1
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Riccardi F, Romano G, Licastro D, Pagani F. Age-dependent regulation of ELP1 exon 20 splicing in Familial Dysautonomia by RNA Polymerase II kinetics and chromatin structure. PLoS One 2024; 19:e0298965. [PMID: 38829854 PMCID: PMC11146744 DOI: 10.1371/journal.pone.0298965] [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: 10/14/2023] [Accepted: 02/01/2024] [Indexed: 06/05/2024] Open
Abstract
Familial Dysautonomia (FD) is a rare disease caused by ELP1 exon 20 skipping. Here we clarify the role of RNA Polymerase II (RNAPII) and chromatin on this splicing event. A slow RNAPII mutant and chromatin-modifying chemicals that reduce the rate of RNAPII elongation induce exon skipping whereas chemicals that create a more relaxed chromatin exon inclusion. In the brain of a mouse transgenic for the human FD-ELP1 we observed on this gene an age-dependent decrease in the RNAPII density profile that was most pronounced on the alternative exon, a robust increase in the repressive marks H3K27me3 and H3K9me3 and a decrease of H3K27Ac, together with a progressive reduction in ELP1 exon 20 inclusion level. In HEK 293T cells, selective drug-induced demethylation of H3K27 increased RNAPII elongation on ELP1 and SMN2, promoted the inclusion of the corresponding alternative exons, and, by RNA-sequencing analysis, induced changes in several alternative splicing events. These data suggest a co-transcriptional model of splicing regulation in which age-dependent changes in H3K27me3/Ac modify the rate of RNAPII elongation and affect processing of ELP1 alternative exon 20.
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Affiliation(s)
- Federico Riccardi
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Giulia Romano
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Danilo Licastro
- Laboratorio di Genomica ed Epigenomica, AREA Science Park, Padriciano, Trieste, Italy
| | - Franco Pagani
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
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2
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Han X, Akinseye L, Sun Z. KDM6A Demethylase Regulates Renal Sodium Excretion and Blood Pressure. Hypertension 2024; 81:541-551. [PMID: 38164755 PMCID: PMC10922853 DOI: 10.1161/hypertensionaha.123.22026] [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: 09/07/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND KDM6A (Lysine-Specific Demethylase 6A) is a specific demethylase for histone 3 lysine (K) 27 trimethylation (H3K27me3). The purpose of this study is to investigate whether KDM6A in renal tubule cells plays a role in the regulation of kidney function and blood pressure. METHODS We first crossed Ksp-Cre+/- and KDM6Aflox/flox mice for generating inducible kidney-specific deletion of KDM6A gene. RESULTS Notably, conditional knockout of KDM6A gene in renal tubule cells (KDM6A-cKO) increased H3K27me3 levels which leads to a decrease in Na excretion and elevation of blood pressure. Further analysis showed that the expression of NKCC2 (Na-K-2Cl cotransporter 2) and NCC (Na-Cl cotransporters) was upregulated which contributes to impaired Na excretion in KDM6A-cKO mice. The expression of AQP2 (aquaporin 2) was also increased in KDM6A-cKO mice, which may facilitate water reabsorption in KDM6A-cKO mice. The expression of Klotho was downregulated while expression of aging markers including p53, p21, and p16 was upregulated in kidneys of KDM6A-cKO mice, indicating that deletion of KDM6A in the renal tubule cells promotes kidney aging. Interestingly, KDM6A-cKO mice developed salt-sensitive hypertension which can be rescued by treatment with Klotho. KDM6A deficiency induced salt-sensitive hypertension likely through downregulation of the Klotho/ERK (extracellular signal-regulated kinase) signaling and upregulation of the WNK (with-no-lysine kinase) signaling. CONCLUSIONS This study provides the first evidence that KDM6A plays an essential role in maintaining normal tubular function and blood pressure. Renal tubule cell specific KDM6A deficiency causes hypertension due to increased H3K27me3 levels and the resultant downregulation of Klotho gene expression which disrupts the Klotho/ERK/NCC/NKCC2 signaling.
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Affiliation(s)
- Xiaobin Han
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Leah Akinseye
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Zhongjie Sun
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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3
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Callegari S, Mirzaei F, Agbaria L, Shariff S, Kantawala B, Moronge D, Ogendi BMO. Zebrafish as an Emerging Model for Sarcopenia: Considerations, Current Insights, and Future Directions. Int J Mol Sci 2023; 24:17018. [PMID: 38069340 PMCID: PMC10707505 DOI: 10.3390/ijms242317018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Sarcopenia poses a significant challenge to public health and can severely impact the quality of life of aging populations. Despite extensive efforts to study muscle degeneration using traditional animal models, there is still a lack of effective diagnostic tools, precise biomarkers, and treatments for sarcopenia. Zebrafish models have emerged as powerful tools in biomedical research, providing unique insights into age-related muscle disorders like sarcopenia. The advantages of using zebrafish models include their rapid growth outside of the embryo, optical transparency during early developmental stages, high reproductive potential, ease of husbandry, compact size, and genetic tractability. By deepening our understanding of the molecular processes underlying sarcopenia, we may develop novel diagnostic tools and effective treatments that can improve the lives of aging individuals affected by this condition. This review aims to explore the unique advantages of zebrafish as a model for sarcopenia research, highlight recent breakthroughs, outline potential avenues for future investigations, and emphasize the distinctive contributions that zebrafish models offer. Our research endeavors to contribute significantly to address the urgent need for practical solutions to reduce the impact of sarcopenia on aging populations, ultimately striving to enhance the quality of life for individuals affected by this condition.
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Affiliation(s)
- Santiago Callegari
- Vascular Medicine Outcomes Laboratory, Cardiology Department, Yale University, New Haven, CT 06510, USA
| | - Foad Mirzaei
- Faculty of General Medicine, Yerevan State Medical University after Mikhtar Heratsi, 2 Koryun, Yerevan 0025, Armenia; (F.M.); (L.A.); (B.K.)
| | - Lila Agbaria
- Faculty of General Medicine, Yerevan State Medical University after Mikhtar Heratsi, 2 Koryun, Yerevan 0025, Armenia; (F.M.); (L.A.); (B.K.)
| | - Sanobar Shariff
- Faculty of General Medicine, Yerevan State Medical University after Mikhtar Heratsi, 2 Koryun, Yerevan 0025, Armenia; (F.M.); (L.A.); (B.K.)
| | - Burhan Kantawala
- Faculty of General Medicine, Yerevan State Medical University after Mikhtar Heratsi, 2 Koryun, Yerevan 0025, Armenia; (F.M.); (L.A.); (B.K.)
| | - Desmond Moronge
- Department of Physiology, Medical College of Georgia, Augusta, GA 30912, USA;
| | - Brian M. O. Ogendi
- Department of Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA;
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4
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Xu A, Teefy BB, Lu RJ, Nozownik S, Tyers AM, Valenzano DR, Benayoun BA. Transcriptomes of aging brain, heart, muscle, and spleen from female and male African turquoise killifish. Sci Data 2023; 10:695. [PMID: 37828039 PMCID: PMC10570339 DOI: 10.1038/s41597-023-02609-x] [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: 06/21/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
The African turquoise killifish is an emerging vertebrate model organism with great potential for aging research due to its naturally short lifespan. Thus far, turquoise killifish aging 'omic' studies have examined a single organ, single sex and/or evaluated samples from non-reference strains. Here, we describe a resource dataset of ribosomal RNA-depleted RNA-seq libraries generated from the brain, heart, muscle, and spleen from both sexes, as well as young and old animals, in the reference GRZ turquoise killifish strain. We provide basic quality control steps and demonstrate the utility of our dataset by performing differential gene expression and gene ontology analyses by age and sex. Importantly, we show that age has a greater impact than sex on transcriptional landscapes across probed tissues. Finally, we confirm transcription of transposable elements (TEs), which are highly abundant and increase in expression with age in brain tissue. This dataset will be a useful resource for exploring gene and TE expression as a function of both age and sex in a powerful naturally short-lived vertebrate model.
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Affiliation(s)
- Alan Xu
- Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, 90089, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ryan J Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, USA
| | - Séverine Nozownik
- Unit of Forensic Genetics, University Center of Legal Medicine, Lausanne, Switzerland
| | - Alexandra M Tyers
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Strasse 9b, 50931, Cologne, Germany
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
| | - Dario R Valenzano
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Strasse 9b, 50931, Cologne, Germany
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, 90089, USA.
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, 90089, USA.
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA.
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5
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Pollina EA, Greer EL. Prometheus unshackled: Liver regeneration makes you young. Mol Cell 2023; 83:1546-1548. [PMID: 37207622 DOI: 10.1016/j.molcel.2023.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/21/2023]
Abstract
In this issue of Molecular Cell, Yang and colleagues1 discover age-dependent increases in broad regions of the repressive histone modification H3K27me3. They also demonstrate partial reversion to younger H3K27me3 patterns and gene expression upon resection of older livers.
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Affiliation(s)
- Elizabeth Ann Pollina
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Eric Lieberman Greer
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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6
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Yang N, Occean JR, Melters DP, Shi C, Wang L, Stransky S, Doyle ME, Cui CY, Delannoy M, Fan J, Slama E, Egan JM, De S, Cunningham SC, de Cabo R, Sidoli S, Dalal Y, Sen P. A hyper-quiescent chromatin state formed during aging is reversed by regeneration. Mol Cell 2023; 83:1659-1676.e11. [PMID: 37116496 PMCID: PMC10228348 DOI: 10.1016/j.molcel.2023.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 02/03/2023] [Accepted: 04/03/2023] [Indexed: 04/30/2023]
Abstract
Epigenetic alterations are a key hallmark of aging but have been limitedly explored in tissues. Here, using naturally aged murine liver as a model and extending to other quiescent tissues, we find that aging is driven by temporal chromatin alterations that promote a refractory cellular state and compromise cellular identity. Using an integrated multi-omics approach and the first direct visualization of aged chromatin, we find that globally, old cells show H3K27me3-driven broad heterochromatinization and transcriptional suppression. At the local level, site-specific loss of H3K27me3 over promoters of genes encoding developmental transcription factors leads to expression of otherwise non-hepatocyte markers. Interestingly, liver regeneration reverses H3K27me3 patterns and rejuvenates multiple molecular and physiological aspects of the aged liver.
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Affiliation(s)
- Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - James R Occean
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Daniël P Melters
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 21224, USA
| | - Changyou Shi
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Lin Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY 10461, USA
| | - Maire E Doyle
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Chang-Yi Cui
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Michael Delannoy
- JHU SOM Microscope Facility, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jinshui Fan
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Eliza Slama
- Department of Surgery, Ascension Saint Agnes Hospital, Baltimore, MD 21229, USA
| | - Josephine M Egan
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Supriyo De
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Steven C Cunningham
- Department of Surgery, Ascension Saint Agnes Hospital, Baltimore, MD 21229, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY 10461, USA
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 21224, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD 21224, USA.
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7
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Therapeutic potential of natural molecules against Alzheimer's disease via SIRT1 modulation. Biomed Pharmacother 2023; 161:114474. [PMID: 36878051 DOI: 10.1016/j.biopha.2023.114474] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease mainly characterized by progressive cognitive dysfunction and memory impairment. Recent studies have shown that regulating silent information regulator 1 (SIRT1) expression has a significant neuroprotective effect, and SIRT1 may become a new therapeutic target for AD. Natural molecules are an important source of drug development for use in AD therapy and may regulate a wide range of biological events by regulating SIRT1 as well as other SIRT1-mediated signaling pathways. This review aims to summarize the correlation between SIRT1 and AD and to identify in vivo and in vitro studies investigating the anti-AD properties of natural molecules as modulators of SIRT1 and SIRT1-mediated signaling pathways. A literature search was conducted for studies published between January 2000 and October 2022 using various literature databases, including Web of Science, PubMed, Google Scholar, Science Direct, and EMBASE. Natural molecules, such as resveratrol, quercetin, icariin, bisdemethoxycurcumin, dihydromyricetin, salidroside, patchouli, sesamin, rhein, ligustilide, tetramethoxyflavanone, 1-theanine, schisandrin, curcumin, betaine, pterostilbene, ampelopsin, schisanhenol, and eriodictyol, have the potential to modulate SIRT1 and SIRT1 signaling pathways, thereby combating AD. The natural molecules modulating SIRT1 discussed in this review provide a potentially novel multi-mechanistic therapeutic strategy for AD. However, future clinical trials need to be conducted to further investigate their beneficial properties and to determine the safety and efficacy of SIRT1 natural activators against AD.
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8
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Teefy B, Malone M, Benayoun BA. Differential Expression Analysis of Nothobranchius furzeri Transposable Elements from RNA-seq Data. Cold Spring Harb Protoc 2023; 2023:35-47. [PMID: 36223994 PMCID: PMC9812909 DOI: 10.1101/pdb.prot107748] [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] [Indexed: 11/06/2022]
Abstract
Transposable elements (TEs) comprise large fractions of eukaryotic genomes, but their repetitive nature and high copy number makes bioinformatic analyses more complex. Here, we report three robust pipelines to analyze TE expression from RNA-seq data in a non-model organism, the African turquoise killifish Nothobranchius furzeri Our protocol can be run with either a genomic or transcriptomic reference depending on available computational resources, with options both for limited memory usage and for more computationally intensive analyses. Our protocol leverages both standard software for classical RNA-seq analysis pipelines as well as software specialized for TEs. This protocol uses input RNA-seq data from Illumina reads and can use data in either single-end or paired-end layout. Here, we show how to start from input RNA-seq data from aging killifish tissues using a publicly available data set from which we take single and paired reads, trim adapters, align and count trimmed reads, and perform differential expression analyses for TEs.
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Affiliation(s)
- Bryan Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
| | - Matthew Malone
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
- Master's program in Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, California 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, California 90089, USA
- USC Stem Cell Initiative, Los Angeles, California 90089, USA
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9
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Abstract
Frailty is a complex syndrome affecting a growing sector of the global population as medical developments have advanced human mortality rates across the world. Our current understanding of frailty is derived from studies conducted in the laboratory as well as the clinic, which have generated largely phenotypic information. Far fewer studies have uncovered biological underpinnings driving the onset and progression of frailty, but the stage is set to advance the field with preclinical and clinical assessment tools, multiomics approaches together with physiological and biochemical methodologies. In this article, we provide comprehensive coverage of topics regarding frailty assessment, preclinical models, interventions, and challenges as well as clinical frameworks and prevalence. We also identify central biological mechanisms that may be at play including mitochondrial dysfunction, epigenetic alterations, and oxidative stress that in turn, affect metabolism, stress responses, and endocrine and neuromuscular systems. We review the role of metabolic syndrome, insulin resistance and visceral obesity, focusing on glucose homeostasis, adenosine monophosphate-activated protein kinase (AMPK), mammalian target of rapamycin (mTOR), and nicotinamide adenine dinucleotide (NAD+ ) as critical players influencing the age-related loss of health. We further focus on how immunometabolic dysfunction associates with oxidative stress in promoting sarcopenia, a key contributor to slowness, weakness, and fatigue. We explore the biological mechanisms involved in stem cell exhaustion that affect regeneration and may contribute to the frailty-associated decline in resilience and adaptation to stress. Together, an overview of the interplay of aging biology with genetic, lifestyle, and environmental factors that contribute to frailty, as well as potential therapeutic targets to lower risk and slow the progression of ongoing disease is covered. © 2022 American Physiological Society. Compr Physiol 12:1-46, 2022.
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Affiliation(s)
- Laís R. Perazza
- Department of Physical Therapy and Athletic Training, Boston University, Boston, Massachusetts, USA
| | - Holly M. Brown-Borg
- Department of Biomedical Sciences, University of North Dakota, Grand Forks, North Dakota, USA
| | - LaDora V. Thompson
- Department of Physical Therapy and Athletic Training, Boston University, Boston, Massachusetts, USA
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10
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Lin Z, Ding Q, Li X, Feng Y, He H, Huang C, Zhu Y. Targeting Epigenetic Mechanisms in Vascular Aging. Front Cardiovasc Med 2022; 8:806988. [PMID: 35059451 PMCID: PMC8764463 DOI: 10.3389/fcvm.2021.806988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/30/2021] [Indexed: 12/28/2022] Open
Abstract
Environment, diseases, lack of exercise, and aged tendency of population have becoming crucial factors that induce vascular aging. Vascular aging is unmodifiable risk factor for diseases like diabetes, hypertension, atherosclerosis, and hyperlipidemia. Effective interventions to combat this vascular function decline is becoming increasingly urgent as the rising hospitalization rate caused by vascular aging-related diseases. Fortunately, recent transformative omics approaches have enabled us to examine vascular aging mechanisms at unprecedented levels and precision, which make our understanding of slowing down or reversing vascular aging become possible. Epigenetic viz. DNA methylation, histone modifications, and non-coding RNA-based mechanisms, is a hallmark of vascular aging, its deregulation leads to aberrant transcription changes in tissues. Epigenetics mechanisms by mediating covalent modifications to DNA and histone proteins, consequently, influence the sensitivity and activities of signaling pathways in cells and tissues. A growing body of evidence supports correlations between epigenetic changes and vascular aging. In this article, we will provide a comprehensive overview of epigenetic changes associated with vascular aging based on the recent findings with a focus on molecular mechanisms of action, strategies to reverse epigenetic changes, and future perspectives.
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Affiliation(s)
- Zhongxiao Lin
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macao SAR, China
- Key Laboratory of Molecular Target and Clinical Pharmacology and National Key Laboratory of Respiratory Diseases, School of Pharmaceutic Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qian Ding
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macao SAR, China
| | - Xinzhi Li
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macao SAR, China
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Hao He
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macao SAR, China
| | - Chuoji Huang
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macao SAR, China
| | - YiZhun Zhu
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macao SAR, China
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China
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11
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Terzibasi Tozzini E, Cellerino A. Nothobranchius annual killifishes. EvoDevo 2020; 11:25. [PMID: 33323125 PMCID: PMC7739477 DOI: 10.1186/s13227-020-00170-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
Annual fishes of the genus Nothobranchius inhabit ephemeral habitats in Eastern and Southeastern Africa. Their life cycle is characterized by very rapid maturation, a posthatch lifespan of a few weeks to months and embryonic diapause to survive the dry season. The species N. furzeri holds the record of the fastest-maturing vertebrate and of the vertebrate with the shortest captive lifespan and is emerging as model organism in biomedical research, evolutionary biology, and developmental biology. Extensive characterization of age-related phenotypes in the laboratory and of ecology, distribution, and demography in the wild are available. Species/populations from habitats differing in precipitation intensity show parallel evolution of lifespan and age-related traits that conform to the classical theories on aging. Genome sequencing and the establishment of CRISPR/Cas9 techniques made this species particularly attractive to investigate the effects genetic and non-genetic intervention on lifespan and aging-related phenotypes. At the same time, annual fishes are a very interesting subject for comparative approaches, including genomics, transcriptomics, and proteomics. The N. furzeri community is highly diverse and rapidly expanding and organizes a biannual meeting.
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Affiliation(s)
| | - Alessandro Cellerino
- Scuola Normale Superiore, Pisa, Italy. .,Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany.
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12
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Barth E, Sieber P, Stark H, Schuster S. Robustness during Aging-Molecular Biological and Physiological Aspects. Cells 2020; 9:E1862. [PMID: 32784503 PMCID: PMC7465392 DOI: 10.3390/cells9081862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the process of aging is still an important challenge to enable healthy aging and to prevent age-related diseases. Most studies in age research investigate the decline in organ functionality and gene activity with age. The focus on decline can even be considered a paradigm in that field. However, there are certain aspects that remain surprisingly stable and keep the organism robust. Here, we present and discuss various properties of robust behavior during human and animal aging, including physiological and molecular biological features, such as the hematocrit, body temperature, immunity against infectious diseases and others. We examine, in the context of robustness, the different theories of how aging occurs. We regard the role of aging in the light of evolution.
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Affiliation(s)
- Emanuel Barth
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Patricia Sieber
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Heiko Stark
- Institute of Zoology and Evolutionary Research with Phyletic Museum, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Stefan Schuster
- Matthias Schleiden Institute, Bioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany;
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13
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Hu CK, Wang W, Brind'Amour J, Singh PP, Reeves GA, Lorincz MC, Alvarado AS, Brunet A. Vertebrate diapause preserves organisms long term through Polycomb complex members. Science 2020; 367:870-874. [PMID: 32079766 DOI: 10.1126/science.aaw2601] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 11/26/2019] [Accepted: 12/23/2019] [Indexed: 12/27/2022]
Abstract
Diapause is a state of suspended development that helps organisms survive extreme environments. How diapause protects living organisms is largely unknown. Using the African turquoise killifish (Nothobranchius furzeri), we show that diapause preserves complex organisms for extremely long periods of time without trade-offs for subsequent adult growth, fertility, and life span. Transcriptome analyses indicate that diapause is an active state, with dynamic regulation of metabolism and organ development genes. The most up-regulated genes in diapause include Polycomb complex members. The chromatin mark regulated by Polycomb, H3K27me3, is maintained at key developmental genes in diapause, and the Polycomb member CBX7 mediates repression of metabolism and muscle genes in diapause. CBX7 is functionally required for muscle preservation and diapause maintenance. Thus, vertebrate diapause is a state of suspended life that is actively maintained by specific chromatin regulators, and this has implications for long-term organism preservation.
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Affiliation(s)
- Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Julie Brind'Amour
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - G Adam Reeves
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Graduate Program of Genetics, Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA. .,Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, CA 94305, USA
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