101
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Song P, Zhao Q, Zou MH. Targeting senescent cells to attenuate cardiovascular disease progression. Ageing Res Rev 2020; 60:101072. [PMID: 32298812 DOI: 10.1016/j.arr.2020.101072] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/19/2022]
Abstract
Cardiovascular disease (CVD) is the most common disease to increase as life expectancy increases. Most high-profile pharmacological treatments for age-related CVD have led to inefficacious results, implying that novel approaches to treating these pathologies are needed. Emerging data have demonstrated that senescent cardiovascular cells, which are characterized by irreversible cell cycle arrest and a distinct senescence-associated secretory phenotype, accumulate in aged or diseased cardiovascular systems, suggesting that they may impair cardiovascular function. This review discusses the evidence implicating senescent cells in cardiovascular ageing, the onset and progression of CVD, and the molecular mechanisms underlying cardiovascular cell senescence. We also review eradication of senescent cardiovascular cells by small-molecule-drug-mediated apoptosis and immune cell-mediated efferocytosis and toxicity as promising and precisely targeted therapeutics for CVD prevention and treatment.
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102
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Bo Otto F, Thumm M. Nucleophagy-Implications for Microautophagy and Health. Int J Mol Sci 2020; 21:ijms21124506. [PMID: 32599961 PMCID: PMC7352367 DOI: 10.3390/ijms21124506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Nucleophagy, the selective subtype of autophagy that targets nuclear material for autophagic degradation, was not only shown to be a model system for the study of selective macroautophagy, but also for elucidating the role of the core autophagic machinery within microautophagy. Nucleophagy also emerged as a system associated with a variety of disease conditions including cancer, neurodegeneration and ageing. Nucleophagic processes are part of natural cell development, but also act as a response to various stress conditions. Upon releasing small portions of nuclear material, micronuclei, the autophagic machinery transfers these micronuclei to the vacuole for subsequent degradation. Despite sharing many cargos and requiring the core autophagic machinery, recent investigations revealed the aspects that set macro- and micronucleophagy apart. Central to the discrepancies found between macro- and micronucleophagy is the nucleus vacuole junction, a large membrane contact site formed between nucleus and vacuole. Exclusion of nuclear pore complexes from the junction and its exclusive degradation by micronucleophagy reveal compositional differences in cargo. Regarding their shared reliance on the core autophagic machinery, micronucleophagy does not involve normal autophagosome biogenesis observed for macronucleophagy, but instead maintains a unique role in overall microautophagy, with the autophagic machinery accumulating at the neck of budding vesicles.
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103
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Ren X, Hu B, Song M, Ding Z, Dang Y, Liu Z, Zhang W, Ji Q, Ren R, Ding J, Chan P, Jiang C, Ye K, Qu J, Tang F, Liu GH. Maintenance of Nucleolar Homeostasis by CBX4 Alleviates Senescence and Osteoarthritis. Cell Rep 2020; 26:3643-3656.e7. [PMID: 30917318 DOI: 10.1016/j.celrep.2019.02.088] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/27/2019] [Accepted: 02/21/2019] [Indexed: 01/12/2023] Open
Abstract
CBX4, a component of polycomb repressive complex 1 (PRC1), plays important roles in the maintenance of cell identity and organ development through gene silencing. However, whether CBX4 regulates human stem cell homeostasis remains unclear. Here, we demonstrate that CBX4 counteracts human mesenchymal stem cell (hMSC) aging via the maintenance of nucleolar homeostasis. CBX4 protein is downregulated in aged hMSCs, whereas CBX4 knockout in hMSCs results in destabilized nucleolar heterochromatin, enhanced ribosome biogenesis, increased protein translation, and accelerated cellular senescence. CBX4 maintains nucleolar homeostasis by recruiting nucleolar protein fibrillarin (FBL) and heterochromatin protein KRAB-associated protein 1 (KAP1) at nucleolar rDNA, limiting the excessive expression of rRNAs. Overexpression of CBX4 alleviates physiological hMSC aging and attenuates the development of osteoarthritis in mice. Altogether, our findings reveal a critical role of CBX4 in counteracting cellular senescence by maintaining nucleolar homeostasis, providing a potential therapeutic target for aging-associated disorders.
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Affiliation(s)
- Xiaoqing Ren
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Boqiang Hu
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China
| | - Moshi Song
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhichao Ding
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujiao Dang
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqi Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Qianzhao Ji
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruotong Ren
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianjian Ding
- Army Diagnosis and Treatment Center for Oral Disease, 306th Hospital of the PLA, Beijing 100101, China
| | - Piu Chan
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China
| | - Keqiong Ye
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Fuchou Tang
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China; Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China.
| | - Guang-Hui Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Beijing Institute for Brain Disorders, Capital Medical University, Beijing 100069, China.
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104
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Tharyan RG, Annibal A, Schiffer I, Laboy R, Atanassov I, Weber AL, Gerisch B, Antebi A. NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin. Nat Metab 2020; 2:387-396. [PMID: 32694663 DOI: 10.1038/s42255-020-0200-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/26/2020] [Indexed: 12/24/2022]
Abstract
Mitochondria are multidimensional organelles whose activities are essential to cellular vitality and organismal longevity, yet underlying regulatory mechanisms spanning these different levels of organization remain elusive1-5. Here we show that Caenorhabditis elegans nuclear transcription factor Y, beta subunit (NFYB-1), a subunit of the NF-Y transcriptional complex6-8, is a crucial regulator of mitochondrial function. Identified in RNA interference (RNAi) screens, NFYB-1 loss leads to perturbed mitochondrial gene expression, reduced oxygen consumption, mitochondrial fragmentation, disruption of mitochondrial stress pathways, decreased mitochondrial cardiolipin levels and abolition of organismal longevity triggered by mitochondrial impairment. Multi-omics analysis reveals that NFYB-1 is a potent repressor of lysosomal prosaposin, a regulator of glycosphingolipid metabolism. Limiting prosaposin expression unexpectedly restores cardiolipin production, mitochondrial function and longevity in the nfyb-1 background. Similarly, cardiolipin supplementation rescues nfyb-1 phenotypes. These findings suggest that the NFYB-1-prosaposin axis coordinates lysosomal to mitochondria signalling via lipid pools to enhance cellular mitochondrial function and organismal health.
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Affiliation(s)
| | - Andrea Annibal
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Isabelle Schiffer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Raymond Laboy
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Ilian Atanassov
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Birgit Gerisch
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- CECAD, University of Cologne, Cologne, Germany.
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105
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The Y chromosome may contribute to sex-specific ageing in Drosophila. Nat Ecol Evol 2020; 4:853-862. [PMID: 32313175 PMCID: PMC7274899 DOI: 10.1038/s41559-020-1179-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/16/2020] [Indexed: 12/03/2022]
Abstract
Heterochromatin suppresses repetitive DNA, and a loss of heterochromatin has been observed in aged cells of several species, including humans and Drosophila. Males often contain substantially more heterochromatic DNA than females, due to the presence of a large, repeat-rich Y chromosome, and male flies generally have shorter average life spans than females. Here we show that repetitive DNA becomes de-repressed more rapidly in old male flies relative to females, and repeats on the Y chromosome are disproportionally mis-expressed during aging. This is associated with a loss of heterochromatin at repetitive elements during aging in male flies, and a general loss of repressive chromatin in aged males away from pericentromeric regions and the Y. By generating flies with different sex chromosome karyotypes (XXY females; X0 and XYY males), we show that repeat de-repression and average lifespan is correlated with the number of Y chromosomes. This suggests that sex-specific chromatin differences may contribute to sex-specific aging in flies.
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106
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Gerisch B, Tharyan RG, Mak J, Denzel SI, Popkes-van Oepen T, Henn N, Antebi A. HLH-30/TFEB Is a Master Regulator of Reproductive Quiescence. Dev Cell 2020; 53:316-329.e5. [PMID: 32302543 DOI: 10.1016/j.devcel.2020.03.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 01/28/2020] [Accepted: 03/15/2020] [Indexed: 12/20/2022]
Abstract
All animals have evolved the ability to survive nutrient deprivation, and nutrient signaling pathways are conserved modulators of health and disease. In C. elegans, late-larval starvation provokes the adult reproductive diapause (ARD), a long-lived quiescent state that enables survival for months without food, yet underlying molecular mechanisms remain unknown. Here, we show that ARD is distinct from other forms of diapause, showing little requirement for canonical longevity pathways, autophagy, and fat metabolism. Instead it requires the HLH-30/TFEB transcription factor to promote the morphological and physiological remodeling involved in ARD entry, survival, and recovery, suggesting that HLH-30 is a master regulator of reproductive quiescence. HLH-30 transcriptome and genetic analyses reveal that Max-like HLH factors, AMP-kinase, mTOR, protein synthesis, and mitochondrial fusion are target processes that promote ARD longevity. ARD thus rewires metabolism to ensure long-term survival and may illuminate similar mechanisms acting in stem cell quiescence and long-term fasting.
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Affiliation(s)
- Birgit Gerisch
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Rebecca George Tharyan
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Jennifer Mak
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Sarah I Denzel
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne 50931, Germany
| | - Till Popkes-van Oepen
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne 50931, Germany
| | - Nadine Henn
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Adam Antebi
- Department of Molecular Genetics of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne 50931, Germany.
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107
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Späth MR, Koehler FC, Hoyer-Allo KJR, Grundmann F, Burst V, Müller RU. Preconditioning strategies to prevent acute kidney injury. F1000Res 2020; 9:F1000 Faculty Rev-237. [PMID: 32269763 PMCID: PMC7135682 DOI: 10.12688/f1000research.21406.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 02/06/2023] Open
Abstract
Acute kidney injury is a common clinical disorder resulting in significantly increased morbidity and mortality. However, despite extensive research, strategies for prevention or treatment are still lacking in routine clinical practice. Already decades ago, several preconditioning strategies (e. g. ischemic/hypoxic preconditioning and calorie restriction) have been published and their extraordinary effectiveness - especially in rodents - has raised the hope for powerful clinical tools to prevent acute kidney injury. However, the underlying mechanisms are still not completely understood and translation to the clinics has not been successful yet. In this review, the most attractive strategies and the current mechanistic concepts are introduced and discussed. Furthermore, we present clinical trials evaluating the feasibility of preconditioning in the clinical setting.
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Affiliation(s)
- Martin Richard Späth
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, 50937, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, NRW, 50931, Germany
| | - Felix Carlo Koehler
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, 50937, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, NRW, 50931, Germany
| | - Karla Johanna Ruth Hoyer-Allo
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, 50937, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, NRW, 50931, Germany
| | - Franziska Grundmann
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, 50937, Germany
| | - Volker Burst
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, 50937, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, NRW, 50937, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, NRW, 50931, Germany
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108
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Immune Clearance of Senescent Cells to Combat Ageing and Chronic Diseases. Cells 2020; 9:cells9030671. [PMID: 32164335 PMCID: PMC7140645 DOI: 10.3390/cells9030671] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/28/2020] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
Senescent cells are generally characterized by permanent cell cycle arrest, metabolic alteration and activation, and apoptotic resistance in multiple organs due to various stressors. Excessive accumulation of senescent cells in numerous tissues leads to multiple chronic diseases, tissue dysfunction, age-related diseases and organ ageing. Immune cells can remove senescent cells. Immunaging or impaired innate and adaptive immune responses by senescent cells result in persistent accumulation of various senescent cells. Although senolytics-drugs that selectively remove senescent cells by inducing their apoptosis-are recent hot topics and are making significant research progress, senescence immunotherapies using immune cell-mediated clearance of senescent cells are emerging and promising strategies to fight ageing and multiple chronic diseases. This short review provides an overview of the research progress to date concerning senescent cell-caused chronic diseases and tissue ageing, as well as the regulation of senescence by small-molecule drugs in clinical trials and different roles and regulation of immune cells in the elimination of senescent cells. Mounting evidence indicates that immunotherapy targeting senescent cells combats ageing and chronic diseases and subsequently extends the healthy lifespan.
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109
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Raz Y, Akker EB, Roest T, Riaz M, Rest O, Suchiman HED, Lakenberg N, Stassen SA, Putten M, Feskens EJM, Reinders MJT, Goeman J, Beekman M, Raz V, Slagboom PE. A data‐driven methodology reveals novel myofiber clusters in older human muscles. FASEB J 2020; 34:5525-5537. [DOI: 10.1096/fj.201902350r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Yotam Raz
- Section of Molecular Epidemiology Leiden University Medical Center Leiden the Netherlands
| | - Erik B. Akker
- Section of Molecular Epidemiology Leiden University Medical Center Leiden the Netherlands
- Leiden Computational Biology Center Leiden University Medical Center Leiden the Netherlands
- The Delft Bioinformatics Lab Delft University of Technology Delft the Netherlands
| | - Tijmen Roest
- Section of Molecular Epidemiology Leiden University Medical Center Leiden the Netherlands
| | - Muhammad Riaz
- Department of Human Genetics Leiden University Medical Center Leiden the Netherlands
| | - Ondine Rest
- Division of Human Nutrition Wageningen University & Research Wageningen the Netherlands
| | - H. Eka D. Suchiman
- Section of Molecular Epidemiology Leiden University Medical Center Leiden the Netherlands
| | - Nico Lakenberg
- Section of Molecular Epidemiology Leiden University Medical Center Leiden the Netherlands
| | - Stefanie A. Stassen
- Section of Gerontology and Geriatrics Leiden University Medical Center Leiden the Netherlands
| | - Maaike Putten
- Department of Human Genetics Leiden University Medical Center Leiden the Netherlands
| | - Edith J. M. Feskens
- Division of Human Nutrition Wageningen University & Research Wageningen the Netherlands
| | - Marcel J. T. Reinders
- Leiden Computational Biology Center Leiden University Medical Center Leiden the Netherlands
- The Delft Bioinformatics Lab Delft University of Technology Delft the Netherlands
| | - Jelle Goeman
- Department of Medical Statistics Leiden University Medical Center Leiden the Netherlands
| | - Marian Beekman
- Section of Molecular Epidemiology Leiden University Medical Center Leiden the Netherlands
| | - Vered Raz
- Department of Human Genetics Leiden University Medical Center Leiden the Netherlands
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110
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Jouvence a small nucleolar RNA required in the gut extends lifespan in Drosophila. Nat Commun 2020; 11:987. [PMID: 32080190 PMCID: PMC7033134 DOI: 10.1038/s41467-020-14784-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/31/2020] [Indexed: 01/06/2023] Open
Abstract
Longevity is influenced by genetic and environmental factors, but the underlying mechanisms remain elusive. Here, we functionally characterise a Drosophila small nucleolar RNA (snoRNA), named jouvence whose loss of function reduces lifespan. The genomic region of jouvence rescues the longevity in mutant, while its overexpression in wild-type increases lifespan. Jouvence is required in enterocytes. In mutant, the epithelium of the gut presents more hyperplasia, while the overexpression of jouvence prevents it. Molecularly, the mutant lack pseudouridylation on 18S and 28S-rRNA, a function rescued by targeted expression of jouvence in the gut. A transcriptomic analysis performed from the gut reveals that several genes are either up- or down-regulated, while restoring the mRNA level of two genes (ninaD or CG6296) rescue the longevity. Since snoRNAs are structurally and functionally well conserved throughout evolution, we identified putative jouvence orthologue in mammals including humans, suggesting that its function in longevity could be conserved. Small non-coding RNAs contribute to the regulation of aging. Here the authors identify a small nucleolar RNA, the snoRNA jouvence, which extends the lifespan of fruit flies through its function in the gut, and is conserved in humans.
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111
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Mammalian oogenesis and female reproductive aging. Aging (Albany NY) 2020; 10:162-163. [PMID: 29410392 PMCID: PMC5842846 DOI: 10.18632/aging.101381] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 02/03/2018] [Indexed: 12/03/2022]
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112
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Papandreou ME, Tavernarakis N. Nucleophagy mediators and mechanisms. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 172:1-14. [PMID: 32620238 DOI: 10.1016/bs.pmbts.2020.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear recycling is essential for cell and organismal homeostasis. Nuclear architecture perturbations, such as nuclear loss or nuclear enlargement, have been observed in several pathological conditions. Apart from proteasomal components which reside in the nucleus, specific autophagic proteins also shuttle between the nucleus and the cytoplasm. Until recently, only the microautophagic degradation of nuclear components had been described. Recent studies, dissecting nuclear material recycling in organisms ranging from yeast to mammals, provide insight relevant to other forms of nucleophagy and the mediators involved. Nucleophagy has also been implicated in pathology. Lamins are degraded in cancer through direct interaction with LC3 in the nucleus. Similarly, in neurodegeneration, Golgi-associated nucleophagy is exacerbated. The physiological role of nucleophagy and its contribution to other pathologies remain to be elucidated. Here we discus recent findings that shed light into the molecular mechanisms and pathways that mediate the autophagic recycling of nuclear material.
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Affiliation(s)
- Margarita-Elena Papandreou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece; Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece; Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Greece.
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113
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Aging and Caloric Restriction Modulate the DNA Methylation Profile of the Ribosomal RNA Locus in Human and Rat Liver. Nutrients 2020; 12:nu12020277. [PMID: 31973116 PMCID: PMC7070571 DOI: 10.3390/nu12020277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 12/21/2022] Open
Abstract
A growing amount of evidence suggests that the downregulation of protein synthesis is an adaptive response during physiological aging, which positively contributes to longevity and can be modulated by nutritional interventions like caloric restriction (CR). The expression of ribosomal RNA (rRNA) is one of the main determinants of translational rate, and epigenetic modifications finely contribute to its regulation. Previous reports suggest that hypermethylation of ribosomal DNA (rDNA) locus occurs with aging, although with some species- and tissue- specificity. In the present study, we experimentally measured DNA methylation of three regions (the promoter, the 5′ of the 18S and the 5′ of 28S sequences) in the rDNA locus in liver tissues from rats at two, four, 10, and 18 months. We confirm previous findings, showing age-related hypermethylation, and describe, for the first time, that this gain in methylation also occurs in human hepatocytes. Furthermore, we show that age-related hypermethylation is enhanced in livers of rat upon CR at two and 10 months, and that at two months a trend towards the reduction of rRNA expression occurs. Collectively, our results suggest that CR modulates age-related regulation of methylation at the rDNA locus, thus providing an epigenetic readout of the pro-longevity effects of CR.
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114
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Chen PH, Chen YT, Chu TY, Ma TH, Wu MH, Lin HH, Chang YS, Tan BCM, Lo SJ. Nucleolar control by a non-apoptotic p53-caspases-deubiquitinylase axis promotes resistance to bacterial infection. FASEB J 2020; 34:1107-1121. [PMID: 31914708 DOI: 10.1096/fj.201901959r] [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: 08/02/2019] [Revised: 10/02/2019] [Accepted: 10/15/2019] [Indexed: 11/11/2022]
Abstract
The nucleolus is best known for its cellular role in regulating ribosome production and growth. More recently, an unanticipated role for the nucleolus in innate immunity has recently emerged whereby downregulation of fibrillarin and nucleolar contraction confers pathogen resistance across taxa. The mechanism of this downregulation, however, remains obscure. Here we report that rather than fibrillarin itself being the proximal factor in this pathway, the key player is a fibrillarin-stabilizing deubiquitinylase USP-33. This was discovered by a candidate-gene search of Caenorhabditis elegans in which CED-3 caspase was revealed to execute targeted cleavage of USP-33, thus destabilizing fibrillarin. We also showed that cep-1 and ced-3 mutant worms altered nucleolar size and decreased antimicrobial peptide gene, spp-1, expression rendering susceptibility to bacterial infection. These phenotypes were reversed by usp-33 knockdown, thus linking the CEP-1-CED-3-USP-33 pathway with nucleolar control and resistance to bacterial infection in worms. Parallel experiments with the human analogs of caspases and USP36 revealed similar roles in coordinating these two processes. In summary, our work outlined a conserved cascade that connects cell death signaling to nucleolar control and innate immune response.
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Affiliation(s)
- Po-Hsiang Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Tung Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tai-Ying Chu
- Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Tian-Hsiang Ma
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Mei-Hsuan Wu
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsi-Hsien Lin
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Szecheng J Lo
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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115
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King GA, Ünal E. The dynamic nuclear periphery as a facilitator of gamete health and rejuvenation. Curr Genet 2020; 66:487-493. [PMID: 31915924 DOI: 10.1007/s00294-019-01050-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 12/26/2022]
Abstract
The nuclear periphery is a hotspot for the accumulation of age-induced damage in eukaryotic cells. The types of damage that occur at the periphery and their phenotypic consequences have begun to be characterized; however, the mechanisms by which cells repair or eliminate nuclear damage remain poorly understood. Using budding yeast meiosis as a natural system to study cellular rejuvenation, we recently discovered a novel nuclear quality control event, in which age-induced damage is sequestered away from dividing chromosomes to a discarded nuclear compartment that we term the GUNC (for "Gametogenesis Uninherited Nuclear Compartment"). Interestingly, extensive nuclear remodeling occurs even in young cells, including a surprising modularity of the nuclear pore complex, suggesting a general contribution to gamete fitness. In this review, we discuss these findings in the context of recent evidence that the nuclear periphery is a highly dynamic region critical for cellular health.
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Affiliation(s)
- Grant A King
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, 94720, USA.
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116
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Moles R, Sarkis S, Galli V, Omsland M, Purcell DFJ, Yurick D, Khoury G, Pise-Masison CA, Franchini G. p30 protein: a critical regulator of HTLV-1 viral latency and host immunity. Retrovirology 2019; 16:42. [PMID: 31852501 PMCID: PMC6921414 DOI: 10.1186/s12977-019-0501-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/29/2019] [Indexed: 12/24/2022] Open
Abstract
The extraordinarily high prevalence of HTLV-1 subtype C (HTLV-1C) in some isolated indigenous communities in Oceania and the severity of the health conditions associated with the virus impress the great need for basic and translational research to prevent and treat HTLV-1 infection. The genome of the virus’s most common subtype, HTLV-1A, encodes structural, enzymatic, and regulatory proteins that contribute to viral persistence and pathogenesis. Among these is the p30 protein encoded by the doubly spliced Tax-orf II mRNA, a nuclear/nucleolar protein with both transcriptional and post-transcriptional activity. The p30 protein inhibits the productive replication cycle via nuclear retention of the mRNA that encodes for both the viral transcriptional trans-activator Tax, and the Rex proteins that regulate the transport of incompletely spliced viral mRNA to the cytoplasm. In myeloid cells, p30 inhibits the PU-1 transcription factor that regulates interferon expression and is a critical mediator of innate and adaptive immunity. Furthermore, p30 alters gene expression, cell cycle progression, and DNA damage responses in T-cells, raising the hypothesis that p30 may directly contribute to T cell transformation. By fine-tuning viral expression while also inhibiting host innate responses, p30 is likely essential for viral infection and persistence. This concept is supported by the finding that macaques, a natural host for the closely genetically related simian T-cell leukemia virus 1 (STLV-1), exposed to an HTLV-1 knockout for p30 expression by a single point mutation do not became infected unless reversion and selection of the wild type HTLV-1 genotype occurs. All together, these data suggest that inhibition of p30 may help to curb and eventually eradicate viral infection by exposing infected cells to an effective host immune response.
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Affiliation(s)
- Ramona Moles
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarkis Sarkis
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Veronica Galli
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Omsland
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - David Yurick
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Georges Khoury
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, Australia
| | - Cynthia A Pise-Masison
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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117
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Bakula D, Ablasser A, Aguzzi A, Antebi A, Barzilai N, Bittner MI, Jensen MB, Calkhoven CF, Chen D, de Grey AD, Feige JN, Georgievskaya A, Gladyshev VN, Golato T, Gudkov AV, Hoppe T, Kaeberlein M, Katajisto P, Kennedy BK, Lal U, Martin-Villalba A, Moskalev AA, Ozerov I, Petr MA, Reason, Rubinsztein DC, Tyshkovskiy A, Vanhaelen Q, Zhavoronkov A, Scheibye-Knudsen M. Latest advances in aging research and drug discovery. Aging (Albany NY) 2019; 11:9971-9981. [PMID: 31770722 PMCID: PMC6914421 DOI: 10.18632/aging.102487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/09/2019] [Indexed: 12/19/2022]
Abstract
An increasing aging population poses a significant challenge to societies worldwide. A better understanding of the molecular, cellular, organ, tissue, physiological, psychological, and even sociological changes that occur with aging is needed in order to treat age-associated diseases. The field of aging research is rapidly expanding with multiple advances transpiring in many previously disconnected areas. Several major pharmaceutical, biotechnology, and consumer companies made aging research a priority and are building internal expertise, integrating aging research into traditional business models and exploring new go-to-market strategies. Many of these efforts are spearheaded by the latest advances in artificial intelligence, namely deep learning, including generative and reinforcement learning. To facilitate these trends, the Center for Healthy Aging at the University of Copenhagen and Insilico Medicine are building a community of Key Opinion Leaders (KOLs) in these areas and launched the annual conference series titled "Aging Research and Drug Discovery (ARDD)" held in the capital of the pharmaceutical industry, Basel, Switzerland (www.agingpharma.org). This ARDD collection contains summaries from the 6th annual meeting that explored aging mechanisms and new interventions in age-associated diseases. The 7th annual ARDD exhibition will transpire 2nd-4th of September, 2020, in Basel.
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Affiliation(s)
- Daniela Bakula
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Ablasser
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Nir Barzilai
- Department of Medicine, Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | | - Cornelis F. Calkhoven
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, AD Groningen, The Netherlands
| | - Danica Chen
- Program in Metabolic Biology, Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | | | - Jerome N. Feige
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Andrei V. Gudkov
- Roswell Park Comprehensive Cancer Center and Genome Protection, Inc., Buffalo, NY 14203, USA
| | - Thorsten Hoppe
- Institute for Genetics and CECAD Research Center, University of Cologne, Cologne, Germany
| | - Matt Kaeberlein
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Pekka Katajisto
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Brian K. Kennedy
- Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University Singapore, Singapore
- Centre for Healthy Ageing, National University Healthy System, Singapore
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Unmesh Lal
- Frost and Sullivan, Frankfurt am Main, Germany
| | | | - Alexey A. Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Ozerov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Rockville, MD 20850, USA
| | - Michael A. Petr
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Reason
- Repair Biotechnologies, Inc., Syracuse, NY 13210, USA
| | - David C. Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, The Keith Peters Building, Cambridge CB2 0XY, UK
- UK Dementia Research Institute, The Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Quentin Vanhaelen
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Rockville, MD 20850, USA
| | - Alex Zhavoronkov
- Pharmaceutical Artificial Intelligence Department, Insilico Medicine, Inc., Rockville, MD 20850, USA
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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118
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Palikyras S, Papantonis A. Modes of phase separation affecting chromatin regulation. Open Biol 2019; 9:190167. [PMID: 31615334 PMCID: PMC6833219 DOI: 10.1098/rsob.190167] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/18/2019] [Indexed: 12/21/2022] Open
Abstract
It has become evident that chromatin in cell nuclei is organized at multiple scales. Significant effort has been devoted to understanding the connection between the nuclear environment and the diverse biological processes taking place therein. A fundamental question is how cells manage to orchestrate these reactions, both spatially and temporally. Recent insights into phase-separated membraneless organelles may be the key for answering this. Of the two models that have been proposed for phase-separated entities, one largely depends on chromatin-protein interactions and the other on multivalent protein-protein and/or protein-RNA ones. Each has its own characteristics, but both would be able to, at least in part, explain chromatin and transcriptional organization. Here, we attempt to give an overview of these two models and their studied examples to date, before discussing the forces that could govern phase separation and prevent it from arising unrestrainedly.
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Affiliation(s)
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center, Georg-August University of Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany
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119
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Blackwell TK, Sewell AK, Wu Z, Han M. TOR Signaling in Caenorhabditis elegans Development, Metabolism, and Aging. Genetics 2019; 213:329-360. [PMID: 31594908 PMCID: PMC6781902 DOI: 10.1534/genetics.119.302504] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 07/18/2019] [Indexed: 12/30/2022] Open
Abstract
The Target of Rapamycin (TOR or mTOR) is a serine/threonine kinase that regulates growth, development, and behaviors by modulating protein synthesis, autophagy, and multiple other cellular processes in response to changes in nutrients and other cues. Over recent years, TOR has been studied intensively in mammalian cell culture and genetic systems because of its importance in growth, metabolism, cancer, and aging. Through its advantages for unbiased, and high-throughput, genetic and in vivo studies, Caenorhabditis elegans has made major contributions to our understanding of TOR biology. Genetic analyses in the worm have revealed unexpected aspects of TOR functions and regulation, and have the potential to further expand our understanding of how growth and metabolic regulation influence development. In the aging field, C. elegans has played a leading role in revealing the promise of TOR inhibition as a strategy for extending life span, and identifying mechanisms that function upstream and downstream of TOR to influence aging. Here, we review the state of the TOR field in C. elegans, and focus on what we have learned about its functions in development, metabolism, and aging. We discuss knowledge gaps, including the potential pitfalls in translating findings back and forth across organisms, but also describe how TOR is important for C. elegans biology, and how C. elegans work has developed paradigms of great importance for the broader TOR field.
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Affiliation(s)
- T Keith Blackwell
- Research Division, Joslin Diabetes Center, Department of Genetics, Harvard Medical School, Harvard Stem Cell Institute, Boston, Massachusetts
| | - Aileen K Sewell
- Department of MCDB, University of Colorado at Boulder, and
- Howard Hughes Medical Institute, Boulder, Colorado
| | - Ziyun Wu
- Research Division, Joslin Diabetes Center, Department of Genetics, Harvard Medical School, Harvard Stem Cell Institute, Boston, Massachusetts
| | - Min Han
- Department of MCDB, University of Colorado at Boulder, and
- Howard Hughes Medical Institute, Boulder, Colorado
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120
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Farley-Barnes KI, Ogawa LM, Baserga SJ. Ribosomopathies: Old Concepts, New Controversies. Trends Genet 2019; 35:754-767. [PMID: 31376929 PMCID: PMC6852887 DOI: 10.1016/j.tig.2019.07.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/02/2019] [Accepted: 07/09/2019] [Indexed: 12/30/2022]
Abstract
Ribosomopathies are a diverse subset of diseases caused by reduced expression of, or mutations in, factors necessary for making ribosomes, the protein translation machinery in the cell. Despite the ubiquitous need for ribosomes in all cell types, ribosomopathies manifest with tissue-specific defects and sometimes increased cancer susceptibility, but few treatments target the underlying cause. By highlighting new research in the field, we review current hypotheses for the basis of this tissue specificity. Based on new work, we broaden our understanding of the role of ribosome biogenesis in diverse tissue types throughout embryonic development. We also pose the question of whether previously described human conditions such as aging can be at least partially attributed to defects in making ribosomes.
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Affiliation(s)
- Katherine I Farley-Barnes
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lisa M Ogawa
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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121
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Sanchez JC, Ollodart A, Large CRL, Clough C, Alvino GM, Tsuchiya M, Crane M, Kwan EX, Kaeberlein M, Dunham MJ, Raghuraman MK, Brewer BJ. Phenotypic and Genotypic Consequences of CRISPR/Cas9 Editing of the Replication Origins in the rDNA of Saccharomyces cerevisiae. Genetics 2019; 213:229-249. [PMID: 31292210 PMCID: PMC6727806 DOI: 10.1534/genetics.119.302351] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 06/28/2019] [Indexed: 12/15/2022] Open
Abstract
The complex structure and repetitive nature of eukaryotic ribosomal DNA (rDNA) is a challenge for genome assembly, thus the consequences of sequence variation in rDNA remain unexplored. However, renewed interest in the role that rDNA variation may play in diverse cellular functions, aside from ribosome production, highlights the need for a method that would permit genetic manipulation of the rDNA. Here, we describe a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based strategy to edit the rDNA locus in the budding yeast Saccharomyces cerevisiae, developed independently but similar to one developed by others. Using this approach, we modified the endogenous rDNA origin of replication in each repeat by deleting or replacing its consensus sequence. We characterized the transformants that have successfully modified their rDNA locus and propose a mechanism for how CRISPR/Cas9-mediated editing of the rDNA occurs. In addition, we carried out extended growth and life span experiments to investigate the long-term consequences that altering the rDNA origin of replication have on cellular health. We find that long-term growth of the edited clones results in faster-growing suppressors that have acquired segmental aneusomy of the rDNA-containing region of chromosome XII or aneuploidy of chromosomes XII, II, or IV. Furthermore, we find that all edited isolates suffer a reduced life span, irrespective of their levels of extrachromosomal rDNA circles. Our work demonstrates that it is possible to quickly, efficiently, and homogeneously edit the rDNA origin via CRISPR/Cas9.
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Affiliation(s)
- Joseph C Sanchez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
- Bioscience Division, Los Alamos National Laboratory, Los Alamos New Mexico 87544
| | - Anja Ollodart
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Christopher R L Large
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Courtnee Clough
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Gina M Alvino
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Mitsuhiro Tsuchiya
- Department of Pathology, University of Washington, Seattle, Washington 98195
| | - Matthew Crane
- Department of Pathology, University of Washington, Seattle, Washington 98195
| | - Elizabeth X Kwan
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Matt Kaeberlein
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
- Department of Pathology, University of Washington, Seattle, Washington 98195
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - M K Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Bonita J Brewer
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
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122
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Cerqueira AV, Lemos B. Ribosomal DNA and the Nucleolus as Keystones of Nuclear Architecture, Organization, and Function. Trends Genet 2019; 35:710-723. [PMID: 31447250 DOI: 10.1016/j.tig.2019.07.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022]
Abstract
The multicopy ribosomal DNA (rDNA) array gives origin to the nucleolus, a large nonmembrane-bound organelle that occupies a substantial volume within the cell nucleus. The rDNA/nucleolus has emerged as a coordinating hub in which seemingly disparate cellular functions converge, and from which a variety of cellular and organismal phenotypes emerge. However, the role of the nucleolus as a determinant and organizer of nuclear architecture and other epigenetic states of the genome is not well understood. We discuss the role of rDNA and the nucleolus in nuclear organization and function - from nucleolus-associated domains (NADs) to the regulation of imprinted loci and X chromosome inactivation, as well as rDNA contact maps that anchor and position the rDNA relative to the rest of the genome. The influence of the nucleolus on nuclear organization undoubtedly modulates diverse biological processes from metabolism to cell proliferation, genome-wide gene expression, maintenance of epigenetic states, and aging.
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Affiliation(s)
- Amanda V Cerqueira
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Bernardo Lemos
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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123
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Chen J, Stark LA. Insights into the Relationship between Nucleolar Stress and the NF-κB Pathway. Trends Genet 2019; 35:768-780. [PMID: 31434627 DOI: 10.1016/j.tig.2019.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
The nuclear organelle the nucleolus and the transcription factor nuclear factor of κ-light-chain-enhancer of activated B cells (NF-κB) are both central to the control of cellular homeostasis, dysregulated in common diseases and implicated in the ageing process. Until recently, it was believed that they acted independently to regulate homeostasis in health and disease. However, there is an emerging body of evidence suggesting that nucleoli and NF-κB signalling converge at multiple levels. Here we will review current understanding of this crosstalk. We will discuss activation of the NF-κB pathway by nucleolar stress and induction of apoptosis by nucleolar sequestration of NF-κB/RelA. We will also discuss the role of TIF-IA, COMMD1, and nucleophosmin, which are key players in this crosstalk, and the therapeutic relevance, particularly with respect to the antitumour effects of aspirin.
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Affiliation(s)
- Jingyu Chen
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland EH4 2XU, UK
| | - Lesley A Stark
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, Scotland EH4 2XU, UK.
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124
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Correll CC, Bartek J, Dundr M. The Nucleolus: A Multiphase Condensate Balancing Ribosome Synthesis and Translational Capacity in Health, Aging and Ribosomopathies. Cells 2019; 8:cells8080869. [PMID: 31405125 PMCID: PMC6721831 DOI: 10.3390/cells8080869] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
Abstract
The nucleolus is the largest membrane-less structure in the eukaryotic nucleus. It is involved in the biogenesis of ribosomes, essential macromolecular machines responsible for synthesizing all proteins required by the cell. The assembly of ribosomes is evolutionarily conserved and is the most energy-consuming cellular process needed for cell growth, proliferation, and homeostasis. Despite the significance of this process, the intricate pathophysiological relationship between the nucleolus and protein synthesis has only recently begun to emerge. Here, we provide perspective on new principles governing nucleolar formation and the resulting multiphase organization driven by liquid-liquid phase separation. With recent advances in the structural analysis of ribosome formation, we highlight the current understanding of the step-wise assembly of pre-ribosomal subunits and the quality control required for proper function. Finally, we address how aging affects ribosome genesis and how genetic defects in ribosome formation cause ribosomopathies, complex diseases with a predisposition to cancer.
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Affiliation(s)
- Carl C Correll
- Center for Proteomics and Molecular Therapeutics, Rosalind Franklin University of Medicine & Science, North Chicago, IL 60064, USA.
| | - Jiri Bartek
- Danish Cancer Society Research Center, Genome Integrity Unit, DK-2100 Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Miroslav Dundr
- Center for Cancer Cell Biology Immunology and Infection, Rosalind Franklin University of Medicine & Science, North Chicago, IL 60064, USA.
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125
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Controlling the material properties and rRNA processing function of the nucleolus using light. Proc Natl Acad Sci U S A 2019; 116:17330-17335. [PMID: 31399547 DOI: 10.1073/pnas.1903870116] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The nucleolus is a prominent nuclear condensate that plays a central role in ribosome biogenesis by facilitating the transcription and processing of nascent ribosomal RNA (rRNA). A number of studies have highlighted the active viscoelastic nature of the nucleolus, whose material properties and phase behavior are a consequence of underlying molecular interactions. However, the ways in which the material properties of the nucleolus impact its function in rRNA biogenesis are not understood. Here we utilize the Cry2olig optogenetic system to modulate the viscoelastic properties of the nucleolus. We show that above a threshold concentration of Cry2olig protein, the nucleolus can be gelled into a tightly linked, low mobility meshwork. Gelled nucleoli no longer coalesce and relax into spheres but nonetheless permit continued internal molecular mobility of small proteins. These changes in nucleolar material properties manifest in specific alterations in rRNA processing steps, including a buildup of larger rRNA precursors and a depletion of smaller rRNA precursors. We propose that the flux of processed rRNA may be actively tuned by the cell through modulating nucleolar material properties, which suggests the potential of materials-based approaches for therapeutic intervention in ribosomopathies.
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126
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King GA, Goodman JS, Schick JG, Chetlapalli K, Jorgens DM, McDonald KL, Ünal E. Meiotic cellular rejuvenation is coupled to nuclear remodeling in budding yeast. eLife 2019; 8:e47156. [PMID: 31397671 PMCID: PMC6711709 DOI: 10.7554/elife.47156] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Production of healthy gametes in meiosis relies on the quality control and proper distribution of both nuclear and cytoplasmic contents. Meiotic differentiation naturally eliminates age-induced cellular damage by an unknown mechanism. Using time-lapse fluorescence microscopy in budding yeast, we found that nuclear senescence factors - including protein aggregates, extrachromosomal ribosomal DNA circles, and abnormal nucleolar material - are sequestered away from chromosomes during meiosis II and subsequently eliminated. A similar sequestration and elimination process occurs for the core subunits of the nuclear pore complex in both young and aged cells. Nuclear envelope remodeling drives the formation of a membranous compartment containing the sequestered material. Importantly, de novo generation of plasma membrane is required for the sequestration event, preventing the inheritance of long-lived nucleoporins and senescence factors into the newly formed gametes. Our study uncovers a new mechanism of nuclear quality control and provides insight into its function in meiotic cellular rejuvenation.
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Affiliation(s)
- Grant A King
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Jay S Goodman
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Jennifer G Schick
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Keerthana Chetlapalli
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Danielle M Jorgens
- Electron Microscope LabUniversity of California, BerkeleyBerkeleyUnited States
| | - Kent L McDonald
- Electron Microscope LabUniversity of California, BerkeleyBerkeleyUnited States
| | - Elçin Ünal
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
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127
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Page MM, Schuster EF, Mudaliar M, Herzyk P, Withers DJ, Selman C. Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in mice. Aging (Albany NY) 2019; 10:1027-1052. [PMID: 29779018 PMCID: PMC5990393 DOI: 10.18632/aging.101446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/08/2018] [Indexed: 11/25/2022]
Abstract
Dietary restriction (DR) is the most widely studied non-genetic intervention capable of extending lifespan across multiple taxa. Modulation of genes, primarily within the insulin/insulin-like growth factor signalling (IIS) and the mechanistic target of rapamycin (mTOR) signalling pathways also act to extend lifespan in model organisms. For example, mice lacking insulin receptor substrate-1 (IRS1) are long-lived and protected against several age-associated pathologies. However, it remains unclear how these particular interventions act mechanistically to produce their beneficial effects. Here, we investigated transcriptional responses in wild-type and IRS1 null mice fed an ad libitum diet (WTAL and KOAL) or fed a 30% DR diet (WTDR or KODR). Using an RNAseq approach we noted a high correlation coefficient of differentially expressed genes existed within the same tissue across WTDR and KOAL mice and many metabolic features were shared between these mice. Overall, we report that significant overlap exists in the tissue-specific transcriptional response between long-lived DR mice and IRS1 null mice. However, there was evidence of disconnect between transcriptional signatures and certain phenotypic measures between KOAL and KODR, in that additive effects on body mass were observed but at the transcriptional level DR induced a unique set of genes in these already long-lived mice.
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Affiliation(s)
- Melissa M Page
- Institute des Sciences de la Vie, Faculty of Sciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Eugene F Schuster
- The Breast Cancer Now Toby Robins Research Centre The Institute of Cancer Research, London, UK
| | - Manikhandan Mudaliar
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Glasgow Molecular Pathology Node, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,Present address: Cerevance, Cambridge Science Park, Cambridge, UK
| | - Pawel Herzyk
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Campus, Bearsden, UK.,Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Dominic J Withers
- MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Colin Selman
- Glasgow Ageing Research Network (GARNER), Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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128
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Chen J, Lobb IT, Morin P, Novo SM, Simpson J, Kennerknecht K, von Kriegsheim A, Batchelor EE, Oakley F, Stark LA. Identification of a novel TIF-IA-NF-κB nucleolar stress response pathway. Nucleic Acids Res 2019; 46:6188-6205. [PMID: 29873780 PMCID: PMC6158704 DOI: 10.1093/nar/gky455] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
Abstract
p53 as an effector of nucleolar stress is well defined, but p53 independent mechanisms are largely unknown. Like p53, the NF-κB transcription factor plays a critical role in maintaining cellular homeostasis under stress. Many stresses that stimulate NF-κB also disrupt nucleoli. However, the link between nucleolar function and activation of the NF-κB pathway is as yet unknown. Here we demonstrate that artificial disruption of the PolI complex stimulates NF-κB signalling. Unlike p53 nucleolar stress response, this effect does not appear to be linked to inhibition of rDNA transcription. We show that specific stress stimuli of NF-κB induce degradation of a critical component of the PolI complex, TIF-IA. This degradation precedes activation of NF-κB and is associated with increased nucleolar size. It is mimicked by CDK4 inhibition and is dependent upon a novel pathway involving UBF/p14ARF and S44 of the protein. We show that blocking TIF-IA degradation blocks stress effects on nucleolar size and NF-κB signalling. Finally, using ex vivo culture, we show a strong correlation between degradation of TIF-IA and activation of NF-κB in freshly resected, human colorectal tumours exposed to the chemopreventative agent, aspirin. Together, our study provides compelling evidence for a new, TIF-IA-NF-κB nucleolar stress response pathway that has in vivo relevance and therapeutic implications.
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Affiliation(s)
- Jingyu Chen
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Rd., Edinburgh EH4 2XU, UK
| | - Ian T Lobb
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Rd., Edinburgh EH4 2XU, UK
| | - Pierre Morin
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Rd., Edinburgh EH4 2XU, UK
| | - Sonia M Novo
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Rd., Edinburgh EH4 2XU, UK
| | - James Simpson
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Rd., Edinburgh EH4 2XU, UK
| | - Kathrin Kennerknecht
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Rd., Edinburgh EH4 2XU, UK
| | - Alex von Kriegsheim
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Rd., Edinburgh EH4 2XU, UK
| | - Emily E Batchelor
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Rd., Edinburgh EH4 2XU, UK
| | - Fiona Oakley
- Liver Research Group, Institute of Cellular Medicine, 4th Floor, William Leech Building, Framlington Place, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
| | - Lesley A Stark
- University of Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Rd., Edinburgh EH4 2XU, UK
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129
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Matos-Perdomo E, Machín F. Nucleolar and Ribosomal DNA Structure under Stress: Yeast Lessons for Aging and Cancer. Cells 2019; 8:cells8080779. [PMID: 31357498 PMCID: PMC6721496 DOI: 10.3390/cells8080779] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/15/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023] Open
Abstract
Once thought a mere ribosome factory, the nucleolus has been viewed in recent years as an extremely sensitive gauge of diverse cellular stresses. Emerging concepts in nucleolar biology include the nucleolar stress response (NSR), whereby a series of cell insults have a special impact on the nucleolus. These insults include, among others, ultra-violet radiation (UV), nutrient deprivation, hypoxia and thermal stress. While these stresses might influence nucleolar biology directly or indirectly, other perturbances whose origin resides in the nucleolar biology also trigger nucleolar and systemic stress responses. Among the latter, we find mutations in nucleolar and ribosomal proteins, ribosomal RNA (rRNA) processing inhibitors and ribosomal DNA (rDNA) transcription inhibition. The p53 protein also mediates NSR, leading ultimately to cell cycle arrest, apoptosis, senescence or differentiation. Hence, NSR is gaining importance in cancer biology. The nucleolar size and ribosome biogenesis, and how they connect with the Target of Rapamycin (TOR) signalling pathway, are also becoming important in the biology of aging and cancer. Simple model organisms like the budding yeast Saccharomyces cerevisiae, easy to manipulate genetically, are useful in order to study nucleolar and rDNA structure and their relationship with stress. In this review, we summarize the most important findings related to this topic.
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Affiliation(s)
- Emiliano Matos-Perdomo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, 38200 Tenerife, Spain
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain.
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200 Tenerife, Spain.
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, 35450 Santa María de Guía, Gran Canaria, Spain.
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130
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PARP1 regulates DNA damage-induced nucleolar-nucleoplasmic shuttling of WRN and XRCC1 in a toxicant and protein-specific manner. Sci Rep 2019; 9:10075. [PMID: 31296950 PMCID: PMC6624289 DOI: 10.1038/s41598-019-46358-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/12/2019] [Indexed: 12/13/2022] Open
Abstract
The prime function of nucleoli is ribogenesis, however, several other, non-canonical functions have recently been identified, including a role in genotoxic stress response. Upon DNA damage, numerous proteins shuttle dynamically between the nucleolus and the nucleoplasm, yet the underlying molecular mechanisms are incompletely understood. Here, we demonstrate that PARP1 and PARylation contribute to genotoxic stress-induced nucleolar-nucleoplasmic shuttling of key genome maintenance factors in HeLa cells. Our work revealed that the RECQ helicase, WRN, translocates from nucleoli to the nucleoplasm upon treatment with the oxidizing agent H2O2, the alkylating agent 2-chloroethyl ethyl sulfide (CEES), and the topoisomerase inhibitor camptothecin (CPT). We show that after treatment with H2O2 and CEES, but not CPT, WRN translocation was dependent on PARP1 protein, yet independent of its enzymatic activity. In contrast, nucleolar-nucleoplasmic translocation of the base excision repair protein, XRCC1, was dependent on both PARP1 protein and its enzymatic activity. Furthermore, gossypol, which inhibits PARP1 activity by disruption of PARP1-protein interactions, abolishes nucleolar-nucleoplasmic shuttling of WRN, XRCC1 and PARP1, indicating the involvement of further upstream factors. In conclusion, this study highlights a prominent role of PARP1 in the DNA damage-induced nucleolar-nucleoplasmic shuttling of genome maintenance factors in HeLa cells in a toxicant and protein-specific manner.
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131
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Chen Y, Li J, Cao F, Lam J, Cheng CC, Yu CH, Huen MS. Nucleolar residence of the seckel syndrome protein TRAIP is coupled to ribosomal DNA transcription. Nucleic Acids Res 2019; 46:10119-10131. [PMID: 30165463 PMCID: PMC6212796 DOI: 10.1093/nar/gky775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022] Open
Abstract
The RING finger protein TRAIP protects genome integrity and its mutation causes Seckel syndrome. TRAIP encodes a nucleolar protein that migrates to UV-induced DNA lesions via a direct interaction with the DNA replication clamp PCNA. Thus far, mechanistically how UV mobilizes TRAIP from the nucleoli remains unknown. We found that PCNA binding is dispensable for the nucleolus-nucleoplasm shuttling of TRAIP following cell exposure to UV irradiation, and that its redistribution did not rely on the master DNA damage kinases ATM and ATR. Interestingly, I-PpoI-induced ribosomal DNA damage led to TRAIP exclusion from the nucleoli, raising the possibility that active ribosomal DNA transcription may underlie TRAIP retention in the nuclear sub-compartments. Accordingly, chemical inhibition of RNA polymerase I activity led to TRAIP diffusion into the nucleoplasm, and was coupled with marked reduction of DNA/RNA hybrids in the nucleoli, suggesting that TRAIP may be sequestered via binding to nucleic acid structures in the nucleoli. Consistently, cell pre-treatment with DNase/RNase effectively released TRAIP from the nucleoli. Taken together, our study defines a bipartite mechanism that drives TRAIP trafficking in response to UV damage, and highlights the nucleolus as a stress sensor that contributes to orchestrating DNA damage responses.
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Affiliation(s)
- Yangzi Chen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Junshi Li
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Fakun Cao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Jason Lam
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Clooney Cy Cheng
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Cheng-Han Yu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Michael Sy Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R.,Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong S.A.R
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132
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Phan T, Khalid F, Iben S. Nucleolar and Ribosomal Dysfunction-A Common Pathomechanism in Childhood Progerias? Cells 2019; 8:E534. [PMID: 31167386 PMCID: PMC6627804 DOI: 10.3390/cells8060534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/21/2019] [Accepted: 06/02/2019] [Indexed: 01/03/2023] Open
Abstract
The nucleolus organizes around the sites of transcription by RNA polymerase I (RNA Pol I). rDNA transcription by this enzyme is the key step of ribosome biogenesis and most of the assembly and maturation processes of the ribosome occur co-transcriptionally. Therefore, disturbances in rRNA transcription and processing translate to ribosomal malfunction. Nucleolar malfunction has recently been described in the classical progeria of childhood, Hutchinson-Gilford syndrome (HGPS), which is characterized by severe signs of premature aging, including atherosclerosis, alopecia, and osteoporosis. A deregulated ribosomal biogenesis with enlarged nucleoli is not only characteristic for HGPS patients, but it is also found in the fibroblasts of "normal" aging individuals. Cockayne syndrome (CS) is also characterized by signs of premature aging, including the loss of subcutaneous fat, alopecia, and cataracts. It has been shown that all genes in which a mutation causes CS, are involved in rDNA transcription by RNA Pol I. A disturbed ribosomal biogenesis affects mitochondria and translates into ribosomes with a reduced translational fidelity that causes endoplasmic reticulum (ER) stress and apoptosis. Therefore, it is speculated that disease-causing disturbances in the process of ribosomal biogenesis may be more common than hitherto anticipated.
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Affiliation(s)
- Tamara Phan
- Department of Dermatology, Ulm University, James-Franck Ring N27, 89081 Ulm, Germany.
| | - Fatima Khalid
- Department of Dermatology, Ulm University, James-Franck Ring N27, 89081 Ulm, Germany.
| | - Sebastian Iben
- Department of Dermatology, Ulm University, James-Franck Ring N27, 89081 Ulm, Germany.
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133
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NOL12 Repression Induces Nucleolar Stress-Driven Cellular Senescence and Is Associated with Normative Aging. Mol Cell Biol 2019; 39:MCB.00099-19. [PMID: 30988155 DOI: 10.1128/mcb.00099-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/06/2019] [Indexed: 02/07/2023] Open
Abstract
The nucleolus is a subnuclear compartment with key roles in rRNA synthesis and ribosome biogenesis, complex processes that require hundreds of proteins and factors. Alterations in nucleolar morphology and protein content have been linked to the control of cell proliferation and stress responses and, recently, further implicated in cell senescence and ageing. In this study, we report the functional role of NOL12 in the nucleolar homeostasis of human primary fibroblasts. NOL12 repression induces specific changes in nucleolar morphology, with increased nucleolar area but reduced nucleolar number, along with nucleolar accumulation and increased levels of fibrillarin and nucleolin. Moreover, NOL12 repression leads to stabilization and activation of p53 in an RPL11-dependent manner, which arrests cells at G2 phase and ultimately leads to senescence. Importantly, we found NOL12 repression in association with nucleolar stress-like responses in human fibroblasts from elderly donors, disclosing it as a biomarker in human chronological aging.
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134
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Keil M, Meyer MT, Dannheisig DP, Maerz LD, Philipp M, Pfister AS. Loss of Peter Pan protein is associated with cell cycle defects and apoptotic events. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:882-895. [DOI: 10.1016/j.bbamcr.2019.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/21/2018] [Accepted: 01/23/2019] [Indexed: 12/19/2022]
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135
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Pfister AS. Emerging Role of the Nucleolar Stress Response in Autophagy. Front Cell Neurosci 2019; 13:156. [PMID: 31114481 PMCID: PMC6503120 DOI: 10.3389/fncel.2019.00156] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Autophagy represents a conserved self-digestion program, which allows regulated degradation of cellular material. Autophagy is activated by cellular stress, serum starvation and nutrient deprivation. Several autophagic pathways have been uncovered, which either non-selectively or selectively target the cellular cargo for lysosomal degradation. Autophagy engages the coordinated action of various key regulators involved in the steps of autophagosome formation, cargo targeting and lysosomal fusion. While non-selective (macro)autophagy is required for removal of bulk material or recycling of nutrients, selective autophagy mediates specific targeting of damaged organelles or protein aggregates. By proper action of the autophagic machinery, cellular homeostasis is maintained. In contrast, failure of this fundamental process is accompanied by severe pathophysiological conditions. Hallmarks of neuropathological disorders are for instance accumulated, mis-folded protein aggregates and damaged mitochondria. The nucleolus has been recognized as central hub in the cellular stress response. It represents a sub-nuclear organelle essential for ribosome biogenesis and also functions as stress sensor by mediating cell cycle arrest or apoptosis. Thus, proper nucleolar function is mandatory for cell growth and survival. Here, I highlight the emerging role of nucleolar factors in the regulation of autophagy. Moreover, I discuss the nucleolar stress response as a novel signaling pathway in the context of autophagy, health and disease.
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Affiliation(s)
- Astrid S Pfister
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Ulm University, Ulm, Germany
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136
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Turi Z, Lacey M, Mistrik M, Moudry P. Impaired ribosome biogenesis: mechanisms and relevance to cancer and aging. Aging (Albany NY) 2019; 11:2512-2540. [PMID: 31026227 PMCID: PMC6520011 DOI: 10.18632/aging.101922] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/04/2019] [Indexed: 02/06/2023]
Abstract
The biosynthesis of ribosomes is a complex process that requires the coordinated action of many factors and a huge energy investment from the cell. Ribosomes are essential for protein production, and thus for cellular survival, growth and proliferation. Ribosome biogenesis is initiated in the nucleolus and includes: the synthesis and processing of ribosomal RNAs, assembly of ribosomal proteins, transport to the cytoplasm and association of ribosomal subunits. The disruption of ribosome biogenesis at various steps, with either increased or decreased expression of different ribosomal components, can promote cell cycle arrest, senescence or apoptosis. Additionally, interference with ribosomal biogenesis is often associated with cancer, aging and age-related degenerative diseases. Here, we review current knowledge on impaired ribosome biogenesis, discuss the main factors involved in stress responses under such circumstances and focus on examples with clinical relevance.
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Affiliation(s)
- Zsofia Turi
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Matthew Lacey
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
| | - Pavel Moudry
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic
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137
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Bouska M, Huang K, Kang P, Bai H. Organelle aging: Lessons from model organisms. J Genet Genomics 2019; 46:171-185. [PMID: 31080045 PMCID: PMC6553499 DOI: 10.1016/j.jgg.2019.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/22/2019] [Accepted: 03/12/2019] [Indexed: 01/07/2023]
Abstract
Most cellular processes descend into failure during aging. While a large collection of longevity pathways has been identified in the past decades, the mechanism for age-related decline of cellular homeostasis and organelle function remains largely unsolved. It is known that many organelles undergo structural and functional changes during normal aging, which significantly contributes to the decline of tissue function at old ages. Since recent studies have revealed an emerging role of organelles as regulatory hubs in maintaining cellular homeostasis, understanding of organelle aging will provide important insights into the cellular basis of organismal aging. Here we review current progress on the characterization of age-dependent structural and functional alterations in the more well-studied organelles, as well as the known mechanisms governing organelle aging in model organisms, with a special focus on the fruit fly Drosophila melanogaster.
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Affiliation(s)
- Mark Bouska
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kerui Huang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ping Kang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Hua Bai
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA.
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138
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Annibal A, Tam H, Latza C, Antebi A. Comparison of ESI-MS/MS and APCI-MS methods for the quantification of folic acid analogs in C. elegans. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:316-327. [PMID: 30675959 DOI: 10.1002/jms.4337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/17/2019] [Accepted: 01/20/2019] [Indexed: 06/09/2023]
Abstract
Folic acid (FA) plays a vital role in central metabolism, including the one carbon cycle, nucleotide, and amino acid biosynthesis. The development of sensitive, accurate analytical methods to measure FA intermediates in tissues is critical to understand their biological roles in diverse physiological and pathological contexts. Here, we developed a highly sensitive method for the simultaneous quantification of FA intermediates in the nematode Caenorhabditis elegans as a model to dissect metabolic networks. The method was further validated by analyzing the worm folate pool upon RNAi knockdown of the dihydrofolate reductase gene dhfr-1. Comparative mass spectrometry behavior of the FA analogs using two different ion sources, electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI), revealed ESI-MS/MS to be more sensitive, but APCI-MS provided more detailed structure inferences, which can elucidate chemical investigation and synthesis of FA analogs. Finally, we report on the use of in vitro oxidation coupled with high-resolution mass spectrometry as a tool to discover new endogenous FA derivatives in the nematode.
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Affiliation(s)
- Andrea Annibal
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Hannah Tam
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Christian Latza
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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139
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Son HG, Altintas O, Kim EJE, Kwon S, Lee SV. Age-dependent changes and biomarkers of aging in Caenorhabditis elegans. Aging Cell 2019; 18:e12853. [PMID: 30734981 PMCID: PMC6413654 DOI: 10.1111/acel.12853] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/28/2018] [Accepted: 09/11/2018] [Indexed: 12/13/2022] Open
Abstract
Caenorhabditis elegans is an exceptionally valuable model for aging research because of many advantages, including its genetic tractability, short lifespan, and clear age‐dependent physiological changes. Aged C. elegans display a decline in their anatomical and functional features, including tissue integrity, motility, learning and memory, and immunity. Caenorhabditis elegans also exhibit many age‐associated changes in the expression of microRNAs and stress‐responsive genes and in RNA and protein quality control systems. Many of these age‐associated changes provide information on the health of the animals and serve as valuable biomarkers for aging research. Here, we review the age‐dependent changes in C. elegans and their utility as aging biomarkers indicative of the physiological status of aging.
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Affiliation(s)
- Heehwa G. Son
- Department of Life Sciences Pohang University of Science and Technology Pohang South Korea
| | - Ozlem Altintas
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang South Korea
| | - Eun Ji E. Kim
- Department of Life Sciences Pohang University of Science and Technology Pohang South Korea
| | - Sujeong Kwon
- Department of Life Sciences Pohang University of Science and Technology Pohang South Korea
| | - Seung‐Jae V. Lee
- Department of Life Sciences Pohang University of Science and Technology Pohang South Korea
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang South Korea
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140
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Nyhus C, Pihl M, Hyttel P, Hall VJ. Evidence for nucleolar dysfunction in Alzheimer's disease. Rev Neurosci 2019; 30:685-700. [PMID: 30849050 DOI: 10.1515/revneuro-2018-0104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/08/2019] [Indexed: 11/15/2022]
Abstract
The nucleolus is a dynamically changing organelle that is central to a number of important cellular functions. Not only is it important for ribosome biogenesis, but it also reacts to stress by instigating a nucleolar stress response and is further involved in regulating the cell cycle. Several studies report nucleolar dysfunction in Alzheimer's disease (AD). Studies have reported a decrease in both total nucleolar volume and transcriptional activity of the nucleolar organizing regions. Ribosomes appear to be targeted by oxidation and reduced protein translation has been reported. In addition, several nucleolar proteins are dysregulated and some of these appear to be implicated in classical AD pathology. Some studies also suggest that the nucleolar stress response may be activated in AD, albeit this latter research is rather limited and requires further investigation. The purpose of this review is to draw the connections of all these studies together and signify that there are clear changes in the nucleolus and the ribosomes in AD. The nucleolus is therefore an organelle that requires more attention than previously given in relation to understanding the biological mechanisms underlying the disease.
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Affiliation(s)
- Caitlin Nyhus
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
| | - Maria Pihl
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
| | - Poul Hyttel
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
| | - Vanessa Jane Hall
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Grønnegårdsvej 7, Frederiksberg C DK-1870, Denmark
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141
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Potapova TA, Gerton JL. Ribosomal DNA and the nucleolus in the context of genome organization. Chromosome Res 2019; 27:109-127. [PMID: 30656516 DOI: 10.1007/s10577-018-9600-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/13/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]
Abstract
The nucleolus constitutes a prominent nuclear compartment, a membraneless organelle that was first documented in the 1830s. The fact that specific chromosomal regions were present in the nucleolus was recognized by Barbara McClintock in the 1930s, and these regions were termed nucleolar organizing regions, or NORs. The primary function of ribosomal DNA (rDNA) is to produce RNA components of ribosomes. Yet, ribosomal DNA also plays a pivotal role in nuclear organization by assembling the nucleolus. This review is focused on the rDNA and associated proteins in the context of genome organization. Recent advances in understanding chromatin organization suggest that chromosomes are organized into topological domains by a DNA loop extrusion process. We discuss the perspective that rDNA may also be organized in topological domains constrained by structural maintenance of chromosome protein complexes such as cohesin and condensin. Moreover, biophysical studies indicate that the nucleolar compartment may be formed by active processes as well as phase separation, a perspective that lends further insight into nucleolar organization. The application of the latest perspectives and technologies to this organelle help further elucidate its role in nuclear structure and function.
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Affiliation(s)
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
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142
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Wang M, Lemos B. Ribosomal DNA harbors an evolutionarily conserved clock of biological aging. Genome Res 2019; 29:325-333. [PMID: 30765617 PMCID: PMC6396418 DOI: 10.1101/gr.241745.118] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/22/2019] [Indexed: 01/17/2023]
Abstract
The ribosomal DNA (rDNA) is the most evolutionarily conserved segment of the genome and gives origin to the nucleolus, an energy intensive nuclear organelle and major hub influencing myriad molecular processes from cellular metabolism to epigenetic states of the genome. The rDNA/nucleolus has been directly and mechanistically implicated in aging and longevity in organisms as diverse as yeasts, Drosophila, and humans. The rDNA is also a significant target of DNA methylation that silences supernumerary rDNA units and regulates nucleolar activity. Here, we introduce an age clock built exclusively with CpG methylation within the rDNA. The ribosomal clock is sufficient to accurately estimate individual age within species, is responsive to genetic and environmental interventions that modulate life-span, and operates across species as distant as humans, mice, and dogs. Further analyses revealed a significant excess of age-associated hypermethylation in the rDNA relative to other segments of the genome, and which forms the basis of the rDNA clock. Our observations identified an evolutionarily conserved marker of aging that is easily ascertained, grounded on nucleolar biology, and could serve as a universal marker to gauge individual age and response to interventions in humans as well as laboratory and wild organisms across a wide diversity of species.
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Affiliation(s)
- Meng Wang
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Bernardo Lemos
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
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143
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Nucleophagy: from homeostasis to disease. Cell Death Differ 2019; 26:630-639. [PMID: 30647432 PMCID: PMC6460388 DOI: 10.1038/s41418-018-0266-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 11/08/2022] Open
Abstract
Nuclear abnormalities are prominent in degenerative disease and progeria syndromes. Selective autophagy of organelles is instrumental in maintaining cell homeostasis and prevention of premature ageing. Although the nucleus is the control centre of the cell by safeguarding our genetic material and controlling gene expression, little is known in relation to nuclear autophagy. Here we present recent discoveries in nuclear recycling, namely nucleophagy in physiology in yeast and nucleophagic events that occur in pathological conditions in mammals. The selective nature of degrading nuclear envelope components, DNA, RNA and nucleoli is highlighted. Potential effects of perturbed nucleophagy in senescence and longevity are examined. Moreover, the open questions that remain to be explored are discussed concerning the conditions, receptors and substrates in homeostatic nucleophagy.
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144
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Alves MJ, Goksel M, Kaya B, Mostafa H, Gygli P, Stephens J, Fair S, Otero JJ, Czeisler CM. CCNA2 Ablation in Aged Mice Results in Abnormal rRNA Granule Accumulation in Hippocampus. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 189:426-439. [PMID: 30579783 DOI: 10.1016/j.ajpath.2018.10.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/20/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Mounting evidence in the literature suggests that RNA-RNA binding protein aggregations can disturb neuronal homeostasis and lead to symptoms associated with normal aging as well as dementia. The specific ablation of cyclin A2 in adult neurons results in neuronal polyribosome aggregations and learning and memory deficits. Detailed histologic and ultrastructural assays of aged mice revealed that post-mitotic hippocampal pyramidal neurons maintain cyclin A2 expression and that proliferative cells in the dentate subgranular zone express cyclin A2. Cyclin A2 loss early during neural development inhibited hippocampal development through canonical/cell-cycle mechanisms, including prolonged cell cycle timing in embryonic hippocampal progenitor cells. However, in mature neurons, cyclin A2 colocalized with dendritic rRNA. Cyclin A2 ablation in adult hippocampus resulted in decreased synaptic density in the hippocampus as well as in accumulation of rRNA granules in dendrite shafts. We conclude that cyclin A2 functions in a noncanonical/non-cell cycle regulatory role to maintain adult pyramidal neuron ribostasis.
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Affiliation(s)
- Michele J Alves
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Mustafa Goksel
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Behiye Kaya
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Hasnaa Mostafa
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Patrick Gygli
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Julie Stephens
- Center for Biostatistics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Summer Fair
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - José J Otero
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio.
| | - Catherine M Czeisler
- Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio.
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145
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Bughio F, Maggert KA. The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance. Chromosome Res 2018; 27:19-30. [PMID: 30511202 DOI: 10.1007/s10577-018-9591-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022]
Abstract
Our goal is to draw a line-hypothetical in its totality but experimentally supported at each individual step-connecting the ribosomal DNA and the phenomenon of transgenerational epigenetic inheritance of induced phenotypes. The reasonableness of this hypothesis is offset by its implication, that many (or most) (or all) of the cases of induced-and-inherited phenotypes that are seen to persist for generations are instead unmapped induced polymorphisms in the ribosomal DNA, and thus are the consequence of the peculiar and enduringly fascinating genetics of the highly transcribed repeat DNA structure at that locus.
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Affiliation(s)
- Farah Bughio
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, USA
- University of Arizona Cancer Center, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Keith A Maggert
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, USA.
- University of Arizona Cancer Center, University of Arizona College of Medicine, Tucson, AZ, USA.
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146
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Stroustrup N. Measuring and modeling interventions in aging. Curr Opin Cell Biol 2018; 55:129-138. [PMID: 30099284 PMCID: PMC6284105 DOI: 10.1016/j.ceb.2018.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023]
Abstract
Many dietary, pharmaceutical, and genetic interventions have been found to increase the lifespan of laboratory animals. Several are now being explored for clinical application. To understand the physiologic action and therapeutic potential of interventions in aging, researchers must build quantitative models. Do interventions delay the onset of aging? Slow it down? Merely ameliorate some of its symptoms? If interventions slow some aging mechanisms but accelerate others, can we detect or predict the systemic consequences? Statistical and analytic models provide a crucial framework in which to answer these questions and clarify the systems-level effect of molecular interventions in aging. This review provides a brief survey of approaches to modeling lifespan data and places them in the context of recent experimental work.
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Affiliation(s)
- Nicholas Stroustrup
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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147
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Crosstalk between NF-κB and Nucleoli in the Regulation of Cellular Homeostasis. Cells 2018; 7:cells7100157. [PMID: 30301139 PMCID: PMC6210184 DOI: 10.3390/cells7100157] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/28/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022] Open
Abstract
Nucleoli are emerging as key sensors of cellular stress and regulators of the downstream consequences on proliferation, metabolism, senescence, and apoptosis. NF-κB signalling is activated in response to a similar plethora of stresses, which leads to modulation of cell growth and death programs. While nucleolar and NF-κB pathways are distinct, it is increasingly apparent that they converge at multiple levels. Exposure of cells to certain insults causes a specific type of nucleolar stress that is characterised by degradation of the PolI complex component, TIF-IA, and increased nucleolar size. Recent studies have shown that this atypical nucleolar stress lies upstream of cytosolic IκB degradation and NF-κB nuclear translocation. Under these stress conditions, the RelA component of NF-κB accumulates within functionally altered nucleoli to trigger a nucleophosmin dependent, apoptotic pathway. In this review, we will discuss these points of crosstalk and their relevance to anti-tumour mechanism of aspirin and small molecule CDK4 inhibitors. We will also briefly the discuss how crosstalk between nucleoli and NF-κB signalling may be more broadly relevant to the regulation of cellular homeostasis and how it may be exploited for therapeutic purpose.
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148
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Tiku V, Kew C, Mehrotra P, Ganesan R, Robinson N, Antebi A. Nucleolar fibrillarin is an evolutionarily conserved regulator of bacterial pathogen resistance. Nat Commun 2018; 9:3607. [PMID: 30190478 PMCID: PMC6127302 DOI: 10.1038/s41467-018-06051-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 07/19/2018] [Indexed: 02/04/2023] Open
Abstract
Innate immunity is the first line of defense against infections. Pathways regulating innate responses can also modulate other processes, including stress resistance and longevity. Increasing evidence suggests a role for the nucleolus in regulating cellular processes implicated in health and disease. Here we show the highly conserved nucleolar protein, fibrillarin, is a vital factor regulating pathogen resistance. Fibrillarin knockdown enhances resistance in C. elegans against bacterial pathogens, higher levels of fibrillarin induce susceptibility to infection. Pathogenic infection reduces nucleolar size, ribsosomal RNA, and fibrillarin levels. Genetic epistasis reveals fibrillarin functions independently of the major innate immunity mediators, suggesting novel mechanisms of pathogen resistance. Bacterial infection also reduces nucleolar size and fibrillarin levels in mammalian cells. Fibrillarin knockdown prior to infection increases intracellular bacterial clearance, reduces inflammation, and enhances cell survival. Collectively, these findings reveal an evolutionarily conserved role of fibrillarin in infection resistance and suggest the nucleolus as a focal point in innate immune responses.
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Affiliation(s)
- Varnesh Tiku
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany.,Department of Infectious Diseases, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Chun Kew
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931, Cologne, Germany
| | - Parul Mehrotra
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931, Cologne, Germany.,VIB-Center for Inflammation Research, VIB - Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Raja Ganesan
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, 50674, Cologne, Germany
| | - Nirmal Robinson
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany. .,Centre for Cancer Biology, University of South Australia, HB11-35 UniSA CRI Building, North Terrace, 5001, Adelaide, Australia.
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931, Cologne, Germany. .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674, Cologne, Germany.
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149
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Abstract
Longer human lives have led to a global burden of late-life disease. However, some older people experience little ill health, a trait that should be extended to the general population. Interventions into lifestyle, including increased exercise and reduction in food intake and obesity, can help to maintain healthspan. Altered gut microbiota, removal of senescent cells, blood factors obtained from young individuals and drugs can all improve late-life health in animals. Application to humans will require better biomarkers of disease risk and responses to interventions, closer alignment of work in animals and humans, and increased use of electronic health records, biobank resources and cohort studies.
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150
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Molenaars M, Janssens GE, Santermans T, Lezzerini M, Jelier R, MacInnes AW, Houtkooper RH. Mitochondrial ubiquinone-mediated longevity is marked by reduced cytoplasmic mRNA translation. Life Sci Alliance 2018; 1. [PMID: 30198021 PMCID: PMC6126614 DOI: 10.26508/lsa.201800082] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This study uses polysomal RNA sequencing to show that the translational efficiency of specific mRNA changes in long-lived Caenorhabditis elegans with reduced ubiquinone synthesis. Mutations in the clk-1 gene impair mitochondrial ubiquinone biosynthesis and extend the lifespan in Caenorhabditis elegans. We demonstrate here that this life extension is linked to the repression of cytoplasmic mRNA translation, independent of the alleged nuclear form of CLK-1. Clk-1 mutations inhibit polyribosome formation similarly to daf-2 mutations that dampen insulin signaling. Comparisons of total versus polysomal RNAs in clk-1(qm30) mutants reveal a reduction in the translational efficiencies of mRNAs coding for elements of the translation machinery and an increase in those coding for the oxidative phosphorylation and autophagy pathways. Knocking down the transcription initiation factor TATA-binding protein-associated factor 4, a protein that becomes sequestered in the cytoplasm during early embryogenesis to induce transcriptional silencing, ameliorates the clk-1 inhibition of polyribosome formation. These results underscore a prominent role for the repression of cytoplasmic protein synthesis in eukaryotic lifespan extension and suggest that mutations impairing mitochondrial function are able to exploit this repression similarly to reductions of insulin signaling. Moreover, this report reveals an unexpected role for TATA-binding protein-associated factor 4 as a repressor of polyribosome formation when ubiquinone biosynthesis is compromised.
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Affiliation(s)
- Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
| | - Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
| | - Toon Santermans
- CMPG - Predictive Genetics and Multicellular Systems, University of Leuven, B-3001 Leuven, Belgium
| | - Marco Lezzerini
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
| | - Rob Jelier
- CMPG - Predictive Genetics and Multicellular Systems, University of Leuven, B-3001 Leuven, Belgium
| | - Alyson W MacInnes
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, Meibergdreef 9, Amsterdam, The Netherlands
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