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Becker J, Bühren V, Schmelzer L, Reckert A, Eickhoff SB, Ritz S, Naue J. Molecular age prediction using skull bone samples from individuals with and without signs of decomposition: a multivariate approach combining analysis of posttranslational protein modifications and DNA methylation. Int J Legal Med 2024:10.1007/s00414-024-03314-z. [PMID: 39256256 DOI: 10.1007/s00414-024-03314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/13/2024] [Indexed: 09/12/2024]
Abstract
The prediction of the chronological age of a deceased individual at time of death can provide important information in case of unidentified bodies. The methodological possibilities in these cases depend on the availability of tissues, whereby bones are preserved for a long time due to their mineralization under normal environmental conditions. Age-dependent changes in DNA methylation (DNAm) as well as the accumulation of pentosidine (Pen) and D-aspartic acid (D-Asp) could be useful molecular markers for age prediction. A combination of such molecular clocks into one age prediction model seems favorable to minimize inter- and intra-individual variation. We therefore developed (I) age prediction models based on the three molecular clocks, (II) examined the improvement of age prediction by combination, and (III) investigated if samples with signs of decomposition can also be examined using these three molecular clocks. Skull bone from deceased individuals was collected to obtain a training dataset (n = 86), and two independent test sets (without signs of decomposition: n = 44, with signs of decomposition: n = 48). DNAm of 6 CpG sites in ELOVL2, KLF14, PDE4C, RPA2, TRIM59 and ZYG11A was analyzed using massive parallel sequencing (MPS). The D-Asp and Pen contents were analyzed by high performance liquid chromatography (HPLC). Age prediction models based on ridge regression were developed resulting in mean absolute errors (MAEs)/root mean square errors (RMSE) of 5.5years /6.6 years (DNAm), 7.7 years /9.3 years (Pen) and 11.7 years /14.6 years (D-Asp) in the test set. Unsurprisingly, a general lower accuracy for the DNAm, D-Asp, and Pen models was observed in samples from decomposed bodies (MAE: 7.4-11.8 years, RMSE: 10.4-15.4 years). This reduced accuracy could be caused by multiple factors with different impact on each molecular clock. To acknowledge general changes due to decomposition, a pilot model for a possible age prediction based on the decomposed samples as training set improved the accuracy evaluated by leave-one-out-cross validation (MAE: 6.6-12 years, RMSE: 8.1-15.9 years). The combination of all three molecular age clocks did reveal comparable MAE and RMSE results to the pure analysis of the DNA methylation for the test set without signs of decomposition. However, an improvement by the combination of all three clocks was possible for the decomposed samples, reducing especially the deviation in case of outliers in samples with very high decomposition and low DNA content. The results demonstrate the general potential in a combined analysis of different molecular clocks in specific cases.
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Affiliation(s)
- J Becker
- Institute of Legal Medicine, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | - V Bühren
- Institute of Legal Medicine, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | - L Schmelzer
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany
| | - A Reckert
- Institute of Legal Medicine, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
| | - S B Eickhoff
- Institute for Systems Neuroscience, University Hospital Duesseldorf, 40225, Duesseldorf, Germany
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Juelich, 52428, Juelich, Germany
| | - S Ritz
- Institute of Legal Medicine, University Hospital Duesseldorf, 40225, Duesseldorf, Germany.
| | - J Naue
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79104, Freiburg, Germany.
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Longtin A, Watowich MM, Sadoughi B, Petersen RM, Brosnan SF, Buetow K, Cai Q, Gurven MD, Highland HM, Huang YT, Kaplan H, Kraft TS, Lim YAL, Long J, Melin AD, Roberson J, Ng KS, Stieglitz J, Trumble BC, Venkataraman VV, Wallace IJ, Wu J, Snyder-Mackler N, Jones A, Bick AG, Lea AJ. Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612068. [PMID: 39314398 PMCID: PMC11419010 DOI: 10.1101/2024.09.09.612068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Characterizing DNA methylation patterns is important for addressing key questions in evolutionary biology, geroscience, and medical genomics. While costs are decreasing, whole-genome DNA methylation profiling remains prohibitively expensive for most population-scale studies, creating a need for cost-effective, reduced representation approaches (i.e., assays that rely on microarrays, enzyme digests, or sequence capture to target a subset of the genome). Most common whole genome and reduced representation techniques rely on bisulfite conversion, which can damage DNA resulting in DNA loss and sequencing biases. Enzymatic methyl sequencing (EM-seq) was recently proposed to overcome these issues, but thorough benchmarking of EM-seq combined with cost-effective, reduced representation strategies has not yet been performed. To do so, we optimized Targeted Methylation Sequencing protocol (TMS)-which profiles ∼4 million CpG sites-for miniaturization, flexibility, and multispecies use at a cost of ∼$80. First, we tested modifications to increase throughput and reduce cost, including increasing multiplexing, decreasing DNA input, and using enzymatic rather than mechanical fragmentation to prepare DNA. Second, we compared our optimized TMS protocol to commonly used techniques, specifically the Infinium MethylationEPIC BeadChip (n=55 paired samples) and whole genome bisulfite sequencing (n=6 paired samples). In both cases, we found strong agreement between technologies (R² = 0.97 and 0.99, respectively). Third, we tested the optimized TMS protocol in three non-human primate species (rhesus macaques, geladas, and capuchins). We captured a high percentage (mean=77.1%) of targeted CpG sites and produced methylation level estimates that agreed with those generated from reduced representation bisulfite sequencing (R² = 0.98). Finally, we applied our protocol to profile age-associated DNA methylation variation in two subsistence-level populations-the Tsimane of lowland Bolivia and the Orang Asli of Peninsular Malaysia-and found age-methylation patterns that were strikingly similar to those reported in high income cohorts, despite known differences in age-health relationships between lifestyle contexts. Altogether, our optimized TMS protocol will enable cost-effective, population-scale studies of genome-wide DNA methylation levels across human and non-human primate species.
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Li X, Meng X, Zhao RR, Xu YH. A genome-wide methylation analysis of Chinese Han patients with chronic insomnia disorder. Sleep Breath 2024:10.1007/s11325-024-03145-7. [PMID: 39186098 DOI: 10.1007/s11325-024-03145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/25/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND As the most common sleep disorder, chronic insomnia disorder (CID) has become a global health burden to the public. However, it remains unclear about the pathogenesis of this disease. Epigenetic changes may provide important insights into the gene-environment interaction in CID. Therefore, this study was conducted to investigate the DNA methylation pattern in CID and reveal the epigenetic mechanism of this disease. METHODS In this study, whole blood DNA was extracted from 8 CID patients (the CID group) and 8 healthy controls (the control group), respectively. Besides, genome-wide DNA methylation was detected by Illumina Human Methylation 850 K Beadchip. Moreover, the sleep quality and insomnia severity were evaluated by the Pittsburgh Sleep Quality Index (PSQI) and Insomnia Severity Index (ISI), respectively. RESULTS A total of 369 differentially methylated positions (DMPs) and 23 differentially methylated regions (DMRs) were identified between the CID and control groups. LHX6 was identified as the most important differentially methylated gene (DMG). The Gene Ontology (GO) analysis results corroborated that DMPs were significantly enriched in 105 GO terms, including cell signaling, homogenous cell adhesion of plasma membrane adhesion molecules, nervous system development, cell adhesion, and calcium ion binding. In addition, it was demonstrated that DMPs were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including the hippo signaling pathway, Ras signaling pathway, and vitamin B6 metabolism. The DMR-related GO analysis results revealed the positive regulation of protein kinase activities. CONCLUSIONS DNA methylation plays a critical role in the development of CID, and LHX6 is validated to be an important DMG.
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Affiliation(s)
- Xiao Li
- Department of Sleep Medicine, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, 453002, China
| | - Xue Meng
- Department of Sleep Medicine, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, 453002, China
| | - Rong-Rong Zhao
- The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
| | - Ya-Hui Xu
- Department of Sleep Medicine, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, 453002, China.
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4
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Watowich MM, Costa CE, Chiou KL, Goldman EA, Petersen RM, Patterson S, Martínez MI, Sterner KN, Horvath JE, Montague MJ, Platt ML, Brent LJN, Higham JP, Lea AJ, Snyder-Mackler N. Immune gene regulation is associated with age and environmental adversity in a nonhuman primate. Mol Ecol 2024:e17445. [PMID: 39032090 DOI: 10.1111/mec.17445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/27/2024] [Accepted: 06/14/2024] [Indexed: 07/22/2024]
Abstract
Phenotypic aging is ubiquitous across mammalian species, suggesting shared underlying mechanisms of aging. Aging is linked to molecular changes to DNA methylation and gene expression, and environmental factors, such as severe external challenges or adversities, can moderate these age-related changes. Yet, it remains unclear whether environmental adversities affect gene regulation via the same molecular pathways as chronological, or 'primary', aging. Investigating molecular aging in naturalistic animal populations can fill this gap by providing insight into shared molecular mechanisms of aging and the effects of a greater diversity of environmental adversities - particularly those that can be challenging to study in humans or laboratory organisms. Here, we characterised molecular aging - specifically, CpG methylation - in a sample of free-ranging rhesus macaques living off the coast of Puerto Rico (n samples = 571, n individuals = 499), which endured a major hurricane during our study. Age was associated with methylation at 78,661 sites (31% of all sites tested). Age-associated hypermethylation occurred more frequently in areas of active gene regulation, while hypomethylation was enriched in regions that show less activity in immune cells, suggesting these regions may become de-repressed in older individuals. Age-associated hypomethylation also co-occurred with increased chromatin accessibility while hypermethylation showed the opposite trend, hinting at a coordinated, multi-level loss of epigenetic stability during aging. We detected 32,048 CpG sites significantly associated with exposure to a hurricane, and these sites overlapped age-associated sites, most strongly in regulatory regions and most weakly in quiescent regions. Together, our results suggest that environmental adversity may contribute to aging-related molecular phenotypes in regions of active gene transcription, but that primary aging has specific signatures in non-regulatory regions.
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Affiliation(s)
- Marina M Watowich
- Department of Biology, University of Washington, Seattle, Washington, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Christina E Costa
- Department of Anthropology, New York University, New York, New York, USA
- New York Consortium in Evolutionary Primatology, New York, New York, USA
| | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Elisabeth A Goldman
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Rachel M Petersen
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Sam Patterson
- Department of Anthropology, New York University, New York, New York, USA
| | - Melween I Martínez
- Caribbean Primate Research Center, Unit of Comparative Medicine, University of Puerto Rico, San Juan, Puerto Rico, USA
| | - Kirstin N Sterner
- Department of Anthropology, University of Oregon, Eugene, Oregon, USA
| | - Julie E Horvath
- Research and Collections Section, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael L Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Psychology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Marketing Department, Wharton School of Business, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - James P Higham
- Department of Anthropology, New York University, New York, New York, USA
- New York Consortium in Evolutionary Primatology, New York, New York, USA
| | - Amanda J Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
- Neurodegenerative Disease Research Center, Arizona State University, Tempe, Arizona, USA
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5
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Kojić D, Spremo J, Đorđievski S, Čelić T, Vukašinović E, Pihler I, Purać J. Spermidine supplementation in honey bees: Autophagy and epigenetic modifications. PLoS One 2024; 19:e0306430. [PMID: 38950057 PMCID: PMC11216588 DOI: 10.1371/journal.pone.0306430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024] Open
Abstract
Polyamines (PAs), including putrescine (Put), spermidine (Spd), and spermine (Spm), are essential polycations with wide-ranging roles in cellular functions. PA levels decline with age, making exogenous PA supplementation, particularly Spd, an intriguing prospect. Previous research in honey bees demonstrated that millimolar Spd added to their diet increased lifespan and reinforced oxidative resilience. The present study is aimed to assess the anti-aging effects of spermidine supplementation at concentrations of 0.1 and 1 mM in honey bees, focusing on autophagy and associated epigenetic changes. Results showed a more pronounced effect at the lower Spd concentration, primarily in the abdomen. Spd induced site-specific histone 3 hypoacetylation at sites K18 and 27, hyperacetylation at K9, with no change at K14 in the entire body. Additionally, autophagy-related genes (ATG3, 5, 9, 13) and genes associated with epigenetic changes (HDAC1, HDAC3, SIRT1, KAT2A, KAT6B, P300, DNMT1A, DNMT1B) were upregulated in the abdomens of honey bees. In conclusion, our findings highlight profound epigenetic changes and autophagy promotion due to spermidine supplementation, contributing to increased honey bee longevity. Further research is needed to fully understand the precise mechanisms and the interplay between epigenetic alterations and autophagy in honey bees, underscoring the significance of autophagy as a geroprotective mechanism.
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Affiliation(s)
- Danijela Kojić
- Faculty of Science, Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Jelena Spremo
- Faculty of Science, Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Srđana Đorđievski
- Faculty of Science, Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Tatjana Čelić
- Faculty of Science, Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Elvira Vukašinović
- Faculty of Science, Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
| | - Ivan Pihler
- Faculty of Agriculture, Department of Animal Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Jelena Purać
- Faculty of Science, Department of Biology and Ecology, University of Novi Sad, Novi Sad, Serbia
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6
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Baranová I, Samec M, Dvorská D, Šťastný I, Janíková K, Kašubová I, Hornáková A, Lukáčová E, Kapinová A, Biringer K, Halašová E, Danková Z. Droplet digital PCR analysis of CDH13 methylation status in Slovak women with invasive ductal breast cancer. Sci Rep 2024; 14:14700. [PMID: 38926485 PMCID: PMC11208553 DOI: 10.1038/s41598-024-65580-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/21/2024] [Indexed: 06/28/2024] Open
Abstract
Identifying novel epigenetic biomarkers is a promising way to improve the clinical management of patients with breast cancer. Our study aimed to determine the methylation pattern of 25 tumor suppressor genes (TSG) and select the best methylation biomarker associated with clinicopathological features in the cohort of Slovak patients diagnosed with invasive ductal carcinoma (IDC). Overall, 166 formalin-fixed, paraffin-embedded (FFPE) tissues obtained from patients with IDC were included in the study. The methylation status of the promoter regions of 25 TSG was analyzed using semiquantitative methylation-specific MLPA (MS-MLPA). We identified CDH13 as the most frequently methylated gene in our cohort of patients. Further analysis by ddPCR confirmed an increased level of methylation in the promoter region of CDH13. A significant difference in CDH13 methylation levels was observed between IDC molecular subtypes LUM A versus HER2 (P = 0.0116) and HER2 versus TNBC (P = 0.0234). In addition, significantly higher methylation was detected in HER2+ versus HER2- tumors (P = 0.0004) and PR- versus PR+ tumors (P = 0.0421). Our results provide evidence that alteration in CDH13 methylation is associated with clinicopathological features in the cohort of Slovak patients with IDC. In addition, using ddPCR as a methylation-sensitive method represents a promising approach characterized by higher precision and technical simplicity to measure the methylation of target CpGs in CDH13 compared to other conventional methods such as MS-MLPA.
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Affiliation(s)
- Ivana Baranová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
- Department of Pathological Physiology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
- Biobank for Cancer and Rare Diseases, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Marek Samec
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia.
- Department of Medical Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia.
| | - Dana Dvorská
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Igor Šťastný
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin and Martin University Hospital, Comenius University in Bratislava, Martin, Slovakia
| | - Katarína Janíková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ivana Kašubová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Hornáková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Lukáčová
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Kapinová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Kamil Biringer
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine in Martin and Martin University Hospital, Comenius University in Bratislava, Martin, Slovakia
| | - Erika Halašová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Danková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
- Biobank for Cancer and Rare Diseases, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
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7
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Olecka M, van Bömmel A, Best L, Haase M, Foerste S, Riege K, Dost T, Flor S, Witte OW, Franzenburg S, Groth M, von Eyss B, Kaleta C, Frahm C, Hoffmann S. Nonlinear DNA methylation trajectories in aging male mice. Nat Commun 2024; 15:3074. [PMID: 38594255 PMCID: PMC11004021 DOI: 10.1038/s41467-024-47316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024] Open
Abstract
Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigate the methylation trajectories of male mouse colon at five different time points of aging. Our study indicates the existence of sudden hypermethylation events at specific stages of life. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 months) and mid-to-late-life (15-24 months) transitions, separating the rodents' life into three stages. These nonlinear methylation dynamics predominantly affect genes associated with the nervous system and enrich in bivalently marked chromatin regions. Based on groups of nonlinearly modified loci, we construct a clock-like classifier STageR (STage of aging estimatoR) that accurately predicts murine epigenetic stage. We demonstrate the universality of our clock in an independent mouse cohort and with publicly available datasets.
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Affiliation(s)
- Maja Olecka
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Alena van Bömmel
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Lena Best
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Madlen Haase
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Silke Foerste
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Konstantin Riege
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Thomas Dost
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Stefano Flor
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Otto W Witte
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Marco Groth
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Björn von Eyss
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Christiane Frahm
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Steve Hoffmann
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
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8
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Di Giorgio E, Ranzino L, Tolotto V, Dalla E, Burelli M, Gualandi N, Brancolini C. Transcription of endogenous retroviruses in senescent cells contributes to the accumulation of double-stranded RNAs that trigger an anti-viral response that reinforces senescence. Cell Death Dis 2024; 15:157. [PMID: 38383514 PMCID: PMC10882003 DOI: 10.1038/s41419-024-06548-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
An important epigenetic switch marks the onset and maintenance of senescence. This allows transcription of the genetic programs that arrest the cell cycle and alter the microenvironment. Transcription of endogenous retroviruses (ERVs) is also a consequence of this epigenetic switch. In this manuscript, we have identified a group of ERVs that are epigenetically silenced in proliferating cells but are upregulated during replicative senescence or during various forms of oncogene-induced senescence, by RAS and Akt, or after HDAC4 depletion. In a HDAC4 model of senescence, removal of the repressive histone mark H3K27me3 is the plausible mechanism that allows the transcription of intergenic ERVs during senescence. We have shown that ERVs contribute to the accumulation of dsRNAs in senescence, which can initiate the antiviral response via the IFIH1-MAVS signaling pathway and thus contribute to the maintenance of senescence. This pathway, and MAVS in particular, plays an active role in shaping the microenvironment and maintaining growth arrest, two essential features of the senescence program.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Liliana Ranzino
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Vanessa Tolotto
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Matteo Burelli
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Nicolò Gualandi
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100, Udine, Italy.
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9
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Tenchov R, Sasso JM, Wang X, Zhou QA. Aging Hallmarks and Progression and Age-Related Diseases: A Landscape View of Research Advancement. ACS Chem Neurosci 2024; 15:1-30. [PMID: 38095562 PMCID: PMC10767750 DOI: 10.1021/acschemneuro.3c00531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 01/04/2024] Open
Abstract
Aging is a dynamic, time-dependent process that is characterized by a gradual accumulation of cell damage. Continual functional decline in the intrinsic ability of living organisms to accurately regulate homeostasis leads to increased susceptibility and vulnerability to diseases. Many efforts have been put forth to understand and prevent the effects of aging. Thus, the major cellular and molecular hallmarks of aging have been identified, and their relationships to age-related diseases and malfunctions have been explored. Here, we use data from the CAS Content Collection to analyze the publication landscape of recent aging-related research. We review the advances in knowledge and delineate trends in research advancements on aging factors and attributes across time and geography. We also review the current concepts related to the major aging hallmarks on the molecular, cellular, and organismic level, age-associated diseases, with attention to brain aging and brain health, as well as the major biochemical processes associated with aging. Major age-related diseases have been outlined, and their correlations with the major aging features and attributes are explored. We hope this review will be helpful for apprehending the current knowledge in the field of aging mechanisms and progression, in an effort to further solve the remaining challenges and fulfill its potential.
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Affiliation(s)
- Rumiana Tenchov
- CAS, a Division of the American Chemical
Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Janet M. Sasso
- CAS, a Division of the American Chemical
Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Xinmei Wang
- CAS, a Division of the American Chemical
Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Qiongqiong Angela Zhou
- CAS, a Division of the American Chemical
Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
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10
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Jiraboonsri S, Hemvipat P, Kamolratanakul S, Bhummaphan N, Siritientong T, Kitkumthorn N, Mutirangura A, Meevassana J. CpG methylation changes in Alu repetitive sequences in normal aging due to diastolic hypertension in human dermal fibroblasts from the facial area. Biomed Rep 2024; 20:5. [PMID: 38222864 PMCID: PMC10784876 DOI: 10.3892/br.2023.1693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/02/2023] [Indexed: 01/16/2024] Open
Abstract
Aging fibroblasts, an important factor contributing to skin aging, are affected by numerous mechanisms, including alterations in DNA methylation and age-related diseases. The current study aimed to investigate the role of Alu methylation in aging fibroblasts and hypertension. The Alu methylation levels in dermal fibroblasts obtained from patients of different ages and blood pressure status were analyzed using the combined bisulfite restriction analysis technique. An inverse correlation was observed between Alu methylation in dermal fibroblasts and patient age. Dermal fibroblasts from the high-normal diastolic blood pressure group had higher Alu methylation levels compared with those from the normal group. The findings of the present study suggest that Alu methylation alterations can be observed with chronological aging and hypertension, and are a potential aging marker or therapeutic target.
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Affiliation(s)
- Suvinai Jiraboonsri
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panicha Hemvipat
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supitcha Kamolratanakul
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Narumol Bhummaphan
- College of Public Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tippawan Siritientong
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
| | - Apiwat Mutirangura
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jiraroch Meevassana
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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11
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Marson F, Zampieri M, Verdone L, Bacalini MG, Ravaioli F, Morandi L, Chiarella SG, Vetriani V, Venditti S, Caserta M, Raffone A, Dotan Ben-Soussan T, Reale A. Quadrato Motor Training (QMT) is associated with DNA methylation changes at DNA repeats: A pilot study. PLoS One 2023; 18:e0293199. [PMID: 37878626 PMCID: PMC10599555 DOI: 10.1371/journal.pone.0293199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/07/2023] [Indexed: 10/27/2023] Open
Abstract
The control of non-coding repeated DNA by DNA methylation plays an important role in genomic stability, contributing to health and healthy aging. Mind-body practices can elicit psychophysical wellbeing via epigenetic mechanisms, including DNA methylation. However, in this context the effects of movement meditations have rarely been examined. Consequently, the current study investigates the effects of a specifically structured movement meditation, called the Quadrato Motor Training (QMT) on psychophysical wellbeing and on the methylation level of repeated sequences. An 8-week daily QMT program was administered to healthy women aged 40-60 years and compared with a passive control group matched for gender and age. Psychological well-being was assessed within both groups by using self-reporting scales, including the Meaning in Life Questionnaire [MLQ] and Psychological Wellbeing Scale [PWB]). DNA methylation profiles of repeated sequences (ribosomal DNA, LINE-1 and Alu) were determined in saliva samples by deep-sequencing. In contrast to controls, the QMT group exhibited increased Search for Meaning, decreased Presence of Meaning and increased Positive Relations, suggesting that QMT may lessen the automatic patterns of thinking. In the QMT group, we also found site-specific significant methylation variations in ribosomal DNA and LINE-1 repeats, consistent with increased genome stability. Finally, the correlations found between changes in methylation and psychometric indices (MLQ and PWB) suggest that the observed epigenetic and psychological changes are interrelated. Collectively, the current results indicate that QMT may improve psychophysical health trajectories by influencing the DNA methylation of specific repetitive sequences.
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Affiliation(s)
- Fabio Marson
- Research Institute for Neuroscience, Education and Didactics, Fondazione Patrizio Paoletti, Assisi, Italy
- Neuroimaging Laboratory, Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Loredana Verdone
- CNR Institute of Molecular Biology and Pathology, National Council of Research (CNR), Rome, Italy
| | - Maria Giulia Bacalini
- Brain Aging Laboratory, IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Francesco Ravaioli
- Dep. of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Luca Morandi
- Dep. of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
- Functional and Molecular Neuroimaging Unit, IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Salvatore Gaetano Chiarella
- Institute of Sciences and Technologies of Cognition (ISTC), National Council of Research (CNR), Rome, Italy
- Department of Psychology, Sapienza University of Rome, Rome, Italy
| | - Valerio Vetriani
- Dept. of Biology and biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Sabrina Venditti
- Dept. of Biology and biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
| | - Micaela Caserta
- CNR Institute of Molecular Biology and Pathology, National Council of Research (CNR), Rome, Italy
| | - Antonino Raffone
- Department of Psychology, Sapienza University of Rome, Rome, Italy
| | - Tal Dotan Ben-Soussan
- Research Institute for Neuroscience, Education and Didactics, Fondazione Patrizio Paoletti, Assisi, Italy
| | - Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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12
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Crochemore C, Chica C, Garagnani P, Lattanzi G, Horvath S, Sarasin A, Franceschi C, Bacalini MG, Ricchetti M. Epigenomic signature of accelerated ageing in progeroid Cockayne syndrome. Aging Cell 2023; 22:e13959. [PMID: 37688320 PMCID: PMC10577576 DOI: 10.1111/acel.13959] [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: 05/17/2022] [Revised: 07/16/2023] [Accepted: 07/31/2023] [Indexed: 09/10/2023] Open
Abstract
Cockayne syndrome (CS) and UV-sensitive syndrome (UVSS) are rare genetic disorders caused by mutation of the DNA repair and multifunctional CSA or CSB protein, but only CS patients display a progeroid and neurodegenerative phenotype, providing a unique conceptual and experimental paradigm. As DNA methylation (DNAm) remodelling is a major ageing marker, we performed genome-wide analysis of DNAm of fibroblasts from healthy, UVSS and CS individuals. Differential analysis highlighted a CS-specific epigenomic signature (progeroid-related; not present in UVSS) enriched in three categories: developmental transcription factors, ion/neurotransmitter membrane transporters and synaptic neuro-developmental genes. A large fraction of CS-specific DNAm changes were associated with expression changes in CS samples, including in previously reported post-mortem cerebella. The progeroid phenotype of CS was further supported by epigenomic hallmarks of ageing: the prediction of DNAm of repetitive elements suggested an hypomethylation of Alu sequences in CS, and the epigenetic clock returned a marked increase in CS biological age respect to healthy and UVSS cells. The epigenomic remodelling of accelerated ageing in CS displayed both commonalities and differences with other progeroid diseases and regular ageing. CS shared DNAm changes with normal ageing more than other progeroid diseases do, and included genes functionally validated for regular ageing. Collectively, our results support the existence of an epigenomic basis of accelerated ageing in CS and unveil new genes and pathways that are potentially associated with the progeroid/degenerative phenotype.
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Affiliation(s)
- Clément Crochemore
- Institut Pasteur, Université Paris Cité, Molecular Mechanisms of Pathological and Physiological Ageing Unit, UMR3738 CNRSParisFrance
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR3738 CNRSParisFrance
- Sup'BiotechVillejuifFrance
| | - Claudia Chica
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HubParisFrance
| | - Paolo Garagnani
- IRCCS Azienda Ospedaliero‐Universitaria di BolognaBolognaItaly
- Department of Medical and Surgical Sciences (DIMEC)University of BolognaBolognaItaly
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli‐Sforza”, Unit of BolognaBolognaItaly
- IRCCS Istituto Ortopedico RizzoliBolognaItaly
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesUSA
- Department of Biostatistics Fielding School of Public HealthUniversity of CaliforniaLos AngelesUSA
| | - Alain Sarasin
- Laboratory of Genetic Stability and Oncogenesis, Institut de Cancérologie Gustave RoussyUniversity Paris‐SudVillejuifFrance
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and MechanicsLobachevsky UniversityNizhniy NovgorodRussia
| | | | - Miria Ricchetti
- Institut Pasteur, Université Paris Cité, Molecular Mechanisms of Pathological and Physiological Ageing Unit, UMR3738 CNRSParisFrance
- Institut Pasteur, Team Stability of Nuclear and Mitochondrial DNA, Stem Cells and Development, UMR3738 CNRSParisFrance
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13
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Kim HS, Jang S, Kim J. Genome-Wide Integrative Transcriptional Profiling Identifies Age-Associated Signatures in Dogs. Genes (Basel) 2023; 14:1131. [PMID: 37372311 DOI: 10.3390/genes14061131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Mammals experience similar stages of embryonic development, birth, infancy, youth, adolescence, maturity, and senescence. While embryonic developmental processes have been extensively researched, many molecular mechanisms regulating the different life stages after birth, such as aging, remain unresolved. We investigated the conserved and global molecular transitions in transcriptional remodeling with age in dogs of 15 breeds, which revealed that genes underlying hormone level regulation and developmental programs were differentially regulated during aging. Subsequently, we show that the candidate genes associated with tumorigenesis also exhibit age-dependent DNA methylation patterns, which might have contributed to the tumor state through inhibiting the plasticity of cell differentiation processes during aging, and ultimately suggesting the molecular events that link the processes of aging and cancer. These results highlight that the rate of age-related transcriptional remodeling is influenced not only by the lifespan, but also by the timing of critical physiological milestones.
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Affiliation(s)
- Hyun Seung Kim
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Subin Jang
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jaemin Kim
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
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14
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Cui H, Xin Y, Cao F, Gan Z, Tian Y, Liu W, Shi P. The correlation between CpG island methylation of hTERT promoter and human age prediction. Leg Med (Tokyo) 2023; 63:102270. [PMID: 37207612 DOI: 10.1016/j.legalmed.2023.102270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
DNA methylation is an epigenetic modification that occurs during the life cycle of individuals. Its degree is closely associated with the methylation status of CpG sites in its promoter region. Based on the previous screening that the hTERT methylation is both related to tumors and age, we suspected that the age inference based on hTERT methylation would be disturbed by the disease of the tested person. Herein, eight CpG sites in the hTERT promoter region were analyzed by real-time methylation-specific PCR, and we found that CpG2, CpG5, and CpG8 were closely related to the tumor (P < 0.05). The remaining five CpG sites had a large error in predicting age alone. Combining them to establish a model yielded better results, with an average age error of 4.35 years. This study provides a reliable and accurate detection method for the DNA methylation status of multiple CpG sites on the hTERT gene promoter, which can be used for the prediction of forensic age and assistant diagnosis of clinical diseases.
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Affiliation(s)
- Hanyue Cui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ye Xin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Fangqi Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Zhongshan North No 1 Road, Shanghai 200083, China
| | - Ziye Gan
- Ulink College of Shanghai, 559 Laiting South Road, Shanghai 201615, China
| | - Yuxiang Tian
- Department of Clinical Laboratory, Shanghai Xuhui District Dahua Hospital, Shanghai 200237, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Zhongshan North No 1 Road, Shanghai 200083, China.
| | - Ping Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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15
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Sgueglia G, Longobardi S, Valerio D, Campitiello MR, Colacurci N, Di Pietro C, Battaglia R, D'Hooghe T, Altucci L, Dell'Aversana C. The impact of epigenetic landscape on ovarian cells in infertile older women undergoing IVF procedures. Clin Epigenetics 2023; 15:76. [PMID: 37143127 PMCID: PMC10161563 DOI: 10.1186/s13148-023-01490-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023] Open
Abstract
The constant decline in fertility and older reproductive age is the major cause of low clinical pregnancy rates in industrialised countries. Epigenetic mechanisms impact on proper embryonic development in women undergoing in vitro fertilisation (IVF) protocols. Here, we describe the main epigenetic modifications that may influence female reproduction and could affect IVF success.
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Affiliation(s)
- Giulia Sgueglia
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Programma di Epigenetica Medica, Azienda Ospedaliera Universitaria, Naples, Italy
| | | | - Domenico Valerio
- Outpatient Fertility Unit, University of Campania 'Luigi Vanvitelli', 80138, Naples, Italy
| | - Maria Rosaria Campitiello
- Department of Obstetrics and Gynecology and Physiopathology of Human Reproduction, ASL Salerno, Salerno, Italy
| | - Nicola Colacurci
- Outpatient Fertility Unit, University of Campania 'Luigi Vanvitelli', 80138, Naples, Italy
- Department of Woman, Child and General and Special Surgery, University of Campania 'Luigi Vanvitelli', 80138, Naples, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics "Giovanni Sichel", University of Catania, 95123, Catania, CT, Italy
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics "Giovanni Sichel", University of Catania, 95123, Catania, CT, Italy
| | | | - Lucia Altucci
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Programma di Epigenetica Medica, Azienda Ospedaliera Universitaria, Naples, Italy.
- BIOGEM, Ariano Irpino, Italy.
- Institute of Experimental Endocrinology and Oncology 'Gaetano Salvatore' (IEOS)-National Research Council (CNR), Naples, Italy.
| | - Carmela Dell'Aversana
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Programma di Epigenetica Medica, Azienda Ospedaliera Universitaria, Naples, Italy.
- Institute of Experimental Endocrinology and Oncology 'Gaetano Salvatore' (IEOS)-National Research Council (CNR), Naples, Italy.
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16
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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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17
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Ji S, Xiong M, Chen H, Liu Y, Zhou L, Hong Y, Wang M, Wang C, Fu X, Sun X. Cellular rejuvenation: molecular mechanisms and potential therapeutic interventions for diseases. Signal Transduct Target Ther 2023; 8:116. [PMID: 36918530 PMCID: PMC10015098 DOI: 10.1038/s41392-023-01343-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 03/16/2023] Open
Abstract
The ageing process is a systemic decline from cellular dysfunction to organ degeneration, with more predisposition to deteriorated disorders. Rejuvenation refers to giving aged cells or organisms more youthful characteristics through various techniques, such as cellular reprogramming and epigenetic regulation. The great leaps in cellular rejuvenation prove that ageing is not a one-way street, and many rejuvenative interventions have emerged to delay and even reverse the ageing process. Defining the mechanism by which roadblocks and signaling inputs influence complex ageing programs is essential for understanding and developing rejuvenative strategies. Here, we discuss the intrinsic and extrinsic factors that counteract cell rejuvenation, and the targeted cells and core mechanisms involved in this process. Then, we critically summarize the latest advances in state-of-art strategies of cellular rejuvenation. Various rejuvenation methods also provide insights for treating specific ageing-related diseases, including cellular reprogramming, the removal of senescence cells (SCs) and suppression of senescence-associated secretory phenotype (SASP), metabolic manipulation, stem cells-associated therapy, dietary restriction, immune rejuvenation and heterochronic transplantation, etc. The potential applications of rejuvenation therapy also extend to cancer treatment. Finally, we analyze in detail the therapeutic opportunities and challenges of rejuvenation technology. Deciphering rejuvenation interventions will provide further insights into anti-ageing and ageing-related disease treatment in clinical settings.
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Affiliation(s)
- Shuaifei Ji
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mingchen Xiong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Huating Chen
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiqiong Liu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Laixian Zhou
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiyue Hong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mengyang Wang
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078, Macau SAR, China.
| | - Xiaobing Fu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
| | - Xiaoyan Sun
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
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18
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Verdone L, Caserta M, Ben-Soussan TD, Venditti S. On the road to resilience: Epigenetic effects of meditation. VITAMINS AND HORMONES 2023; 122:339-376. [PMID: 36863800 DOI: 10.1016/bs.vh.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Many environmental and lifestyle related factors may influence the physiology of the brain and body by acting on fundamental molecular pathways, such as the hypothalamus-pituitary-adrenal axis (HPA) and the immune system. For example, stressful conditions created by adverse early-life events, unhealthy habits and low socio-economic status may favor the onset of diseases linked to neuroendocrine dysregulation, inflammation and neuroinflammation. Beside pharmacological treatments used in clinical settings, much attention has been given to complementary treatments such as mind-body techniques involving meditation that rely on the activation of inner resources to regain health. At the molecular level, the effects of both stress and meditation are elicited epigenetically through a set of mechanisms that regulate gene expression as well as the circulating neuroendocrine and immune effectors. Epigenetic mechanisms constantly reshape genome activities in response to external stimuli, representing a molecular interface between organism and environment. In the present work, we aimed to review the current knowledge on the correlation between epigenetics, gene expression, stress and its possible antidote, meditation. After introducing the relationship between brain, physiology, and epigenetics, we will proceed to describe three basic epigenetic mechanisms: chromatin covalent modifications, DNA methylation and non-coding RNAs. Subsequently, we will give an overview of the physiological and molecular aspects related to stress. Finally, we will address the epigenetic effects of meditation on gene expression. The results of the studies reported in this review demonstrate that mindful practices modulate the epigenetic landscape, leading to increased resilience. Therefore, these practices can be considered valuable tools that complement pharmacological treatments when coping with pathologies related to stress.
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Affiliation(s)
- Loredana Verdone
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Rome, Italy.
| | - Micaela Caserta
- Institute of Molecular Biology and Pathology, National Research Council (CNR), Rome, Italy
| | - Tal Dotan Ben-Soussan
- Cognitive Neurophysiology Laboratory, Research Institute for Neuroscience, Education and Didactics, Patrizio Paoletti Foundation for Development and Communication, Assisi, Italy
| | - Sabrina Venditti
- Dept. of Biology and biotechnologies, Sapienza University of Rome, Rome, Italy.
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Meyer BS, Moiron M, Caswara C, Chow W, Fedrigo O, Formenti G, Haase B, Howe K, Mountcastle J, Uliano-Silva M, Wood J, Jarvis ED, Liedvogel M, Bouwhuis S. Sex-specific changes in autosomal methylation rate in ageing common terns. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.982443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Senescence, an age-related decline in survival and/or reproductive performance, occurs in species across the tree of life. Molecular mechanisms underlying this within-individual phenomenon are still largely unknown, but DNA methylation changes with age are among the candidates. Using a longitudinal approach, we investigated age-specific changes in autosomal methylation of common terns, relatively long-lived migratory seabirds known to show senescence. We collected blood at 1-, 3- and/or 4-year intervals, extracted DNA from the erythrocytes and estimated autosomal DNA methylation by mapping Reduced Representative Bisulfite Sequencing reads to a de novo assembled reference genome. We found autosomal methylation levels to decrease with age within females, but not males, and no evidence for selective (dis)appearance of birds of either sex in relation to their methylation level. Moreover, although we found positions in the genome to consistently vary in their methylation levels, individuals did not show such strong consistent variance. These results pave the way for studies at the level of genome features or specific positions, which should elucidate the functional consequences of the patterns observed, and how they translate to the ageing phenotype.
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20
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Histone Modifications in Alzheimer's Disease. Genes (Basel) 2023; 14:genes14020347. [PMID: 36833274 PMCID: PMC9956192 DOI: 10.3390/genes14020347] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/11/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Since Late-onset Alzheimer's disease (LOAD) derives from a combination of genetic variants and environmental factors, epigenetic modifications have been predicted to play a role in the etiopathology of LOAD. Along with DNA methylation, histone modifications have been proposed as the main epigenetic modifications that contribute to the pathologic mechanisms of LOAD; however, little is known about how these mechanisms contribute to the disease's onset or progression. In this review, we highlighted the main histone modifications and their functional role, including histone acetylation, histone methylation, and histone phosphorylation, as well as changes in such histone modifications that occur in the aging process and mainly in Alzheimer's disease (AD). Furthermore, we pointed out the main epigenetic drugs tested for AD treatment, such as those based on histone deacetylase (HDAC) inhibitors. Finally, we remarked on the perspectives around the use of such epigenetics drugs for treating AD.
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21
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Furrer D, Dragic D, Chang SL, Fournier F, Droit A, Jacob S, Diorio C. Association between genome-wide epigenetic and genetic alterations in breast cancer tissue and response to HER2-targeted therapies in HER2-positive breast cancer patients: new findings and a systematic review. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:995-1015. [PMID: 36627894 PMCID: PMC9771759 DOI: 10.20517/cdr.2022.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/25/2022] [Accepted: 10/08/2022] [Indexed: 01/12/2023]
Abstract
Recent evidence suggests that genetic and epigenetic mechanisms might be associated with acquired resistance to cancer therapies. The aim of this study was to assess the association of genome-wide genetic and epigenetic alterations with the response to anti-HER2 agents in HER2-positive breast cancer patients. PubMed was screened for articles published until March 2021 on observational studies investigating the association of genome-wide genetic and epigenetic alterations, measured in breast cancer tissues or blood, with the response to targeted treatment in HER2-positive breast cancer patients. Sixteen studies were included in the review along with ours, in which we compared the genome-wide DNA methylation pattern in breast tumor tissues of patients who acquired resistance to treatment (case group, n = 6) to that of patients who did not develop resistance (control group, n = 6). Among genes identified as differentially methylated between the breast cancer tissue of cases and controls, one of them, PRKACA, was also reported as differentially expressed in two studies included in the review. Although included studies were heterogeneous in terms of methodology and study population, our review suggests that genes of the PI3K pathway may play an important role in developing resistance to anti-HER2 agents in breast cancer patients. Genome-wide genetic and epigenetic alterations measured in breast cancer tissue or blood might be promising markers of resistance to anti-HER2 agents in HER2-positive breast cancer patients. Further studies are needed to confirm these data.
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Affiliation(s)
- Daniela Furrer
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine sociale et préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Dzevka Dragic
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine sociale et préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Université Paris-Saclay, UVSQ, Inserm, CESP U1018, Exposome and Heredity Team, Gustave Roussy, Villejuif 94807, France
| | - Sue-Ling Chang
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada
| | - Frédéric Fournier
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Arnaud Droit
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Simon Jacob
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de biologie moléculaire, de biochimie médicale et de pathologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Centre des Maladies du Sein, Hôpital du Saint-Sacrement, Québec, QC G1S 4L8, Canada
| | - Caroline Diorio
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine sociale et préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Centre des Maladies du Sein, Hôpital du Saint-Sacrement, Québec, QC G1S 4L8, Canada.,Correspondence to: Prof. Caroline Diorio, Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, 1050 chemin Ste-Foy, Québec, QC G1S 4L8, Canada. E-mail:
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22
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Zhao L, Hou C, Yan N. Neuroinflammation in retinitis pigmentosa: Therapies targeting the innate immune system. Front Immunol 2022; 13:1059947. [PMID: 36389729 PMCID: PMC9647059 DOI: 10.3389/fimmu.2022.1059947] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is an important cause of irreversible blindness worldwide and lacks effective treatment strategies. Although mutations are the primary cause of RP, research over the past decades has shown that neuroinflammation is an important cause of RP progression. Due to the abnormal activation of immunity, continuous sterile inflammation results in neuron loss and structural destruction. Therapies targeting inflammation have shown their potential to attenuate photoreceptor degeneration in preclinical models. Regardless of variations in genetic background, inflammatory modulation is emerging as an important role in the treatment of RP. We summarize the evidence for the role of inflammation in RP and mention therapeutic strategies where available, focusing on the modulation of innate immune signals, including TNFα signaling, TLR signaling, NLRP3 inflammasome activation, chemokine signaling and JAK/STAT signaling. In addition, we describe epigenetic regulation, the gut microbiome and herbal agents as prospective treatment strategies for RP in recent advances.
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Affiliation(s)
- Ling Zhao
- Research Laboratory of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Chen Hou
- Research Laboratory of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Naihong Yan
- Research Laboratory of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China,*Correspondence: Naihong Yan,
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23
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ROS: Basic Concepts, Sources, Cellular Signaling, and its Implications in Aging Pathways. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1225578. [PMID: 36312897 PMCID: PMC9605829 DOI: 10.1155/2022/1225578] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022]
Abstract
Reactive oxygen species (ROS) are bioproducts of cellular metabolism. There is a range of molecules with oxidizing properties known as ROS. Despite those molecules being implied negatively in aging and numerous diseases, their key role in cellular signaling is evident. ROS control several biological processes such as inflammation, proliferation, and cell death. The redox signaling underlying these cellular events is one characteristic of the new generation of scientists aimed at defining the role of ROS in the cellular environment. The control of redox potential, which includes the balance of the sources of ROS and the antioxidant system, implies an important target for understanding the cells' fate derived from redox signaling. In this review, we summarized the chemical, the redox balance, the signaling, and the implications of ROS in biological aging.
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24
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Alimohammadi M, Makaremi S, Rahimi A, Asghariazar V, Taghadosi M, Safarzadeh E. DNA methylation changes and inflammaging in aging-associated diseases. Epigenomics 2022; 14:965-986. [PMID: 36043685 DOI: 10.2217/epi-2022-0143] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aging as an inevitable phenomenon is associated with pervasive changes in physiological functions. There is a relationship between aging and the increase of several chronic diseases. Most age-related disorders are accompanied by an underlying chronic inflammatory state, as demonstrated by local infiltration of inflammatory cells and greater levels of proinflammatory cytokines in the bloodstream. Within inflammaging, many epigenetic events, especially DNA methylation, change. During the aging process, due to aberrations of DNA methylation, biological processes are disrupted, leading to the emergence or progression of a variety of human diseases, including cancer, neurodegenerative disorders, cardiovascular disease and diabetes. The focus of this review is on DNA methylation, which is involved in inflammaging-related activities, and how its dysregulation leads to human disorders.
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Affiliation(s)
- Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 1983969411, Iran
| | - Shima Makaremi
- School of Medicine & Allied Medical Sciences, Ardabil University of Medical Sciences, Ardabil, 5618985991, Iran
| | - Ali Rahimi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, 5618985991, Iran
| | - Vahid Asghariazar
- Deputy of Research & Technology, Ardabil University of Medical Sciences, Ardabil, 5618985991, Iran
| | - Mahdi Taghadosi
- Department of Immunology, Kermanshah University of Medical Sciences, Kermanshah, 6714869914, Iran
| | - Elham Safarzadeh
- Department of Microbiology, Parasitology, & Immunology, Ardabil University of Medical Sciences, Ardabil, 5618985991, Iran
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25
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Govender P, Ghai M, Okpeku M. Sex-specific DNA methylation: impact on human health and development. Mol Genet Genomics 2022; 297:1451-1466. [PMID: 35969270 DOI: 10.1007/s00438-022-01935-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
Abstract
Human evolution has shaped gender differences between males and females. Over the years, scientific studies have proposed that epigenetic modifications significantly influence sex-specific differences. The evolution of sex chromosomes with epigenetics as the driving force may have led to one sex being more adaptable than the other when exposed to various factors over time. Identifying and understanding sex-specific differences, particularly in DNA methylation, will help determine how each gender responds to factors, such as disease susceptibility, environmental exposure, brain development and neurodegeneration. From a medicine and health standpoint, sex-specific methylation studies have shed light on human disease severity, progression, and response to therapeutic intervention. Interesting findings in gender incongruent individuals highlight the role of genetic makeup in influencing DNA methylation differences. Sex-specific DNA methylation studies will empower the biotechnology and pharmaceutical industry with more knowledge to identify biomarkers, design and develop sex bias drugs leading to better treatment in men and women based on their response to different diseases.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
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26
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Reimann B, Martens DS, Wang C, Ghantous A, Herceg Z, Plusquin M, Nawrot TS. Interrelationships and determinants of aging biomarkers in cord blood. J Transl Med 2022; 20:353. [PMID: 35945616 PMCID: PMC9361565 DOI: 10.1186/s12967-022-03541-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Increasing evidence supports the concept of prenatal programming as an early factor in the aging process. DNA methylation age (DNAm age), global genome-wide DNA methylation (global methylation), telomere length (TL), and mitochondrial DNA content (mtDNA content) have independently been shown to be markers of aging, but their interrelationship and determinants at birth remain uncertain. METHODS We assessed the inter-correlation between the aging biomarkers DNAm age, global methylation, TL and mtDNA content using Pearson's correlation in 190 cord blood samples of the ENVIRONAGE birth cohort. TL and mtDNA content was measured via qPCR, while the DNA methylome was determined using the human 450K methylation Illumina microarray. Subsequently, DNAm age was calculated according to Horvath's epigenetic clock, and mean global, promoter, gene-body, and intergenic DNA methylation were determined. Path analysis, a form of structural equation modeling, was performed to disentangle the complex causal relationships among the aging biomarkers and their potential determinants. RESULTS DNAm age was inversely correlated with global methylation (r = -0.64, p < 0.001) and mtDNA content (r = - 0.16, p = 0.027). Cord blood TL was correlated with mtDNA content (r = 0.26, p < 0.001) but not with global methylation or DNAm age. Path analysis showed the strongest effect for global methylation on DNAm age with a decrease of 0.64 standard deviations (SD) in DNAm age for each SD (0.01%) increase in global methylation (p < 0.001). Among the applied covariates, newborn sex and season of delivery were the strongest determinants of aging biomarkers. CONCLUSIONS We provide insight into molecular aging signatures at the start of life, including their interrelations and determinants, showing that cord blood DNAm age is inversely associated with global methylation and mtDNA content but not with newborn telomere length. Our findings demonstrate that cord blood TL and DNAm age relate to different pathways/mechanisms of biological aging and can be influenced by environmental factors already at the start of life. These findings are relevant for understanding fetal programming and for the early prevention of noncommunicable diseases.
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Affiliation(s)
- Brigitte Reimann
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), Lyon, France
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium.
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
- School of Public Health, Occupational and Environmental Medicine, KU Leuven, Leuven, Belgium
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27
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Beal AP, Hackerott S, Feldheim K, Gruber SH, Eirin‐Lopez JM. Age group DNA methylation differences in lemon sharks ( Negaprion brevirostris): Implications for future age estimation tools. Ecol Evol 2022; 12:e9226. [PMID: 36052296 PMCID: PMC9425014 DOI: 10.1002/ece3.9226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 11/11/2022] Open
Abstract
Age information is often non-existent for most shark populations due to a lack of measurable physiological and morphological traits that can be used to estimate age. Recently, epigenetic clocks have been found to accurately estimate age for mammals, birds, and fish. However, since these clocks rely, among other things, on the availability of reference genomes, their application is hampered in non-traditional model organisms lacking such molecular resources. The technique known as Methyl-Sensitive Amplified Polymorphism (MSAP) has emerged as a valid alternative for studying DNA methylation biomarkers when reference genome information is missing, and large numbers of samples need to be processed. Accordingly, the MSAP technique was used in the present study to characterize global DNA methylation patterns in lemon sharks from three different age groups (juveniles, subadults, and adults). The obtained results reveal that, while MSAP analyses lack enough resolution as a standalone approach to infer age in these organisms, the global DNA methylation patterns observed using this technique displayed significant differences between age groups. Overall, these results confer that DNA methylation does change with age in sharks like what has been seen for other vertebrates and that MSAP could be useful as part of an epigenetics pipeline to infer the broad range of ages found in large samples sizes.
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Affiliation(s)
- Andria Paige Beal
- Environmental Epigenetics Laboratory, Institute of EnvironmentFlorida International UniversityMiamiFloridaUSA
| | - Serena Hackerott
- Environmental Epigenetics Laboratory, Institute of EnvironmentFlorida International UniversityMiamiFloridaUSA
| | - Kevin Feldheim
- Pritzker Laboratory for Molecular Systematics and EvolutionField Museum of Natural HistoryChicagoIllinoisUSA
| | | | - Jose M. Eirin‐Lopez
- Environmental Epigenetics Laboratory, Institute of EnvironmentFlorida International UniversityMiamiFloridaUSA
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28
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Kocamaz D, Franzke C, Gröger N, Braun K, Bock J. Early Life Stress-Induced Epigenetic Programming of Hippocampal NPY-Y2 Receptor Gene Expression Changes in Response to Adult Stress. Front Cell Neurosci 2022; 16:936979. [PMID: 35846564 PMCID: PMC9283903 DOI: 10.3389/fncel.2022.936979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Early Life Stress (ELS) can critically influence brain development and future stress responses and thus represents an important risk factor for mental health and disease. Neuropeptide Y (NPY) is discussed to be a key mediator of resilient vs. vulnerable adaptations and specifically, the NPY-Y2 receptor (Y2R) may be involved in the pathophysiology of depression due to its negative regulation of NPY-release. The present study addressed the hypotheses that ELS and adult stress (AS) affect the expression of hippocampal Y2R and that exposure to ELS induces an epigenetically mediated programming effect towards a consecutive stress exposure in adulthood. The specific aims were to investigate if (i) ELS or AS as single stressors induce changes in Y2 receptor gene expression in the hippocampus, (ii) the predicted Y2R changes are epigenetically mediated via promoter-specific DNA-methylation, (iii) the ELS-induced epigenetic changes exert a programming effect on Y2R gene expression changes in response to AS, and finally (iv) if the predicted alterations are sex-specific. Animals were assigned to the following experimental groups: (1) non-stressed controls (CON), (2) only ELS exposure (ELS), (3) only adult stress exposure (CON+AS), and (4) exposure to ELS followed by AS (ELS+AS). Using repeated maternal separation in mice as an ELS and swim stress as an AS we found that both stressors affected Y2R gene expression in the hippocampus of male mice but not in females. Specifically, upregulated expression was found in the CON+AS group. In addition, exposure to both stressors ELS+AS significantly reduced Y2R gene expression when compared to CON+AS. The changes in Y2R expression were paralleled by altered DNA-methylation patterns at the Y2R promoter, specifically, a decrease in mean DNA-methylation in the CON+AS males compared to the non-AS exposed groups and an increase in the ELS+AS males compared to the CON+AS males. Also, a strong negative correlation of mean DNA-methylation with Y2R expression was found. Detailed CpG-site-specific analysis of DNA-methylation revealed that ELS induced increased DNA-methylation only at specific CpG-sites within the Y2R promoter. It is tempting to speculate that these ELS-induced CpG-site-specific changes represent a “buffering” programming effect against elevations of Y2R expression induced by AS.
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Affiliation(s)
- Derya Kocamaz
- Department of Zoology/Developmental Neurobiology, Institute of Biology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Caroline Franzke
- Department of Zoology/Developmental Neurobiology, Institute of Biology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Nicole Gröger
- Department of Zoology/Developmental Neurobiology, Institute of Biology, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Katharina Braun
- Department of Zoology/Developmental Neurobiology, Institute of Biology, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Jörg Bock
- Center for Behavioral Brain Sciences, Magdeburg, Germany
- PG “Epigenetics and Structural Plasticity,” Institute of Biology, Otto von Guericke University Magdeburg, Magdeburg, Germany
- *Correspondence: Jörg Bock,
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29
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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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30
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Sumner JA, Gambazza S, Gao X, Baccarelli AA, Uddin M, McLaughlin KA. Epigenetics of early-life adversity in youth: cross-sectional and longitudinal associations. Clin Epigenetics 2022; 14:48. [PMID: 35395780 PMCID: PMC8994405 DOI: 10.1186/s13148-022-01269-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/31/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Altered DNA methylation (DNAm) may be one pathway through which early-life adversity (ELA) contributes to adverse mental and physical health outcomes. This study investigated whether the presence versus absence of ELA experiences reflecting the dimensions of threat and deprivation were associated with epigenome-wide DNAm cross-sectionally and longitudinally in a community-based sample of children and adolescents. METHODS In 113 youths aged 8-16 years with wide variability in ELA, we examined associations of abuse (physical, sexual, emotional; indicating threat-related experiences) and neglect (emotional, physical; indicating deprivation-related experiences) with DNAm assessed with the Illumina EPIC BeadChip array, with DNA derived from saliva. In cross-sectional epigenome-wide analyses, we investigated associations of lifetime abuse and neglect with DNAm at baseline. In longitudinal epigenome-wide analyses, we examined whether experiencing abuse and neglect over an approximately 2-year follow-up were each associated with change in DNAm from baseline to follow-up. RESULTS In cross-sectional analyses adjusting for lifetime experience of neglect, lifetime experience of abuse was associated with DNAm for four cytosine-phosphodiester-guanine (CpG) sites (cg20241299: coefficient = 0.023, SE = 0.004; cg08671764: coefficient = 0.018, SE = 0.003; cg27152686: coefficient = - 0.069, SE = 0.012; cg24241897: coefficient = - 0.003, SE = 0.001; FDR < .05). In longitudinal analyses, experiencing neglect over follow-up was associated with an increase in DNAm for one CpG site, adjusting for abuse over follow-up (cg03135983: coefficient = 0.036, SE = 0.006; FDR < .05). CONCLUSIONS In this study, we identified examples of epigenetic patterns associated with ELA experiences of threat and deprivation that were already observable in youth. We provide novel evidence for change in DNAm over time in relation to ongoing adversity and that experiences reflecting distinct ELA dimensions may be characterized by unique epigenetic patterns.
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Affiliation(s)
- Jennifer A Sumner
- Department of Psychology, University of California, Los Angeles, Psychology Building 1285, Box 951563, Los Angeles, CA, 90095-1563, USA.
| | - Simone Gambazza
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Healthcare Professions Department, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Xu Gao
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
- Department of Occupational and Environmental Health Sciences, Peking University, Beijing, China
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
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Shared genetic and epigenetic changes link aging and cancer. Trends Cell Biol 2022; 32:338-350. [PMID: 35144882 DOI: 10.1016/j.tcb.2022.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/28/2021] [Accepted: 01/07/2022] [Indexed: 12/12/2022]
Abstract
Aging is a universal biological process that increases the risk of multiple diseases including cancer. Growing evidence shows that alterations in the genome and epigenome, driven by similar mechanisms, are found in both aged cells and cancer cells. In this review, we detail the genetic and epigenetic changes associated with normal aging and the mechanisms responsible for these changes. By highlighting genetic and epigenetic alterations in the context of tumorigenesis, cancer progression, and the aging tumor microenvironment, we examine the possible impacts of the normal aging process on malignant transformation. Finally, we examine the implications of age-related genetic and epigenetic alterations in both tumors and patients for the treatment of cancer.
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32
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Sleep Health among Racial/Ethnic groups and Strategies to achieve Sleep Health Equity. Respir Med 2022. [DOI: 10.1007/978-3-030-93739-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Nayeri Rad A, Shams G, Avelar RA, Morowvat MH, Ghasemi Y. Potential senotherapeutic candidates and their combinations derived from transcriptional connectivity and network measures. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Sahabi S, Jafari-Gharabaghlou D, Zarghami N. A new insight into cell biological and biochemical changes through aging. Acta Histochem 2022; 124:151841. [PMID: 34995929 DOI: 10.1016/j.acthis.2021.151841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/17/2022]
Abstract
After several years of extensive research, the main cause of aging is yet elusive. There are some theories about aging, such as stem cell aging, senescent cells accumulation, and neuro-endocrine theories. None of them is able to explain all changes that happen in cells and body through aging. By finding out the main cause of aging, it will be much easier to control, prevent and even reverse the aging process. Our cells, regardless of their replicative capacity, get old through aging and they have almost the same epigenetic age. Different cell signaling pathways contribute to aging. The most important one is mTORC1 that becomes hyperactive in cells that undergo aging. Other significant changes with age are lysosome accumulation, impaired autophagy, and mitophagy. Immune system undergoes gradual changes through aging including a shift from lymphoid to myeloid lineage production as well as increased IL-6 and TNF-α which lead to age-related weight loss and meta-inflammation. Additionally, our endocrine system also experiences some changes that should be taken into consideration when looking for the main cause of aging in the human body. In this review, we planned to summarize some of the changes that happen in cells and the body through aging.
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35
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Martínez-Iglesias O, Naidoo V, Cacabelos N, Cacabelos R. Epigenetic Biomarkers as Diagnostic Tools for Neurodegenerative Disorders. Int J Mol Sci 2021; 23:13. [PMID: 35008438 PMCID: PMC8745005 DOI: 10.3390/ijms23010013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetics is the study of heritable changes in gene expression that occur without alterations to the DNA sequence, linking the genome to its surroundings. The accumulation of epigenetic alterations over the lifespan may contribute to neurodegeneration. The aim of the present study was to identify epigenetic biomarkers for improving diagnostic efficacy in patients with neurodegenerative diseases. We analyzed global DNA methylation, chromatin remodeling/histone modifications, sirtuin (SIRT) expression and activity, and the expression of several important neurodegeneration-related genes. DNA methylation, SIRT expression and activity and neuregulin 1 (NRG1), microtubule-associated protein tau (MAPT) and brain-derived neurotrophic factor (BDNF) expression were reduced in buffy coat samples from patients with neurodegenerative disorders. Our data suggest that these epigenetic biomarkers may be useful in clinical practical for the diagnosis, surveillance, and prognosis of disease activity in patients with neurodegenerative diseases.
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Affiliation(s)
- Olaia Martínez-Iglesias
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, Bergondo, 15165 Corunna, Spain; (V.N.); (N.C.); (R.C.)
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36
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Endlicher R, Drahota Z, Kučera O, Červinková Z. Age-Dependent Changes in the Function of Mitochondrial Membrane Permeability Transition Pore in Rat Liver Mitochondria. Physiol Res 2021. [DOI: 10.33549//physiolres.934734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mitochondria play an important role in the cell aging process. Changes in calcium homeostasis and/or increased reactive oxygen species (ROS) production lead to the opening of mitochondrial permeability transition pore (MPTP), depolarization of the inner mitochondrial membrane, and decrease of ATP production. Our work aimed to monitor age-related changes in the Ca2+ ion effect on MPTP and the ability of isolated rat liver mitochondria to accumulate calcium. The mitochondrial calcium retention capacity (CRC) was found to be significantly affected by the age of rats. Measurement of CRC values of the rat liver mitochondria showed two periods when 3 to17-week old rats were tested. 3-week and 17-week old rats showed lower CRC values than 7-week old animals. Similar changes were observed while testing calcium-induced swelling of rat liver mitochondria. These findings indicate that the mitochondrial energy production system is more resistant to calcium-induced MPTP opening accompanied by the damaging effect of ROS in adult rats than in young and aged animals.
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Affiliation(s)
| | | | | | - Z. Červinková
- Department of Physiology, Faculty of Medicine in Hradec Králové, Charles University, Hradec Kralove, Czech Republic.
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Mc Auley MT. DNA methylation in genes associated with the evolution of ageing and disease: A critical review. Ageing Res Rev 2021; 72:101488. [PMID: 34662746 DOI: 10.1016/j.arr.2021.101488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/30/2021] [Accepted: 10/12/2021] [Indexed: 12/28/2022]
Abstract
Ageing is characterised by a physical decline in biological functioning which results in a progressive risk of mortality with time. As a biological phenomenon, it is underpinned by the dysregulation of a myriad of complex processes. Recently, however, ever-increasing evidence has associated epigenetic mechanisms, such as DNA methylation (DNAm) with age-onset pathologies, including cancer, cardiovascular disease, and Alzheimer's disease. These diseases compromise healthspan. Consequently, there is a medical imperative to understand the link between epigenetic ageing, and healthspan. Evolutionary theory provides a unique way to gain new insights into epigenetic ageing and health. This review will: (1) provide a brief overview of the main evolutionary theories of ageing; (2) discuss recent genetic evidence which has revealed alleles that have pleiotropic effects on fitness at different ages in humans; (3) consider the effects of DNAm on pleiotropic alleles, which are associated with age related disease; (4) discuss how age related DNAm changes resonate with the mutation accumulation, disposable soma and programmed theories of ageing; (5) discuss how DNAm changes associated with caloric restriction intersect with the evolution of ageing; and (6) conclude by discussing how evolutionary theory can be used to inform investigations which quantify age-related DNAm changes which are linked to age onset pathology.
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Affiliation(s)
- Mark Tomás Mc Auley
- Faculty of Science and Engineering, University of Chester, Exton Park, Chester CH1 4BJ, UK.
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38
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Zagkos L, Roberts J, Auley MM. A mathematical model which examines age-related stochastic fluctuations in DNA maintenance methylation. Exp Gerontol 2021; 156:111623. [PMID: 34774717 DOI: 10.1016/j.exger.2021.111623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 10/19/2022]
Abstract
Due to its complexity and its ubiquitous nature the ageing process remains an enduring biological puzzle. Many molecular mechanisms and biochemical process have become synonymous with ageing. However, recent findings have pinpointed epigenetics as having a key role in ageing and healthspan. In particular age related changes to DNA methylation offer the possibility of monitoring the trajectory of biological ageing and could even be used to predict the onset of diseases such as cancer, Alzheimer's disease and cardiovascular disease. At the molecular level emerging evidence strongly suggests the regulatory processes which govern DNA methylation are subject to intracellular stochasticity. It is challenging to fully understand the impact of stochasticity on DNA methylation levels at the molecular level experimentally. An ideal solution is to use mathematical models to capture the essence of the stochasticity and its outcomes. In this paper we present a novel stochastic model which accounts for specific methylation levels within a gene promoter. Uncertainty of the eventual site-specific methylation levels for different values of methylation age, depending on the initial methylation levels were analysed. Our model predicts the observed bistable levels in CpG islands. In addition, simulations with various levels of noise indicate that uncertainty predominantly spreads through the hypermethylated region of stability, especially for large values of input noise. A key outcome of the model is that CpG islands with high to intermediate methylation levels tend to be more susceptible to dramatic DNA methylation changes due to increasing methylation age.
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Affiliation(s)
- Loukas Zagkos
- Department of Mathematics, School of Science and Engineering, University of Chester, Thornton Science Park, Chester CH2 4NU, UK; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London W2 1PG, UK.
| | - Jason Roberts
- Department of Mathematics, School of Science and Engineering, University of Chester, Thornton Science Park, Chester CH2 4NU, UK
| | - Mark Mc Auley
- Department of Chemical Engineering, School of Science and Engineering, University of Chester, Thornton Science Park, Chester CH2 4NU, UK
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Anifandis G, Samara M, Simopoulou M, Messini CI, Chatzimeletiou K, Thodou E, Daponte A, Georgiou I. Insights into the Role of Telomeres in Human Embryological Parameters. Opinions Regarding IVF. J Dev Biol 2021; 9:jdb9040049. [PMID: 34842724 PMCID: PMC8628962 DOI: 10.3390/jdb9040049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Telomeres promote genome integrity by protecting chromosome ends from the activation of the DNA damage response and protecting chromosomes from the loss of coding sequences due to the end replication problem. Telomere length (TL) is progressively shortened as age progresses, thus resulting in cellular senescence. Therefore, TL is in strong adverse linear correlation with aging. Mounting evidence supports the notion that telomeres and male/female infertility are in a close relationship, posing the biology of telomeres as a hot topic in the era of human-assisted reproduction. Specifically, the length of sperm telomeres is gradually increasing as men get older, while the telomere length of the oocytes seems not to follow similar patterns with that of sperm. Nonetheless, the telomere length of the embryos during the cleavage stages seems to have a paternal origin, but the telomere length can be further extended by telomerase activity during the blastocyst stage. The latter has been proposed as a new molecular biomarker with strong predictive value regarding male infertility. As far as the role of telomeres in assisted reproduction, the data is limited but the length of telomeres in both gametes seems to be affected mainly by the cause of infertility rather than the assisted reproductive therapy (ART) procedure itself. The present review aims to shed more light into the role of telomeres in human embryological parameters, including gametes and embryos and also presents opinions regarding the association between telomeres and in vitro fertilization (IVF).
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Affiliation(s)
- George Anifandis
- Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41222 Larisa, Greece; (C.I.M.); (A.D.)
- Correspondence:
| | - Maria Samara
- Department of Anatomical Pathology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41222 Larisa, Greece; (M.S.); (E.T.)
| | - Mara Simopoulou
- Laboratory of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Christina I. Messini
- Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41222 Larisa, Greece; (C.I.M.); (A.D.)
| | - Katerina Chatzimeletiou
- Unit for Human Reproduction, 1st Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences, Aristotelian University of Thessaloniki, 56403 Thessaloniki, Greece;
| | - Eleni Thodou
- Department of Anatomical Pathology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41222 Larisa, Greece; (M.S.); (E.T.)
| | - Alexandros Daponte
- Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41222 Larisa, Greece; (C.I.M.); (A.D.)
| | - Ioannis Georgiou
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece;
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Lin WY, Wang YC, Teng IH, Liu C, Lou XY. Associations of five obesity metrics with epigenetic age acceleration: Evidence from 2,474 Taiwan Biobank participants. Obesity (Silver Spring) 2021; 29:1731-1738. [PMID: 34472716 DOI: 10.1002/oby.23255] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Obesity is associated with epigenetic age acceleration (EAA), resulting in an increased risk of many age-related disorders. However, most studies have focused on the relationship of EAA with BMI. Whether any other obesity metric is more relevant to EAA remains unknown. METHODS Here, the methylation ages of 2,474 Taiwan Biobank (TWB) participants were calculated according to Levine's phenotypic age (PhenoAge) and Lu's GrimAge. Residuals from regressing methylation age on chronological age were used to quantify PhenoEAA and GrimEAA. Five obesity metrics were evaluated, namely BMI, body fat percentage, waist circumference, hip circumference, and waist-hip ratio. Sex-stratified EAA was regressed on each of the five obesity metrics. RESULTS For male individuals, an increase of one SD in waist-hip ratio (0.06) was associated with a 0.602-year PhenoEAA (p = 6.3E-6) and a 0.481-year GrimEAA (p = 1.2E-8). For female individuals, every SD increase in BMI (3.7 kg/m2 ) was associated with a 0.600-year PhenoEAA (p = 3.3E-5) and a 0.305-year GrimEAA (p = 3.1E-5). CONCLUSIONS "Abdominal obesity" and "general obesity" are significantly associated with male and female EAA, respectively. The prevention of abdominal obesity and general obesity is associated with a lower risk of EAA in men and women, respectively.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
- Master of Public Health Degree Program, College of Public Health, National Taiwan University, Taipei, Taiwan
- Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yu-Cyuan Wang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - I-Hsuan Teng
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chi Liu
- Master Program in Statistics, National Taiwan University, Taipei, Taiwan
| | - Xiang-Yang Lou
- Department of Biostatistics, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA
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41
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Habibe JJ, Clemente-Olivo MP, de Vries CJ. How (Epi)Genetic Regulation of the LIM-Domain Protein FHL2 Impacts Multifactorial Disease. Cells 2021; 10:2611. [PMID: 34685595 PMCID: PMC8534169 DOI: 10.3390/cells10102611] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 01/13/2023] Open
Abstract
Susceptibility to complex pathological conditions such as obesity, type 2 diabetes and cardiovascular disease is highly variable among individuals and arises from specific changes in gene expression in combination with external factors. The regulation of gene expression is determined by genetic variation (SNPs) and epigenetic marks that are influenced by environmental factors. Aging is a major risk factor for many multifactorial diseases and is increasingly associated with changes in DNA methylation, leading to differences in gene expression. Four and a half LIM domains 2 (FHL2) is a key regulator of intracellular signal transduction pathways and the FHL2 gene is consistently found as one of the top hyper-methylated genes upon aging. Remarkably, FHL2 expression increases with methylation. This was demonstrated in relevant metabolic tissues: white adipose tissue, pancreatic β-cells, and skeletal muscle. In this review, we provide an overview of the current knowledge on regulation of FHL2 by genetic variation and epigenetic DNA modification, and the potential consequences for age-related complex multifactorial diseases.
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Affiliation(s)
- Jayron J. Habibe
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, and Amsterdam Gastroenterology, Endocrinology and Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.J.H.); (M.P.C.-O.)
- Department of Physiology, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, 1081 HV Amsterdam, The Netherlands
| | - Maria P. Clemente-Olivo
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, and Amsterdam Gastroenterology, Endocrinology and Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.J.H.); (M.P.C.-O.)
| | - Carlie J. de Vries
- Department of Medical Biochemistry, Amsterdam University Medical Centers, Amsterdam Cardiovascular Sciences, and Amsterdam Gastroenterology, Endocrinology and Metabolism, 1105 AZ Amsterdam, The Netherlands; (J.J.H.); (M.P.C.-O.)
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42
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Checknita D, Tiihonen J, Hodgins S, Nilsson KW. Associations of age, sex, sexual abuse, and genotype with monoamine oxidase a gene methylation. J Neural Transm (Vienna) 2021; 128:1721-1739. [PMID: 34424394 PMCID: PMC8536631 DOI: 10.1007/s00702-021-02403-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022]
Abstract
Epigenome-wide studies report higher methylation among women than men with decreasing levels with age. Little is known about associations of sex and age with methylation of monoamine oxidase A (MAOA). Methylation of the first exonic and partial first intronic region of MAOA has been shown to strengthen associations of interactions of MAOA-uVNTR genotypes and adversity with aggression and substance misuse. Our study examined associations of sex and age with MAOA first exon and intron methylation levels in 252 women and 157 men aged 14–73 years. Participants included adolescents recruited at a substance misuse clinic, their siblings and parents, and healthy women. Women showed ~ 50% higher levels of exonic, and ~ 15% higher intronic, methylation than men. Methylation levels were similar between younger (M = 22.7 years) and older (M = 46.1 years) participants, and stable across age. Age modified few associations of methylation levels with sex. MAOA genotypes modified few associations of methylation with sex and age. Higher methylation levels among women were not explained by genotype, nor interaction of genotype and sexual abuse. Findings were similar after adjusting for lifetime diagnoses of substance dependence (women = 24.3%; men = 34.2%). Methylation levels were higher among women who experienced sexual abuse than women who did not. Results extend on prior studies by showing that women display higher levels of methylation than men within first intronic/exonic regions of MAOA, which did not decrease with age in either sex. Findings were not conditioned by genotype nor interactions of genotype and trauma, and indicate X-chromosome inactivation.
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Affiliation(s)
- David Checknita
- Department of Neuroscience, Uppsala University, Uppsala, Sweden. .,Department of Clinical Neuroscience, Karolinska Institutet, Psychiatry Building R5:00 c/o Jari Tiihonen, Karolinska Universitetssjukhuset, 171 76, Stockholm, Sweden. .,Centre for Clinical Research, Västmanland County Council, Uppsala University, Uppsala, Sweden.
| | - Jari Tiihonen
- Department of Clinical Neuroscience, Karolinska Institutet, Psychiatry Building R5:00 c/o Jari Tiihonen, Karolinska Universitetssjukhuset, 171 76, Stockholm, Sweden.,Center for Psychiatry Research, Stockholm City Council, Stockholm, Sweden.,Department of Forensic Psychiatry, Niuvanniemi Hospital, University of Eastern Finland, Kuopio, Finland
| | - Sheilagh Hodgins
- Department of Clinical Neuroscience, Karolinska Institutet, Psychiatry Building R5:00 c/o Jari Tiihonen, Karolinska Universitetssjukhuset, 171 76, Stockholm, Sweden.,Département de Psychiatrie et Addictologie, Centre de Recherche de l'Institut Universitaire en Santé Mentale de Montréal, Université de Montréal, Montréal, QC, Canada
| | - Kent W Nilsson
- Department of Neuroscience, Uppsala University, Uppsala, Sweden.,Centre for Clinical Research, Västmanland County Council, Uppsala University, Uppsala, Sweden
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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Willscher E, Hopp L, Kreuz M, Schmidt M, Hakobyan S, Arakelyan A, Hentschel B, Jones DTW, Pfister SM, Loeffler M, Loeffler-Wirth H, Binder H. High-Resolution Cartography of the Transcriptome and Methylome Landscapes of Diffuse Gliomas. Cancers (Basel) 2021; 13:3198. [PMID: 34206856 PMCID: PMC8268631 DOI: 10.3390/cancers13133198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 02/01/2023] Open
Abstract
Molecular mechanisms of lower-grade (II-III) diffuse gliomas (LGG) are still poorly understood, mainly because of their heterogeneity. They split into astrocytoma- (IDH-A) and oligodendroglioma-like (IDH-O) tumors both carrying mutations(s) at the isocitrate dehydrogenase (IDH) gene and into IDH wild type (IDH-wt) gliomas of glioblastoma resemblance. We generated detailed maps of the transcriptomes and DNA methylomes, revealing that cell functions divided into three major archetypic hallmarks: (i) increased proliferation in IDH-wt and, to a lesser degree, IDH-O; (ii) increased inflammation in IDH-A and IDH-wt; and (iii) the loss of synaptic transmission in all subtypes. Immunogenic properties of IDH-A are diverse, partly resembling signatures observed in grade IV mesenchymal glioblastomas or in grade I pilocytic astrocytomas. We analyzed details of coregulation between gene expression and DNA methylation and of the immunogenic micro-environment presumably driving tumor development and treatment resistance. Our transcriptome and methylome maps support personalized, case-by-case views to decipher the heterogeneity of glioma states in terms of data portraits. Thereby, molecular cartography provides a graphical coordinate system that links gene-level information with glioma subtypes, their phenotypes, and clinical context.
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Affiliation(s)
- Edith Willscher
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Lydia Hopp
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Markus Kreuz
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Siras Hakobyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Arsen Arakelyan
- Research Group of Bioinformatics, Institute of Molecular Biology of the National Academy of Sciences of the Republic of Armenia, 7 Hasratyan Str., Yerevan 0014, Armenia; (S.H.); (A.A.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
| | - Bettina Hentschel
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - David T. W. Jones
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Stefan M. Pfister
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120 Heidelberg, Germany
| | - Markus Loeffler
- IMISE, Institute for Medical Informatics, Statistics and Epidemiology, Universität of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (M.K.); (B.H.); (M.L.)
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany; (E.W.); (L.H.); (M.S.)
- Armenian Bioinformatics Institute (ABI), 7 Hasratyan Str., Yerevan 0014, Armenia; (D.T.W.J.); (S.M.P.)
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45
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Srikulwong U, Phanchai W, Srepusharawoot P, Sakonsinsiri C, Puangmali T. Computational Insights into Molecular Adsorption Characteristics of Methylated DNA on Graphene Oxide for Multicancer Early Detection. J Phys Chem B 2021; 125:6697-6708. [PMID: 34110832 DOI: 10.1021/acs.jpcb.1c02808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA methylation is an epigenetic modification involving the transfer of a methyl group to cytosine residues of a DNA molecule. Altered DNA methylation of certain genes is associated with several diseases including cancer. Nanomaterials, such as graphene oxide (GO), offer great potential as sensing elements for methylated DNA (mDNA) detection due to their distinct properties. Understanding molecular interactions between mDNA and GO can make provision for developing a universal cancer screening test. Molecular dynamics (MD) simulation and density functional theory (DFT) calculation have been employed for investigating their detailed macro- and microscale interactions. Based upon the MD simulation, different adsorption levels of methylated and unmethylated DNAs on GO were represented by a contacting surface area (CSA), which depends on surrounding conditions (in water or a MgCl2 solution). In water, the CSAs of the methylated and unmethylated single-stranded DNA (ssDNA) were ≈13 and ≈5 nm2, respectively, representing more preferable adsorption on GO for the methylated ssDNA. In the presence of divalent ions (Mg2+), the CSAs of both methylated and unmethylated DNA molecules were ≈8 nm2, suggesting that there was no significant difference in adsorption in a saline solution. To reveal the electrical property of GO covered by either methylated or unmethylated DNA, its electronic structure was investigated by the DFT calculation. The energy gaps of pristine graphene (pG) and GO adsorbed by 5-methylcytosine (5mC) were 1.6 and 12.9 meV, respectively, while cytosine adsorption resulted in lower energy gaps (1.2 meV for pG and 9.5 meV for GO). When comparing methylated DNA-covered GO with that covered with unmethylated DNA, remarkable differences in electrical conductivity, which were caused by the electronic structure of GO, were observed. These findings will provide a new route for an efficient detection method of DNA methylation, which can further be used to develop a universal cancer test.
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Affiliation(s)
- Unnop Srikulwong
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Witthawat Phanchai
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Pornjuk Srepusharawoot
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Theerapong Puangmali
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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Zupkovitz G, Kabiljo J, Kothmayer M, Schlick K, Schöfer C, Lagger S, Pusch O. Analysis of Methylation Dynamics Reveals a Tissue-Specific, Age-Dependent Decline in 5-Methylcytosine Within the Genome of the Vertebrate Aging Model Nothobranchius furzeri. Front Mol Biosci 2021; 8:627143. [PMID: 34222326 PMCID: PMC8242171 DOI: 10.3389/fmolb.2021.627143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 06/02/2021] [Indexed: 12/12/2022] Open
Abstract
Erosion of the epigenetic DNA methylation landscape is a widely recognized hallmark of aging. Emerging advances in high throughput sequencing techniques, in particular DNA methylation data analysis, have resulted in the establishment of precise human and murine age prediction tools. In vertebrates, methylation of cytosine at the C5 position of CpG dinucleotides is executed by DNA methyltransferases (DNMTs) whereas the process of enzymatic demethylation is highly dependent on the activity of the ten-eleven translocation methylcytosine dioxygenase (TET) family of enzymes. Here, we report the identification of the key players constituting the DNA methylation machinery in the short-lived teleost aging model Nothobranchius furzeri. We present a comprehensive spatio-temporal expression profile of the methylation-associated enzymes from embryogenesis into late adulthood, thereby covering the complete killifish life cycle. Data mining of the N. furzeri genome produced five dnmt gene family orthologues corresponding to the mammalian DNMTs (DNMT1, 2, 3A, and 3B). Comparable to other teleost species, N. furzeri harbors multiple genomic copies of the de novo DNA methylation subfamily. A related search for the DNMT1 recruitment factor UHRF1 and TET family members resulted in the identification of N. furzeri uhrf1, tet1, tet2, and tet3. Phylogenetic analysis revealed high cross-species similarity on the amino acid level of all individual dnmts, tets, and uhrf1, emphasizing a high degree of functional conservation. During early killifish development all analyzed dnmts and tets showed a similar expression profile characterized by a strong increase in transcript levels after fertilization, peaking either at embryonic day 6 or at the black eye stage of embryonic development. In adult N. furzeri, DNA methylation regulating enzymes showed a ubiquitous tissue distribution. Specifically, we observed an age-dependent downregulation of dnmts, and to some extent uhrf1, which correlated with a significant decrease in global DNA methylation levels in the aging killifish liver and muscle. The age-dependent DNA methylation profile and spatio-temporal expression characteristics of its enzymatic machinery reported here may serve as an essential platform for the identification of an epigenetic aging clock in the new vertebrate model system N. furzeri.
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Affiliation(s)
- Gordin Zupkovitz
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.,Department of Life Science Engineering, University of Applied Sciences Technikum Wien, Vienna, Austria.,City of Vienna Competence Team Aging Tissue, Vienna, Austria
| | - Julijan Kabiljo
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria.,Department of General Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Michael Kothmayer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Katharina Schlick
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Christian Schöfer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Sabine Lagger
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Oliver Pusch
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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Li T, Wei Y, Qu M, Mou L, Miao J, Xi M, Liu Y, He R. Formaldehyde and De/Methylation in Age-Related Cognitive Impairment. Genes (Basel) 2021; 12:genes12060913. [PMID: 34199279 PMCID: PMC8231798 DOI: 10.3390/genes12060913] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/31/2021] [Accepted: 06/10/2021] [Indexed: 12/19/2022] Open
Abstract
Formaldehyde (FA) is a highly reactive substance that is ubiquitous in the environment and is usually considered as a pollutant. In the human body, FA is a product of various metabolic pathways and participates in one-carbon cycle, which provides carbon for the synthesis and modification of bio-compounds, such as DNA, RNA, and amino acids. Endogenous FA plays a role in epigenetic regulation, especially in the methylation and demethylation of DNA, histones, and RNA. Recently, epigenetic alterations associated with FA dysmetabolism have been considered as one of the important features in age-related cognitive impairment (ARCI), suggesting the potential of using FA as a diagnostic biomarker of ARCI. Notably, FA plays multifaceted roles, and, at certain concentrations, it promotes cell proliferation, enhances memory formation, and elongates life span, effects that could also be involved in the aetiology of ARCI. Further investigation of and the regulation of the epigenetics landscape may provide new insights about the aetiology of ARCI and provide novel therapeutic targets.
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Affiliation(s)
- Ting Li
- Bayannur Hospital, Bayannur 015000, China;
| | - Yan Wei
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
| | - Meihua Qu
- Translational Medical Center, Weifang Second People’s Hospital, The Second Affiliated Hospital of Weifang Medical University, Weifang 261041, China;
| | - Lixian Mou
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
| | - Junye Miao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
| | - Mengqi Xi
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China; (M.X.); (Y.L.)
| | - Ying Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China; (M.X.); (Y.L.)
| | - Rongqiao He
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (Y.W.); (L.M.); (J.M.)
- Correspondence:
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Cykowiak M, Krajka-Kuźniak V, Baer-Dubowska W. Combinations of Phytochemicals More Efficiently than Single Components Activate Nrf2 and Induce the Expression of Antioxidant Enzymes in Pancreatic Cancer Cells. Nutr Cancer 2021; 74:996-1011. [PMID: 34120541 DOI: 10.1080/01635581.2021.1933097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 01/25/2021] [Accepted: 04/30/2021] [Indexed: 12/21/2022]
Abstract
Cancer prevention particularly related to aging can be improved by the use of phytochemicals combinations. In this study, we evaluated the effect of phenethyl isothiocyanate (PEITC), xanthohumol (XAN), indole-3-carbinol (I3C), and resveratrol (RES) and their combinations on the Nrf2 signaling pathway. Human pancreatic cancer cells MIA-Pa-Ca-2 were treated with the phytochemicals alone or their equimolar mixture for 24 h and activation of Nrf2 and expression of its target genes were evaluated. Phytochemicals alone enhanced Nrf2 activation and expression, but their combinations were more efficient. The mixture of XAN and PEITC was found to be the most potent modulator of the Nrf2 pathway. Moreover, increased levels of P-Nrf2 and P-JNK and decreased level of P-GSK-3β suggested possible activation of Nrf2 through modulation of these kinases. The combinations of XAN with PEITC and RES with PEITC increased mostly the expression of SOD, GSTP, CAT, and GPx. XAN and PEITC mixture induced the cell cycle arrest in G0/G1 phase and increased apoptotic and autophagy markers. These results indicate that combinations of phytochemicals resembling that occurring in natural diets may efficiently modulate the signaling pathways, which proper function is important for pancreatic cancer prophylaxis or improving the results of conventional therapy.
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Affiliation(s)
- Marta Cykowiak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Poznań, Poland
| | - Violetta Krajka-Kuźniak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Poznań, Poland
| | - Wanda Baer-Dubowska
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Poznań, Poland
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49
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Different epigenetic signatures of newborn telomere length and telomere attrition rate in early life. Aging (Albany NY) 2021; 13:14630-14650. [PMID: 34086604 PMCID: PMC8221291 DOI: 10.18632/aging.203117] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/17/2021] [Indexed: 12/22/2022]
Abstract
Telomere length (TL) and telomere shortening are biological indicators of aging, and epigenetic associates have been found for TL in adults. However, the role of epigenetic signatures in setting newborn TL and early life telomere dynamics is unknown. In the present study, based on 247 participating newborns from the ENVIRONAGE birth cohort, whole-genome DNA methylation, profiled on the Illumina MethylationEPIC BeadChip microarray, and TL were measured in cord blood. In a follow-up visit at a mean age of 4.58 years, leukocyte TL was evaluated. We combined an epigenome-wide association study and a statistical learning method with re-sampling to select CpGs and their two-way interactions to model baseline (cord blood) TL and early-life telomere attrition rate, where distinct epigenetic signatures were identified for the two outcomes. In addition, a stronger epigenetic regulation was suggested in setting newborn TL than that of telomere dynamics in early life: 47 CpGs and 7 between-CpG interactions explained 76% of the variance in baseline TLs, while 72% of the total variance in telomere attrition rate was explained by 31 CpGs and 5 interactions. Functional enrichment analysis based on the selected CpGs in the two models revealed GLUT4 translocation and immune cell signaling pathways, respectively. These CpGs and interactions, as well as the cellular pathways, are potential novel targets of further investigation of telomere biology and aging.
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50
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Bravo-Moreno A. Reproductive agency, assisted reproductive technology & obstetric violence. Health Care Women Int 2021; 43:806-826. [PMID: 33960876 DOI: 10.1080/07399332.2021.1883026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In this article, I draw on ethnographic research I conducted in the UK and Spain. I analyse the experiences of women who chose to become mothers with the assistance of reproductive technologies (ART). All the women intended to have a natural birth in hospital and they reported that hospitals categorised their pregnancies as high-risk on the basis of their age (35-47 years) and the use of ART. How do these women deal with their reproductive treatment? How does hospital culture impact on women's birthing bodies and psyche? What are the struggles they undergo to defend their wish to have a "natural" birth?
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Affiliation(s)
- Ana Bravo-Moreno
- Thomas Coram Research Unit, University College London, London, UK.,Department of Social Anthropology, Universidad de Granada, Granada, Spain
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