and autoimmunity that characterize both the state and diseases of aging. Here, we review the epigenetic mechanisms involved in the development of immune senescence and autoimmunity in old age.
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Affiliation(s)
- Donna Ray
- Division of Rheumatology, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, United States
| | - Raymond Yung
- Division of Geriatric and Palliative Medicine, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, United States.
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The VEGFA156b isoform is dysregulated in senescent endothelial cells and may be associated with prevalent and incident coronary heart disease. Clin Sci (Lond) 2018; 132:313-325. [PMID: 29330351 DOI: 10.1042/cs20171556] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/15/2017] [Accepted: 01/08/2018] [Indexed: 12/19/2022]
Abstract
Coronary heart disease (CHD) is a leading cause of morbidity in people over 65 years of age; >40% of all deaths are due to this condition. The association between increasing age and CHD is well documented; the accumulation of senescent cells in cardiac and vascular tissues may represent one factor underpinning this observation. We aimed to identify senescence-related expression changes in primary human senescent cardiomyocytes and endothelial cells and to relate transcript expression in peripheral blood leucocytes to prevalent and incident CHD in the InCHIANTI study of aging. We quantified splicing factor expression and splicing patterns of candidate transcripts in proliferative and senescent later passage endothelial cells and cardiomyocytes using qRTPCR. Senescence-associated isoforms also expressed in peripheral blood leucocytes were then examined for associations with CHD status in 134 pairs of age, sex and BMI-matched CHD cases and controls. Splicing factor expression was dysregulated in senescent cardiomyocytes, as previously reported for endothelial cells, as was the expression of alternatively expressed cardiac and vascular candidate genes in both cell types. We found nominal associations between the expression of VEGFA156b and FNI-EIIIIA isoforms in peripheral blood mRNA and CHD status. Dysregulated splicing factor expression is a key feature of senescent cardiomyocytes and endothelial cells. Altered splicing of key cardiac or endothelial genes may contribute to the risk of CHD in the human population.
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Abstract
Social epigenomics is an area of science that evaluates why and how different social factors and processes affect different components of the epigenome. As it happens with most of the new areas in science, social epigenetics being a relatively new area, only limited progress has been made. However, the potential of implicating social epigenomics in improving health and health related policies is tremendous. Epidemiologic studies evaluating social, behavior, family, and environmental factors have helped understand social inequality and develop the area of social epigenomics. Most of the information in social epidemiology has been gathered from genetic studies. Now the time has come that we may apply similar approaches in social epigenomics because technologies of determining methylation, histone, and noncoding RNA profiling are well developed. The focus of this chapter is to understand the role of epigenetic regulation in social experiences at various stages in life due to altered function of genes and affecting health in populations with different races/ethnicity. Here we discuss the current challenges and opportunities in the field.
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Affiliation(s)
- Krishna Banaudha
- Department of Biochemistry and Molecular Biology, School of Medicine and Public Health, George Washington University, Washington, DC, USA.
| | - Vineet Kumar
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
| | - Mukesh Verma
- Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, MD, USA
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Karpinski P, Pesz K, Sasiadek MM. Pan-cancer analysis reveals presence of pronounced DNA methylation drift in CpG island methylator phenotype clusters. Epigenomics 2017; 9:1341-1352. [PMID: 28960094 DOI: 10.2217/epi-2017-0070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AIM To provide characteristics of major genomic correlates in CpG island methylator phenotype-high (CIMP-H) subgroups in relation to corresponding non-CIMP-H subgroups by use of phenotypic, DNA methylation and RNAseq data. MATERIALS & METHODS Twenty-three datasets generated by The Cancer Genome Atlas project encompassing over 7200 unique samples were analyzed. We identified 23 CIMP-H clusters by use of unsupervised clustering. RESULTS & CONCLUSION More than 90% of CIMP-H clusters were significantly associated with accelerated epigenetic mitotic clock, demethylation of enhancer sites, backbone and repetitive sequences. Pronounced epigenetic drift observed in majority of CIMP-H subgroups may be related to increased cell division rate, which leads to expansion of DNA methylation errors. This may explain pan-cancer mechanism of establishing CIMP-H in majority of tissue types.
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Affiliation(s)
- Pawel Karpinski
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Karolina Pesz
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
| | - Maria M Sasiadek
- Department of Genetics, Wroclaw Medical University, Wroclaw, Poland
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Abstract
In mammals, caloric restriction consistently results in extended lifespan. Epigenetic information encoded by DNA methylation is tightly regulated, but shows a striking drift associated with age that includes both gains and losses of DNA methylation at various sites. Here, we report that epigenetic drift is conserved across species and the rate of drift correlates with lifespan when comparing mice, rhesus monkeys, and humans. Twenty-two to 30-year-old rhesus monkeys exposed to 30% caloric restriction since 7–14 years of age showed attenuation of age-related methylation drift compared to ad libitum-fed controls such that their blood methylation age appeared 7 years younger than their chronologic age. Even more pronounced effects were seen in 2.7–3.2-year-old mice exposed to 40% caloric restriction starting at 0.3 years of age. The effects of caloric restriction on DNA methylation were detectable across different tissues and correlated with gene expression. We propose that epigenetic drift is a determinant of lifespan in mammals. Caloric restriction has been shown to increase lifespan in mammals. Here, the authors provide evidence that age-related methylation drift correlates with lifespan and that caloric restriction in mice and rhesus monkeys results in attenuation of age-related methylation drift.
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