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Rieckher M, Gallrein C, Alquezar-Artieda N, Bourached-Silva N, Vaddavalli PL, Mares D, Backhaus M, Blindauer T, Greger K, Wiesner E, Pontel LB, Schumacher B. Distinct DNA repair mechanisms prevent formaldehyde toxicity during development, reproduction and aging. Nucleic Acids Res 2024; 52:8271-8285. [PMID: 38894680 DOI: 10.1093/nar/gkae519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Formaldehyde (FA) is a recognized environmental and metabolic toxin implicated in cancer development and aging. Inherited mutations in the FA-detoxifying enzymes ADH5 and ALDH2 genes lead to FA overload in the severe multisystem AMeD syndrome. FA accumulation causes genome damage including DNA-protein-, inter- and intra-strand crosslinks and oxidative lesions. However, the influence of distinct DNA repair systems on organismal FA resistance remains elusive. We have here investigated the consequence of a range of DNA repair mutants in a model of endogenous FA overload generated by downregulating the orthologs of human ADH5 and ALDH2 in C. elegans. We have focused on the distinct components of nucleotide excision repair (NER) during developmental growth, reproduction and aging. Our results reveal three distinct modes of repair of FA-induced DNA damage: Transcription-coupled repair (TCR) operating NER-independently during developmental growth or through NER during adulthood, and, in concert with global-genome (GG-) NER, in the germline and early embryonic development. Additionally, we show that the Cockayne syndrome B (CSB) factor is involved in the resolution of FA-induced DNA-protein crosslinks, and that the antioxidant and FA quencher N-acetyl-l-cysteine (NAC) reverses the sensitivity of detoxification and DNA repair defects during development, suggesting a therapeutic intervention to revert FA-pathogenic consequences.
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Affiliation(s)
- Matthias Rieckher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Christian Gallrein
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Natividad Alquezar-Artieda
- Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Catalonia, Spain
| | - Nour Bourached-Silva
- Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Catalonia, Spain
| | - Pavana Lakshmi Vaddavalli
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Devin Mares
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Maria Backhaus
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Timon Blindauer
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Ksenia Greger
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Eva Wiesner
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Lucas B Pontel
- Josep Carreras Leukaemia Research Institute (IJC), Ctra de Can Ruti, Camí de les Escoles s/n, 08916 Badalona, Barcelona, Catalonia, Spain
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET - Partner Institute of the Max Planck Society, C1425FQD, Buenos Aires, Argentina
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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2
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Ropert B, Gallrein C, Schumacher B. DNA repair deficiencies and neurodegeneration. DNA Repair (Amst) 2024; 138:103679. [PMID: 38640601 DOI: 10.1016/j.dnarep.2024.103679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024]
Abstract
Neurodegenerative diseases are the second most prevalent cause of death in industrialized countries. Alzheimer's Disease is the most widespread and also most acknowledged form of dementia today. Together with Parkinson's Disease they account for over 90 % cases of neurodegenerative disorders caused by proteopathies. Far less known are the neurodegenerative pathologies in DNA repair deficiency syndromes. Such diseases like Cockayne - or Werner Syndrome are described as progeroid syndromes - diseases that cause the premature ageing of the affected persons, and there are clear implications of such diseases in neurologic dysfunction and degeneration. In this review, we aim to draw the attention on commonalities between proteopathy-associated neurodegeneration and neurodegeneration caused by DNA repair defects and discuss how mitochondria are implicated in the development of both disorder classes. Furthermore, we highlight how nematodes are a valuable and indispensable model organism to study conserved neurodegenerative processes in a fast-forward manner.
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Affiliation(s)
- Baptiste Ropert
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany
| | - Christian Gallrein
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, Jena 07745, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, Cologne 50931, Germany.
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3
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Ange JS, Weng Y, Stevenson ME, Kaletsky R, Moore RS, Zhou S, Murphy CT. Adult Single-nucleus Neuronal Transcriptomes of Insulin Signaling Mutants Reveal Regulators of Behavior and Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579364. [PMID: 38370779 PMCID: PMC10871314 DOI: 10.1101/2024.02.07.579364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The insulin/insulin-like signaling (IIS) pathway regulates many of C. elegans' adult functions, including learning and memory 1 . While whole-worm and tissue-specific transcriptomic analyses have identified IIS targets 2,3 , a higher-resolution single-cell approach is required to identify changes that confer neuron-specific improvements in the long-lived insulin receptor mutant, daf-2 . To understand how behaviors that are controlled by a small number of neurons change in daf-2 mutants, we used the deep resolution of single-nucleus RNA sequencing to define each neuron type's transcriptome in adult wild-type and daf-2 mutants. First, we found surprising differences between wild-type L4 larval neurons and young adult neurons in chemoreceptor expression, synaptic genes, and learning and memory genes. These Day 1 adult neuron transcriptomes allowed us to identify adult AWC-specific regulators of chemosensory function and to predict neuron-to-neuron peptide/receptor pairs. We then identified gene expression changes that correlate with daf-2's improved cognitive functions, particularly in the AWC sensory neuron that controls learning and associative memory 4 , and used behavioral assays to test their roles in cognitive function. Combining deep single-neuron transcriptomics, genetic manipulation, and behavioral analyses enabled us to identify genes that may function in a single adult neuron to control behavior, including conserved genes that function in learning and memory. One-Sentence Summary Single-nucleus sequencing of adult wild-type and daf-2 C. elegans neurons reveals functionally relevant transcriptional changes, including regulators of chemosensation, learning, and memory.
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Culberson JW, Kopel J, Sehar U, Reddy PH. Urgent needs of caregiving in ageing populations with Alzheimer's disease and other chronic conditions: Support our loved ones. Ageing Res Rev 2023; 90:102001. [PMID: 37414157 PMCID: PMC10756323 DOI: 10.1016/j.arr.2023.102001] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
The ageing process begins at birth. It is a life-long process, and its exact origins are still unknown. Several hypotheses attempt to describe the normal ageing process, including hormonal imbalance, formation of reactive oxygen species, DNA methylation & DNA damage accumulation, loss of proteostasis, epigenetic alterations, mitochondrial dysfunction, senescence, inflammation, and stem cell depletion. With increased lifespan in elderly individuals, the prevalence of age-related diseases including, cancer, diabetes, obesity, hypertension, Alzheimer's, Alzheimer's disease and related dementias, Parkinson's, and other mental illnesses are increased. These increased age-related illnesses, put tremendous pressure & burden on caregivers, family members, and friends who are living with patients with age-related diseases. As medical needs evolve, the caregiver is expected to experience an increase in duties and challenges, which may result in stress on themselves, and impact their own family life. In the current article, we assess the biological mechanisms of ageing and its effect on body systems, exploring lifestyle and ageing, with a specific focus on age-related disorders. We also discussed the history of caregiving and specific challenges faced by caregivers in the presence of multiple comorbidities. We also assessed innovative approaches to funding caregiving, and efforts to improve the medical system to better organize chronic care efforts, while improving the skill and efficiency of both informal and formal caregivers. We also discussed the role of caregiving in end-of-life care. Our critical analysis strongly suggests that there is an urgent need for caregiving in aged populations and support from local, state, and federal agencies.
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Affiliation(s)
- John W Culberson
- Department of Family and Community Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Jonathan Kopel
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ujala Sehar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA; Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
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5
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Freeman TF, Zhao Q, Surya A, Rothe R, Cenik ES. Ribosome biogenesis disruption mediated chromatin structure changes revealed by SRAtac, a customizable end to end analysis pipeline for ATAC-seq. BMC Genomics 2023; 24:512. [PMID: 37658321 PMCID: PMC10472662 DOI: 10.1186/s12864-023-09576-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 08/11/2023] [Indexed: 09/03/2023] Open
Abstract
The nucleolus is a large nuclear body that serves as the primary site for ribosome biogenesis. Recent studies have suggested that it also plays an important role in organizing chromatin architecture. However, to establish a causal relationship between nucleolar ribosome assembly and chromatin architecture, genetic tools are required to disrupt nucleolar ribosome biogenesis. In this study, we used ATAC-seq to investigate changes in chromatin accessibility upon specific depletion of two ribosome biogenesis components, RPOA-2 and GRWD-1, in the model organism Caenorhabditis elegans. To facilitate the analysis of ATAC-seq data, we introduced two tools: SRAlign, an extensible NGS data processing workflow, and SRAtac, a customizable end-to-end ATAC-seq analysis pipeline. Our results revealed highly comparable changes in chromatin accessibility following both RPOA-2 and GRWD-1 perturbations. However, we observed a weak correlation between changes in chromatin accessibility and gene expression. While our findings corroborate the idea of a feedback mechanism between ribosomal RNA synthesis, nucleolar ribosome large subunit biogenesis, and chromatin structure during the L1 stage of C. elegans development, they also prompt questions regarding the functional impact of these alterations on gene expression.
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Affiliation(s)
- Trevor F Freeman
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Agustian Surya
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Reed Rothe
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA.
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6
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Sarkar GC, Rautela U, Goyala A, Datta S, Anand N, Singh A, Singh P, Chamoli M, Mukhopadhyay A. DNA damage signals from somatic uterine tissue arrest oogenesis through activated DAF-16. Development 2023; 150:dev201472. [PMID: 37577954 DOI: 10.1242/dev.201472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/21/2023] [Indexed: 08/15/2023]
Abstract
Germ line integrity is crucial for progeny fitness. Organisms deploy the DNA damage response (DDR) signaling to protect the germ line from genotoxic stress, facilitating the cell-cycle arrest of germ cells and DNA repair or their apoptosis. Cell-autonomous regulation of germ line quality in response to DNA damage is well studied; however, how quality is enforced cell non-autonomously on sensing somatic DNA damage is less known. Using Caenorhabditis elegans, we show that DDR disruption, only in the uterus, when insulin/IGF-1 signaling (IIS) is low, arrests oogenesis in the pachytene stage of meiosis I, in a FOXO/DAF-16 transcription factor-dependent manner. Without FOXO/DAF-16, germ cells of the IIS mutant escape the arrest to produce poor-quality oocytes, showing that the transcription factor imposes strict quality control during low IIS. Activated FOXO/DAF-16 senses DDR perturbations during low IIS to lower ERK/MPK-1 signaling below a threshold to promote germ line arrest. Altogether, we elucidate a new surveillance role for activated FOXO/DAF-16 that ensures optimal germ cell quality and progeny fitness in response to somatic DNA damage.
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Affiliation(s)
- Gautam Chandra Sarkar
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Umanshi Rautela
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anita Goyala
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sudeshna Datta
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nikhita Anand
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anupama Singh
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Prachi Singh
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manish Chamoli
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Arnab Mukhopadhyay
- Molecular Aging Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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7
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Zhao Q, Rangan R, Weng S, Özdemir C, Sarinay Cenik E. Inhibition of ribosome biogenesis in the epidermis is sufficient to trigger organism-wide growth quiescence independently of nutritional status in C. elegans. PLoS Biol 2023; 21:e3002276. [PMID: 37651423 PMCID: PMC10499265 DOI: 10.1371/journal.pbio.3002276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 09/13/2023] [Accepted: 07/26/2023] [Indexed: 09/02/2023] Open
Abstract
Interorgan communication is crucial for multicellular organismal growth, development, and homeostasis. Cell nonautonomous inhibitory cues, which limit tissue-specific growth alterations, are not well characterized due to cell ablation approach limitations. In this study, we employed the auxin-inducible degradation system in C. elegans to temporally and spatially modulate ribosome biogenesis, through depletion of essential factors (RPOA-2, GRWD-1, or TSR-2). Our findings reveal that embryo-wide inhibition of ribosome biogenesis induces a reversible early larval growth quiescence, distinguished by a unique gene expression signature that is different from starvation or dauer stages. When ribosome biogenesis is inhibited in volumetrically similar tissues, including body wall muscle, epidermis, pharynx, intestine, or germ line, it results in proportionally stunted growth across the organism to different degrees. We show that specifically inhibiting ribosome biogenesis in the epidermis is sufficient to trigger an organism-wide growth quiescence. Epidermis-specific ribosome depletion leads to larval growth quiescence at the L3 stage, reduces organism-wide protein synthesis, and induced cell nonautonomous gene expression alterations. Further molecular analysis reveals overexpression of secreted proteins, suggesting an organism-wide regulatory mechanism. We find that UNC-31, a dense-core vesicle (DCV) pathway component, plays a significant role in epidermal ribosome biogenesis-mediated growth quiescence. Our tissue-specific knockdown experiments reveal that the organism-wide growth quiescence induced by epidermal-specific ribosome biogenesis inhibition is suppressed by reducing unc-31 expression in the epidermis, but not in neurons or body wall muscles. Similarly, IDA-1, a membrane-associated protein of the DCV, is overexpressed, and its knockdown in epidermis suppresses the organism-wide growth quiescence in response to epidermal ribosome biogenesis inhibition. Finally, we observe an overall increase in DCV puncta labeled by IDA-1 when epidermal ribosome biogenesis is inhibited, and these puncta are present in or near epidermal cells. In conclusion, these findings suggest a novel mechanism of nutrition-independent multicellular growth coordination initiated from the epidermis tissue upon ribosome biogenesis inhibition.
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Affiliation(s)
- Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Rekha Rangan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Shinuo Weng
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Cem Özdemir
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
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8
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Cerón J. Caenorhabditis elegans for research on cancer hallmarks. Dis Model Mech 2023; 16:dmm050079. [PMID: 37278614 PMCID: PMC10259857 DOI: 10.1242/dmm.050079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023] Open
Abstract
After decades of research, our knowledge of the complexity of cancer mechanisms, elegantly summarized as 'hallmarks of cancer', is expanding, as are the therapeutic opportunities that this knowledge brings. However, cancer still needs intense research to diminish its tremendous impact. In this context, the use of simple model organisms such as Caenorhabditis elegans, in which the genetics of the apoptotic pathway was discovered, can facilitate the investigation of several cancer hallmarks. Amenable for genetic and drug screens, convenient for fast and efficient genome editing, and aligned with the 3Rs ('Replacement, Reduction and Refinement') principles for ethical animal research, C. elegans plays a significant role in unravelling the intricate network of cancer mechanisms and presents a promising option in clinical diagnosis and drug discovery.
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Affiliation(s)
- Julián Cerón
- Modeling Human Diseases in C. elegans Group – Genes, Disease and Therapy Program, Bellvitge Biomedical Research Institute – IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
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9
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Kang H, Hasselbeck S, Taškova K, Wang N, Oosten LNV, Mrowka R, Utikal J, Andrade-Navarro MA, Wang J, Wölfl S, Cheng X. Development of a next-generation endogenous OCT4 inducer and its anti-aging effect in vivo. Eur J Med Chem 2023; 257:115513. [PMID: 37253308 DOI: 10.1016/j.ejmech.2023.115513] [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: 03/24/2023] [Revised: 05/05/2023] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
The identification of small molecules capable of replacing transcription factors has been a longstanding challenge in the generation of human chemically induced pluripotent stem cells (iPSCs). Recent studies have shown that ectopic expression of OCT4, one of the master pluripotency regulators, compromised the developmental potential of resulting iPSCs, This highlights the importance of finding endogenous OCT4 inducers for the generation of clinical-grade human iPSCs. Through a cell-based high throughput screen, we have discovered several new OCT4-inducing compounds (O4Is). In this work, we prepared metabolically stable analogues, including O4I4, which activate endogenous OCT4 and associated signaling pathways in various cell lines. By combining these with a transcription factor cocktail consisting of SOX2, KLF4, MYC, and LIN28 (referred to as "CSKML") we achieved to reprogram human fibroblasts into a stable and authentic pluripotent state without the need for exogenous OCT4. In Caenorhabditis elegans and Drosophila, O4I4 extends lifespan, suggesting the potential application of OCT4-inducing compounds in regenerative medicine and rejuvenation therapy.
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Affiliation(s)
- Han Kang
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany
| | - Sebastian Hasselbeck
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, Germany
| | - Katerina Taškova
- Faculty of Biology, Johannes Gutenberg University Mainz, Germany
| | - Nessa Wang
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany
| | - Luuk N van Oosten
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany
| | - Ralf Mrowka
- Experimentelle Nephrologie, KIM III, Universitätsklinikum, Jena, Germany
| | - Jochen Utikal
- Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Jichang Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Stefan Wölfl
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany
| | - Xinlai Cheng
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt am Main, Germany; Frankfurt Cancer Institute, Germany.
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10
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Bujarrabal-Dueso A, Sendtner G, Meyer DH, Chatzinikolaou G, Stratigi K, Garinis GA, Schumacher B. The DREAM complex functions as conserved master regulator of somatic DNA-repair capacities. Nat Struct Mol Biol 2023; 30:475-488. [PMID: 36959262 PMCID: PMC10113156 DOI: 10.1038/s41594-023-00942-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/08/2023] [Indexed: 03/25/2023]
Abstract
The DNA-repair capacity in somatic cells is limited compared with that in germ cells. It has remained unknown whether not only lesion-type-specific, but overall repair capacities could be improved. Here we show that the DREAM repressor complex curbs the DNA-repair capacities in somatic tissues of Caenorhabditis elegans. Mutations in the DREAM complex induce germline-like expression patterns of multiple mechanisms of DNA repair in the soma. Consequently, DREAM mutants confer resistance to a wide range of DNA-damage types during development and aging. Similarly, inhibition of the DREAM complex in human cells boosts DNA-repair gene expression and resistance to distinct DNA-damage types. DREAM inhibition leads to decreased DNA damage and prevents photoreceptor loss in progeroid Ercc1-/- mice. We show that the DREAM complex transcriptionally represses essentially all DNA-repair systems and thus operates as a highly conserved master regulator of the somatic limitation of DNA-repair capacities.
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Affiliation(s)
- Arturo Bujarrabal-Dueso
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Georg Sendtner
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - David H Meyer
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
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11
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Gui T, Burgering BMT. FOXOs: masters of the equilibrium. FEBS J 2022; 289:7918-7939. [PMID: 34610198 PMCID: PMC10078705 DOI: 10.1111/febs.16221] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 01/14/2023]
Abstract
Forkhead box O (FOXO) transcription factors (TFs) are a subclass of the larger family of forkhead TFs. Mammalians express four members FOXO1, FOXO3, FOXO4, and FOXO6. The interest in FOXO function stems mostly from their observed role in determining lifespan, where in model organisms, increased FOXO activity results in extended lifespan. FOXOs act as downstream of several signaling pathway and are extensively regulated through post-translational modifications. The transcriptional program activated by FOXOs in various cell types, organisms, and under various conditions has been described and has shed some light on what the critical transcriptional targets are in mediating FOXO function. At the cellular level, these studies have revealed a role for FOXOs in cell metabolism, cellular redox, cell proliferation, DNA repair, autophagy, and many more. The general picture that emerges hereof is that FOXOs act to preserve equilibrium, and they are important for cellular homeostasis. Here, we will first briefly summarize the general knowledge of FOXO regulation and possible functions. We will use genomic stability to illustrate how FOXOs ensure homeostasis. Genomic stability is critical for maintaining genetic integrity, and therefore preventing disease. However, genomic mutations need to occur during lifetime to enable evolution, yet their accumulation is believed to be causative to aging. Therefore, the role of FOXO in genomic stability may underlie its role in lifespan and aging. Finally, we will come up with questions on some of the unknowns in FOXO function, the answer(s) to which we believe will further our understanding of FOXO function and ultimately may help to understand lifespan and its consequences.
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Affiliation(s)
- Tianshu Gui
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht and the Oncode Institute, The Netherlands
| | - Boudewijn M T Burgering
- Molecular Cancer Research, Center Molecular Medicine, University Medical Center Utrecht and the Oncode Institute, The Netherlands
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12
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Servello FA, Fernandes R, Eder M, Harris N, Martin OMF, Oswal N, Lindberg A, Derosiers N, Sengupta P, Stroustrup N, Apfeld J. Neuronal temperature perception induces specific defenses that enable C. elegans to cope with the enhanced reactivity of hydrogen peroxide at high temperature. eLife 2022; 11:e78941. [PMID: 36226814 PMCID: PMC9635881 DOI: 10.7554/elife.78941] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/12/2022] [Indexed: 11/30/2022] Open
Abstract
Hydrogen peroxide is the most common reactive chemical that organisms face on the microbial battlefield. The rate with which hydrogen peroxide damages biomolecules required for life increases with temperature, yet little is known about how organisms cope with this temperature-dependent threat. Here, we show that Caenorhabditis elegans nematodes use temperature information perceived by sensory neurons to cope with the temperature-dependent threat of hydrogen peroxide produced by the pathogenic bacterium Enterococcus faecium. These nematodes preemptively induce the expression of specific hydrogen peroxide defenses in response to perception of high temperature by a pair of sensory neurons. These neurons communicate temperature information to target tissues expressing those defenses via an insulin/IGF1 hormone. This is the first example of a multicellular organism inducing their defenses to a chemical when they sense an inherent enhancer of the reactivity of that chemical.
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Affiliation(s)
| | - Rute Fernandes
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Matthias Eder
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Nathan Harris
- Department of Biology, Brandeis UniversityWalthamUnited States
| | - Olivier MF Martin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Natasha Oswal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Anders Lindberg
- Biology Department, Northeastern UniversityBostonUnited States
| | | | - Piali Sengupta
- Department of Biology, Brandeis UniversityWalthamUnited States
| | - Nicholas Stroustrup
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Javier Apfeld
- Biology Department, Northeastern UniversityBostonUnited States
- Bioengineering Department, Northeastern UniversityBostonUnited States
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13
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Iakovou E, Kourti M. A Comprehensive Overview of the Complex Role of Oxidative Stress in Aging, The Contributing Environmental Stressors and Emerging Antioxidant Therapeutic Interventions. Front Aging Neurosci 2022; 14:827900. [PMID: 35769600 PMCID: PMC9234325 DOI: 10.3389/fnagi.2022.827900] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/10/2022] [Indexed: 12/15/2022] Open
Abstract
Introduction Aging is a normal, inevitable, irreversible, and progressive process which is driven by internal and external factors. Oxidative stress, that is the imbalance between prooxidant and antioxidant molecules favoring the first, plays a key role in the pathophysiology of aging and comprises one of the molecular mechanisms underlying age-related diseases. However, the oxidative stress theory of aging has not been successfully proven in all animal models studying lifespan, meaning that altering oxidative stress/antioxidant defense systems did not always lead to a prolonged lifespan, as expected. On the other hand, animal models of age-related pathological phenotypes showed a well-correlated relationship with the levels of prooxidant molecules. Therefore, it seems that oxidative stress plays a more complicated role than the one once believed and this role might be affected by the environment of each organism. Environmental factors such as UV radiation, air pollution, and an unbalanced diet, have also been implicated in the pathophysiology of aging and seem to initiate this process more rapidly and even at younger ages. Aim The purpose of this review is to elucidate the role of oxidative stress in the physiology of aging and the effect of certain environmental factors in initiating and sustaining this process. Understanding the pathophysiology of aging will contribute to the development of strategies to postpone this phenomenon. In addition, recent studies investigating ways to alter the antioxidant defense mechanisms in order to prevent aging will be presented. Conclusions Careful exposure to harmful environmental factors and the use of antioxidant supplements could potentially affect the biological processes driving aging and slow down the development of age-related diseases. Maybe a prolonged lifespan could not be achieved by this strategy alone, but a longer healthspan could also be a favorable target.
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Affiliation(s)
- Evripides Iakovou
- Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
| | - Malamati Kourti
- Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
- Angiogenesis and Cancer Drug Discovery Group, Basic and Translational Cancer Research Center, Department of Life Sciences, European University Cyprus, Nicosia, Cyprus
- *Correspondence: Malamati Kourti
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14
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Guimarães Nunes IJ, Feltes BC, David MZ, Dorn M. Gene Expression Variation Analysis (GEVA): a new R package to evaluate variations in differential expression in multiple biological conditions. J Biomed Inform 2022; 129:104053. [DOI: 10.1016/j.jbi.2022.104053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
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15
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Hamsanathan S, Anthonymuthu T, Han S, Shinglot H, Siefken E, Sims A, Sen P, Pepper HL, Snyder NW, Bayir H, Kagan V, Gurkar AU. Integrated -omics approach reveals persistent DNA damage rewires lipid metabolism and histone hyperacetylation via MYS-1/Tip60. SCIENCE ADVANCES 2022; 8:eabl6083. [PMID: 35171671 PMCID: PMC8849393 DOI: 10.1126/sciadv.abl6083] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Although DNA damage is intricately linked to metabolism, the metabolic alterations that occur in response to DNA damage are not well understood. We use a DNA repair-deficient model of ERCC1-XPF in Caenorhabditis elegans to gain insights on how genotoxic stress drives aging. Using multi-omic approach, we discover that nuclear DNA damage promotes mitochondrial β-oxidation and drives a global loss of fat depots. This metabolic shift to β-oxidation generates acetyl-coenzyme A to promote histone hyperacetylation and an associated change in expression of immune-effector and cytochrome genes. We identify the histone acetyltransferase MYS-1, as a critical regulator of this metabolic-epigenetic axis. We show that in response to DNA damage, polyunsaturated fatty acids, especially arachidonic acid (AA) and AA-related lipid mediators, are elevated and this is dependent on mys-1. Together, these findings reveal that DNA damage alters the metabolic-epigenetic axis to drive an immune-like response that can promote age-associated decline.
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Affiliation(s)
- Shruthi Hamsanathan
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Tamil Anthonymuthu
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
- Adeptrix Corp., Beverly, MA 01915, USA
| | - Suhao Han
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Himaly Shinglot
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Ella Siefken
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Austin Sims
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Hannah L. Pepper
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Hulya Bayir
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
- Department of Environmental Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Valerian Kagan
- Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
- Department of Environmental Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Aditi U. Gurkar
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr., Pittsburgh, PA 15219, USA
- Division of Geriatric Medicine, Department of Medicine, University of Pittsburgh School of Medicine, 3471 Fifth Avenue, Kaufmann Medical Building Suite 500, Pittsburgh, PA 15213, USA
- Geriatric Research, Education and Clinical Center, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA 15240, USA
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16
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Regulation and functions of membrane lipids: Insights from Caenorhabditis elegans. BBA ADVANCES 2022; 2:100043. [PMID: 37082601 PMCID: PMC10074978 DOI: 10.1016/j.bbadva.2022.100043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/28/2021] [Accepted: 01/12/2022] [Indexed: 02/08/2023] Open
Abstract
The Caenorhabditis elegans plasma membrane is composed of glycerophospholipids and sphingolipids with a small cholesterol. The C. elegans obtain the majority of the membrane lipids by modifying fatty acids present in the bacterial diet. The metabolic pathways of membrane lipid biosynthesis are well conserved across the animal kingdom. In C. elegans CDP-DAG and Kennedy pathway produce glycerophospholipids. Meanwhile, the sphingolipids are synthesized through a different pathway. They have evolved remarkably diverse mechanisms to maintain membrane lipid homeostasis. For instance, the lipid bilayer stress operates to accomplish homeostasis during any perturbance in the lipid composition. Meanwhile, the PAQR-2/IGLR-2 complex works with FLD-1 to balance unsaturated to saturated fatty acids to maintain membrane fluidity. The loss of membrane lipid homeostasis is observed in many human genetic and metabolic disorders. Since C. elegans conserved such genes and pathways, it can be used as a model organism.
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17
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Guédon R, Maremonti E, Armant O, Galas S, Brede DA, Lecomte-Pradines C. A systems biology analysis of reproductive toxicity effects induced by multigenerational exposure to ionizing radiation in C. elegans. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 225:112793. [PMID: 34544019 DOI: 10.1016/j.ecoenv.2021.112793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Understanding the effects of chronic exposure to pollutants over generations is of primary importance for the protection of humans and the environment; however, to date, knowledge on the molecular mechanisms underlying multigenerational adverse effects is scarce. We employed a systems biology approach to analyze effects of chronic exposure to gamma radiation at molecular, tissue and individual levels in the nematode Caenorhabditis elegans. Our data show a decrease of 23% in the number of offspring on the first generation F0 and more than 40% in subsequent generations F1, F2 and F3. To unveil the impact on the germline, an in-depth analysis of reproductive processes involved in gametes formation was performed for all four generations. We measured a decrease in the number of mitotic germ cells accompanied by increased cell-cycle arrest in the distal part of the gonad. Further impact on the germline was manifested by decreased sperm quantity and quality. In order to obtain insight in the molecular mechanisms leading to decreased fecundity, gene expression was investigated via whole genome RNA sequencing. The transcriptomic analysis revealed modulation of transcription factors, as well as genes involved in stress response, unfolded protein response, lipid metabolism and reproduction. Furthermore, a drastic increase in the number of differentially expressed genes involved in defense response was measured in the last two generations, suggesting a cumulative stress effect of ionizing radiation exposure. Transcription factor binding site enrichment analysis and the use of transgenic strain identified daf-16/FOXO as a master regulator of genes differentially expressed in response to radiation. The presented data provide new knowledge with respect to the molecular mechanisms involved in reproductive toxic effects and accumulated stress resulting from multigenerational exposure to ionizing radiation.
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Affiliation(s)
- Rémi Guédon
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV, SRTE, Laboratoire d'ECOtoxicologie des radionucléides (LECO), Cadarache, France
| | - Erica Maremonti
- Centre for Environmental Radioactivity (CERAD), Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Olivier Armant
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV, SRTE, Laboratoire d'ECOtoxicologie des radionucléides (LECO), Cadarache, France
| | - Simon Galas
- Institut des biomolecules Max Mousseron (IBMM), University of Montpellier, Centre National de Recherche Scientifique (CNRS), ENSCM, Montpellier, France
| | - Dag Anders Brede
- Centre for Environmental Radioactivity (CERAD), Faculty of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), 1432 Ås, Norway
| | - Catherine Lecomte-Pradines
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PRP-ENV, SRTE, Laboratoire d'ECOtoxicologie des radionucléides (LECO), Cadarache, France.
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18
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Context-specific regulation of lysosomal lipolysis through network-level diverting of transcription factor interactions. Proc Natl Acad Sci U S A 2021; 118:2104832118. [PMID: 34607947 DOI: 10.1073/pnas.2104832118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2021] [Indexed: 11/18/2022] Open
Abstract
Plasticity in multicellular organisms involves signaling pathways converting contexts-either natural environmental challenges or laboratory perturbations-into context-specific changes in gene expression. Congruently, the interactions between the signaling molecules and transcription factors (TF) regulating these responses are also context specific. However, when a target gene responds across contexts, the upstream TF identified in one context is often inferred to regulate it across contexts. Reconciling these stable TF-target gene pair inferences with the context-specific nature of homeostatic responses is therefore needed. The induction of the Caenorhabditis elegans genes lipl-3 and lipl-4 is observed in many genetic contexts and is essential to survival during fasting. We find DAF-16/FOXO mediating lipl-4 induction in all contexts tested; hence, lipl-4 regulation seems context independent and compatible with across-context inferences. In contrast, DAF-16-mediated regulation of lipl-3 is context specific. DAF-16 reduces the induction of lipl-3 during fasting, yet it promotes it during oxidative stress. Through discrete dynamic modeling and genetic epistasis, we define that DAF-16 represses HLH-30/TFEB-the main TF activating lipl-3 during fasting. Contrastingly, DAF-16 activates the stress-responsive TF HSF-1 during oxidative stress, which promotes C. elegans survival through induction of lipl-3 Furthermore, the TF MXL-3 contributes to the dominance of HSF-1 at the expense of HLH-30 during oxidative stress but not during fasting. This study shows how context-specific diverting of functional interactions within a molecular network allows cells to specifically respond to a large number of contexts with a limited number of molecular players, a mode of transcriptional regulation we name "contextualized transcription."
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19
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Marchal L, Hamsanathan S, Karthikappallil R, Han S, Shinglot H, Gurkar AU. Analysis of representative mutants for key DNA repair pathways on healthspan in Caenorhabditis elegans. Mech Ageing Dev 2021; 200:111573. [PMID: 34562508 DOI: 10.1016/j.mad.2021.111573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 08/26/2021] [Accepted: 09/21/2021] [Indexed: 12/30/2022]
Abstract
Although the link between DNA damage and aging is well accepted, the role of different DNA repair proteins on functional/physiological aging is not well-defined. Here, using Caenorhabditis elegans, we systematically examined the effect of three DNA repair genes involved in key genome stability pathways. We assayed multiple health proxies including molecular, functional and resilience measures to define healthspan. Loss of XPF-1/ERCC-1, a protein involved in nucleotide excision repair (NER), homologous recombination (HR) and interstrand crosslink (ICL) repair, showed the highest impairment of functional and stress resilience measures along with a shortened lifespan. brc-1 mutants, with a well-defined role in HR and ICL are short-lived and highly sensitive to acute stressors, specifically oxidative stress. In contrast, ICL mutant, fcd-2 did not impact lifespan or most healthspan measures. Our efforts also uncover that DNA repair mutants show high sensitivity to oxidative stress with age, suggesting that this measure could act as a primary proxy for healthspan. Together, these data suggest that impairment of multiple DNA repair genes can drive functional/physiological aging. Further studies to examine specific DNA repair genes in a tissue specific manner will help dissect the importance and mechanistic role of these repair systems in biological aging.
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Affiliation(s)
- Lucile Marchal
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA, 15219, USA
| | - Shruthi Hamsanathan
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA, 15219, USA
| | - Roshan Karthikappallil
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA, 15219, USA; Medical Sciences Division, University of Oxford, Oxford, UK
| | - Suhao Han
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA, 15219, USA
| | - Himaly Shinglot
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA, 15219, USA
| | - Aditi U Gurkar
- Aging Institute of UPMC and the University of Pittsburgh School of Medicine, 100 Technology Dr, Pittsburgh, PA, 15219, USA; Division of Geriatric Medicine, Department of Medicine, University of Pittsburgh School of Medicine, 3471 Fifth Avenue, Kaufmann Medical Building Suite 500, Pittsburgh, PA, 15213, USA; Geriatric Research, Education and Clinical Centre, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA, 15240, USA.
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20
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Rieckher M, Garinis GA, Schumacher B. Molecular pathology of rare progeroid diseases. Trends Mol Med 2021; 27:907-922. [PMID: 34272172 DOI: 10.1016/j.molmed.2021.06.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022]
Abstract
Progeroid syndromes (PSs) are characterized by the premature onset of age-related pathologies. The genetic mutations underlying PSs are functionally linked to genome maintenance and repair, supporting the causative role of DNA damage accumulation in aging. Recent advances from studies in animal models of PSs have provided new insight into the role of DNA repair mechanisms in human disease and the physiological adaptations to accumulating DNA damage during aging. The molecular pathology of PSs is reminiscent of the natural aging process, highlighting the relevance for a wide range of age-related diseases. Recent progress has led to the development of novel therapeutic strategies against age-related diseases that are relevant to rare diseases as well as the general aging population.
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Affiliation(s)
- Matthias Rieckher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013, Heraklion, Crete, Greece; Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany.
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21
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Immunomodulatory effect of pentagalloyl glucose in LPS-stimulated RAW264.7 macrophages and PAO1-induced Caenorhabditis elegans. Exp Gerontol 2021; 150:111388. [PMID: 33957261 DOI: 10.1016/j.exger.2021.111388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 11/23/2022]
Abstract
Pentagalloyl glucose (PGG) is a valuable natural compound with an array of biological activities, but the immunomodulatory effect and mechanism have not been fully validated yet. In this study, to elucidate comprehensively the function of immunomodulation and its underlying mechanism of PGG in vitro and in vivo, two model systems were conducted, which including lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages cells and Pseudomonas aeruginosa (PAO1)-induced Caenorhabditis elegans (C. elegans). Current results showed that PGG significantly inhibited secretions of tumor necrosis factor-α (TNF-α), interleukin-1 beta (IL-1β), interleukin-6 (IL-6) and mediator nitric oxide (NO) in LPS-stimulated RAW264.7 cells. In addition, the expression of genes nitric oxide synthase (iNOS), TNF-α, IL-1β and IL-6 in LPS- stimulated RAW264.7 cells was reduced by PGG. In vivo assay showed that lifespan of PAO1-induced C. elegans was enhanced significantly by 14.1% under the pre-treatment of PGG, which was abrogated in toxin sensitive mdt-15 mutant. Similarly, the PGG showed a benefit on 41.2% significant extension longevity in C. elegans under pathogenic PA14. And the nuclear localization of DAF-16 of strain TJ356 was significantly increased in PAO1-induced C. elegans by PGG. Further, PGG modulated several signaling pathways to enhance immunomodulation in C. elegans including DBL-1, DAF-2/DAF-16, and mitogen-activated protein (MAP) kinase pathways. Furthermore, other genes involved in immunomodulatory response in C. elegans were remarkably regulated such as lys-1, lys-2, spp-18, egl-9, and hif-1. Our study suggested that PGG have potential to develop into novel immunomodulatory nutraceutical.
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22
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Khanna A, Sellegounder D, Kumar J, Chamoli M, Vargas M, Chinta SJ, Rane A, Nelson C, Peiris TH, Brem R, Andersen J, Lithgow G, Kapahi P. Trimethylamine modulates dauer formation, neurodegeneration, and lifespan through tyra-3/daf-11 signaling in Caenorhabditis elegans. Aging Cell 2021; 20:e13351. [PMID: 33819374 PMCID: PMC8135002 DOI: 10.1111/acel.13351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 02/10/2021] [Accepted: 03/05/2021] [Indexed: 11/27/2022] Open
Abstract
In the nematode Caenorhabditis elegans, signals derived from bacteria in the diet, the animal's major nutrient source, can modulate both behavior and healthspan. Here we describe a dual role for trimethylamine (TMA), a human gut flora metabolite, which acts as a nutrient signal and a neurotoxin. TMA and its associated metabolites are produced by the human gut microbiome and have been suggested to serve as risk biomarkers for diabetes and cardiovascular diseases. We demonstrate that the tyramine receptor TYRA-3, a conserved G protein-coupled receptor (GPCR), is required to sense TMA and mediate its responses. TMA activates guanylyl cyclase DAF-11 signaling through TYRA-3 in amphid neurons (ASK) and ciliated neurons (BAG) to mediate food-sensing behavior. Bacterial mutants deficient in TMA production enhance dauer formation, extend lifespan, and are less preferred as a food source. Increased levels of TMA lead to neural damage in models of Parkinson's disease and shorten lifespan. Our results reveal conserved signaling pathways modulated by TMA in C. elegans that are likely to be relevant for its effects in mammalian systems.
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Affiliation(s)
- Amit Khanna
- Buck Institute for Research on Aging Novato CA USA
- Dovetail Genomics LLC Scotts Valley CA USA
| | | | | | | | | | - Shankar J. Chinta
- Buck Institute for Research on Aging Novato CA USA
- Touro University California Vallejo CA USA
| | - Anand Rane
- Buck Institute for Research on Aging Novato CA USA
| | | | | | - Rachel Brem
- Buck Institute for Research on Aging Novato CA USA
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23
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Pees B, Yang W, Kloock A, Petersen C, Peters L, Fan L, Friedrichsen M, Butze S, Zárate-Potes A, Schulenburg H, Dierking K. Effector and regulator: Diverse functions of C. elegans C-type lectin-like domain proteins. PLoS Pathog 2021; 17:e1009454. [PMID: 33793670 PMCID: PMC8051790 DOI: 10.1371/journal.ppat.1009454] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 04/16/2021] [Accepted: 03/05/2021] [Indexed: 11/22/2022] Open
Abstract
In C. elegans, 283 clec genes encode a highly diverse family of C-type lectin-like domain (CTLD) proteins. Since vertebrate CTLD proteins have characterized functions in defense responses against pathogens and since expression of C. elegans clec genes is pathogen-dependent, it is generally assumed that clec genes function in C. elegans immune defenses. However, little is known about the relative contribution and exact function of CLEC proteins in C. elegans immunity. Here, we focused on the C. elegans clec gene clec-4, whose expression is highly upregulated by pathogen infection, and its paralogs clec-41 and clec-42. We found that, while mutation of clec-4 resulted in enhanced resistance to the Gram-positive pathogen Bacillus thuringiensis MYBt18247 (Bt247), inactivation of clec-41 and clec-42 by RNAi enhanced susceptibility to Bt247. Further analyses revealed that enhanced resistance of clec-4 mutants to Bt247 was due to an increase in feeding cessation on the pathogen and consequently a decrease in pathogen load. Moreover, clec-4 mutants exhibited feeding deficits also on non-pathogenic bacteria that were in part reflected in the clec-4 gene expression profile, which overlapped with gene sets affected by starvation or mutation in nutrient sensing pathways. However, loss of CLEC-4 function only mildly affected life-history traits such as fertility, indicating that clec-4 mutants are not subjected to dietary restriction. While CLEC-4 function appears to be associated with the regulation of feeding behavior, we show that CLEC-41 and CLEC-42 proteins likely function as bona fide immune effector proteins that have bacterial binding and antimicrobial capacities. Together, our results exemplify functional diversification within clec gene paralogs. C-type lectin-like domain (CTLD) containing proteins fulfill various and fundamental tasks in the human and mouse immune system. Genes encoding CTLD proteins are present in all animal genomes, in some cases in very large numbers and highly diversified. While the function of several vertebrate CTLD proteins is well characterized, experimental evidence of an immune function of most invertebrate CTLD proteins is missing, although their role in immunity is usually assumed. We here explore the immune function of three related CTLD proteins in the model nematode Caenorhabditis elegans. We find that they play diverse roles in C. elegans immunity, functioning as antimicrobial immune effector proteins that are important for defense against pathogen infection and probably directly interact with bacteria, but also regulators of feeding behavior that more indirectly affect C. elegans pathogen resistance. Such insight into the functional consequence of invertebrate CTLD protein diversification contributes to our understanding of the evolution of innate and invertebrate immune systems.
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Affiliation(s)
- Barbara Pees
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Department of Comparative Immunobiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Wentao Yang
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Anke Kloock
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Carola Petersen
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Department of Comparative Immunobiology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Lena Peters
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Li Fan
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Meike Friedrichsen
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Sabrina Butze
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Alejandra Zárate-Potes
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- * E-mail:
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24
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Schumacher B, Pothof J, Vijg J, Hoeijmakers JH. The central role of DNA damage in the ageing process. Nature 2021; 592:695-703. [PMID: 33911272 PMCID: PMC9844150 DOI: 10.1038/s41586-021-03307-7] [Citation(s) in RCA: 362] [Impact Index Per Article: 120.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023]
Abstract
Ageing is a complex, multifaceted process leading to widespread functional decline that affects every organ and tissue, but it remains unknown whether ageing has a unifying causal mechanism or is grounded in multiple sources. Phenotypically, the ageing process is associated with a wide variety of features at the molecular, cellular and physiological level-for example, genomic and epigenomic alterations, loss of proteostasis, declining overall cellular and subcellular function and deregulation of signalling systems. However, the relative importance, mechanistic interrelationships and hierarchical order of these features of ageing have not been clarified. Here we synthesize accumulating evidence that DNA damage affects most, if not all, aspects of the ageing phenotype, making it a potentially unifying cause of ageing. Targeting DNA damage and its mechanistic links with the ageing phenotype will provide a logical rationale for developing unified interventions to counteract age-related dysfunction and disease.
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Affiliation(s)
- Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Cologne, Germany. .,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA,Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jan H.J. Hoeijmakers
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany,Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands,Princess Máxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands
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25
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Gartner A, Engebrecht J. DNA repair, recombination, and damage signaling. Genetics 2021; 220:6522877. [PMID: 35137093 PMCID: PMC9097270 DOI: 10.1093/genetics/iyab178] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/10/2021] [Indexed: 01/09/2023] Open
Abstract
DNA must be accurately copied and propagated from one cell division to the next, and from one generation to the next. To ensure the faithful transmission of the genome, a plethora of distinct as well as overlapping DNA repair and recombination pathways have evolved. These pathways repair a large variety of lesions, including alterations to single nucleotides and DNA single and double-strand breaks, that are generated as a consequence of normal cellular function or by external DNA damaging agents. In addition to the proteins that mediate DNA repair, checkpoint pathways have also evolved to monitor the genome and coordinate the action of various repair pathways. Checkpoints facilitate repair by mediating a transient cell cycle arrest, or through initiation of cell suicide if DNA damage has overwhelmed repair capacity. In this chapter, we describe the attributes of Caenorhabditis elegans that facilitate analyses of DNA repair, recombination, and checkpoint signaling in the context of a whole animal. We review the current knowledge of C. elegans DNA repair, recombination, and DNA damage response pathways, and their role during development, growth, and in the germ line. We also discuss how the analysis of mutational signatures in C. elegans is helping to inform cancer mutational signatures in humans.
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Affiliation(s)
- Anton Gartner
- Department for Biological Sciences, IBS Center for Genomic Integrity, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea,Corresponding author: (A.G.); (J.E.)
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA,Corresponding author: (A.G.); (J.E.)
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26
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Principles of the Molecular and Cellular Mechanisms of Aging. J Invest Dermatol 2021; 141:951-960. [PMID: 33518357 DOI: 10.1016/j.jid.2020.11.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022]
Abstract
Aging can be defined as a state of progressive functional decline accompanied by an increase in mortality. Time-dependent accumulation of cellular damage, namely lesions and mutations in the DNA and misfolded proteins, impair organellar and cellular function. Ensuing cell fate alterations lead to the accumulation of dysfunctional cells and hamper homeostatic processes, thus limiting regenerative potential; trigger low-grade inflammation; and alter intercellular and intertissue communication. The accumulation of molecular damage together with modifications in the epigenetic landscape, dysregulation of gene expression, and altered endocrine communication, drive the aging process and establish age as the main risk factor for age-associated diseases and multimorbidity.
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27
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Deng J, Bai X, Tang H, Pang S. DNA damage promotes ER stress resistance through elevation of unsaturated phosphatidylcholine in Caenorhabditis elegans. J Biol Chem 2021; 296:100095. [PMID: 33208465 PMCID: PMC7949029 DOI: 10.1074/jbc.ra120.016083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 01/04/2023] Open
Abstract
DNA damage triggers the cellular adaptive response to arrest proliferation and repair DNA damage; when damage is too severe to be repaired, apoptosis is initiated to prevent the spread of genomic insults. However, how cells endure DNA damage to maintain cell function remains largely unexplored. By using Caenorhabditis elegans as a model, we report that DNA damage elicits cell maintenance programs, including the unfolded protein response of the endoplasmic reticulum (UPRER). Mechanistically, sublethal DNA damage unexpectedly suppresses apoptotic genes in C. elegans, which in turn increases the activity of the inositol-requiring enzyme 1/X-box binding protein 1 (IRE-1/XBP-1) branch of the UPRER by elevating unsaturated phosphatidylcholine. In addition, UPRER activation requires silencing of the lipid regulator skinhead-1 (SKN-1). DNA damage suppresses SKN-1 activity to increase unsaturated phosphatidylcholine and activate UPRER. These findings reveal the UPRER activation as an organismal adaptive response that is important to maintain cell function during DNA damage.
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Affiliation(s)
- Jianhui Deng
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Bai
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Haiqing Tang
- School of Life Sciences, Chongqing University, Chongqing, China.
| | - Shanshan Pang
- School of Life Sciences, Chongqing University, Chongqing, China.
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28
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Tissue-Specific DNA Repair Activity of ERCC-1/XPF-1. Cell Rep 2021; 34:108608. [PMID: 33440146 DOI: 10.1016/j.celrep.2020.108608] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 10/30/2020] [Accepted: 12/15/2020] [Indexed: 01/14/2023] Open
Abstract
Hereditary DNA repair defects affect tissues differently, suggesting that in vivo cells respond differently to DNA damage. Knowledge of the DNA damage response, however, is largely based on in vitro and cell culture studies, and it is currently unclear whether DNA repair changes depending on the cell type. Here, we use in vivo imaging of the nucleotide excision repair (NER) endonuclease ERCC-1/XPF-1 in C. elegans to demonstrate tissue-specific NER activity. In oocytes, XPF-1 functions as part of global genome NER (GG-NER) to ensure extremely rapid removal of DNA-helix-distorting lesions throughout the genome. In contrast, in post-mitotic neurons and muscles, XPF-1 participates in NER of transcribed genes only. Strikingly, muscle cells appear more resistant to the effects of DNA damage than neurons. These results suggest a tissue-specific organization of the DNA damage response and may help to better understand pleiotropic and tissue-specific consequences of accumulating DNA damage.
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29
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Fan X, Zeng Y, Fan Z, Cui L, Song W, Wu Q, Gao Y, Yang D, Mao X, Zeng B, Zhang M, Ni Q, Li Y, Wang T, Li D, Yang M. Dihydromyricetin promotes longevity and activates the transcription factors FOXO and AOP in Drosophila. Aging (Albany NY) 2020; 13:460-476. [PMID: 33291074 PMCID: PMC7835053 DOI: 10.18632/aging.202156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022]
Abstract
Drugs or compounds have been shown to promote longevity in various approaches. We used Drosophila to explore novel natural compounds can be applied to anti-aging. Here we reported that a flavonoid named Dihydromyricetin can increase stress that tolerance and lipid levels, slow down gut dysfunction and extend Drosophila lifespan. Dihydromyricetin can also lessen pERK and pAKT signaling, consequently activating FOXO and AOP to modulate longevity. Our results suggested that DHM could be used as an effective compound for anti-aging intervention, which could likely be applied to both mammals and humans.
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Affiliation(s)
- Xiaolan Fan
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yao Zeng
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Ziqiang Fan
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Liang Cui
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Wenhao Song
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Qi Wu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Yue Gao
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Deying Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xueping Mao
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zeng
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingwang Zhang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qingyong Ni
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tao Wang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingyao Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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30
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Lopes AFC, Bozek K, Herholz M, Trifunovic A, Rieckher M, Schumacher B. A C. elegans model for neurodegeneration in Cockayne syndrome. Nucleic Acids Res 2020; 48:10973-10985. [PMID: 33021672 PMCID: PMC7641758 DOI: 10.1093/nar/gkaa795] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/08/2020] [Accepted: 09/27/2020] [Indexed: 12/22/2022] Open
Abstract
Cockayne syndrome (CS) is a congenital syndrome characterized by growth and mental retardation, and premature ageing. The complexity of CS and mammalian models warrants simpler metazoan models that display CS-like phenotypes that could be studied in the context of a live organism. Here, we provide a characterization of neuronal and mitochondrial aberrations caused by a mutation in the csb-1 gene in Caenorhabditis elegans. We report a progressive neurodegeneration in adult animals that is enhanced upon UV-induced DNA damage. The csb-1 mutants show dysfunctional hyperfused mitochondria that degrade upon DNA damage, resulting in diminished respiratory activity. Our data support the role of endogenous DNA damage as a driving factor of CS-related neuropathology and underline the role of mitochondrial dysfunction in the disease.
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Affiliation(s)
- Amanda F C Lopes
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Katarzyna Bozek
- Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
| | - Marija Herholz
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Matthias Rieckher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
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31
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Wang S, Meyer DH, Schumacher B. H3K4me2 regulates the recovery of protein biosynthesis and homeostasis following DNA damage. Nat Struct Mol Biol 2020; 27:1165-1177. [DOI: 10.1038/s41594-020-00513-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 09/02/2020] [Indexed: 01/08/2023]
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32
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Al Zouabi L, Bardin AJ. Stem Cell DNA Damage and Genome Mutation in the Context of Aging and Cancer Initiation. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036210. [PMID: 31932318 DOI: 10.1101/cshperspect.a036210] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Adult stem cells fuel tissue homeostasis and regeneration through their unique ability to self-renew and differentiate into specialized cells. Thus, their DNA provides instructions that impact the tissue as a whole. Since DNA is not an inert molecule, but rather dynamic, interacting with a myriad of chemical and physical factors, it encounters damage from both endogenous and exogenous sources. Damage to DNA introduces deviations from its normal intact structure and, if left unrepaired, may result in a genetic mutation. In turn, mutant genomes of stem and progenitor cells are inherited in cells of the lineage, thus eroding the genetic information that maintains homeostasis of the somatic cell population. Errors arising in stem and progenitor cells will have a substantially larger impact on the tissue in which they reside than errors occurring in postmitotic differentiated cells. Therefore, maintaining the integrity of genomic DNA within our stem cells is essential to protect the instructions necessary for rebuilding healthy tissues during homeostatic renewal. In this review, we will first discuss DNA damage arising in stem cells and cell- and tissue-intrinsic mechanisms that protect against harmful effects of this damage. Secondly, we will examine how erroneous DNA repair and persistent DNA damage in stem and progenitor cells impact stem cells and tissues in the context of cancer initiation and aging. Finally, we will discuss the use of invertebrate and vertebrate model systems to address unanswered questions on the role that DNA damage and mutation may play in aging and precancerous conditions.
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Affiliation(s)
- Lara Al Zouabi
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75248 Paris, France.,Sorbonne Universités, UPMC University, Paris 6, France
| | - Allison J Bardin
- Institut Curie, PSL Research University, CNRS UMR 3215, INSERM U934, Stem Cells and Tissue Homeostasis Group, 75248 Paris, France.,Sorbonne Universités, UPMC University, Paris 6, France
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33
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DNA Damage Response and Metabolic Reprogramming in Health and Disease. Trends Genet 2020; 36:777-791. [PMID: 32684438 DOI: 10.1016/j.tig.2020.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/08/2023]
Abstract
Nuclear DNA damage contributes to cellular malfunction and the premature onset of age-related diseases, including cancer. Until recently, the canonical DNA damage response (DDR) was thought to represent a collection of nuclear processes that detect, signal and repair damaged DNA. However, recent evidence suggests that beyond nuclear events, the DDR rewires an intricate network of metabolic circuits, fine-tunes protein synthesis, trafficking, and secretion as well as balances growth with defense strategies in response to genotoxic insults. In this review, we discuss how the active DDR signaling mobilizes extranuclear and systemic responses to promote cellular homeostasis and organismal survival in health and disease.
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34
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DAF-16 and SMK-1 Contribute to Innate Immunity During Adulthood in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2020; 10:1521-1539. [PMID: 32161087 PMCID: PMC7202018 DOI: 10.1534/g3.120.401166] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Aging is accompanied by a progressive decline in immune function termed "immunosenescence". Deficient surveillance coupled with the impaired function of immune cells compromises host defense in older animals. The dynamic activity of regulatory modules that control immunity appears to underlie age-dependent modifications to the immune system. In the roundworm Caenorhabditis elegans levels of PMK-1 p38 MAP kinase diminish over time, reducing the expression of immune effectors that clear bacterial pathogens. Along with the PMK-1 pathway, innate immunity in C. elegans is regulated by the insulin signaling pathway. Here we asked whether DAF-16, a Forkhead box (FOXO) transcription factor whose activity is inhibited by insulin signaling, plays a role in host defense later in life. While in younger C. elegans DAF-16 is inactive unless stimulated by environmental insults, we found that even in the absence of acute stress the transcriptional activity of DAF-16 increases in an age-dependent manner. Beginning in the reproductive phase of adulthood, DAF-16 upregulates a subset of its transcriptional targets, including genes required to kill ingested microbes. Accordingly, DAF-16 has little to no role in larval immunity, but functions specifically during adulthood to confer resistance to bacterial pathogens. We found that DAF-16-mediated immunity in adults requires SMK-1, a regulatory subunit of the PP4 protein phosphatase complex. Our data suggest that as the function of one branch of the innate immune system of C. elegans (PMK-1) declines over time, DAF-16-mediated immunity ramps up to become the predominant means of protecting adults from infection, thus reconfiguring immunity later in life.
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35
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Robin JD, Jacome Burbano M, Peng H, Croce O, Thomas JL, Laberthonniere C, Renault V, Lototska L, Pousse M, Tessier F, Bauwens S, Leong W, Sacconi S, Schaeffer L, Magdinier F, Ye J, Gilson E. Mitochondrial function in skeletal myofibers is controlled by a TRF2-SIRT3 axis over lifetime. Aging Cell 2020; 19:e13097. [PMID: 31991048 PMCID: PMC7059141 DOI: 10.1111/acel.13097] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/23/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
Telomere shortening follows a developmentally regulated process that leads to replicative senescence of dividing cells. However, whether telomere changes are involved in postmitotic cell function and aging remains elusive. In this study, we discovered that the level of the TRF2 protein, a key telomere-capping protein, declines in human skeletal muscle over lifetime. In cultured human myotubes, TRF2 downregulation did not trigger telomere dysfunction, but suppressed expression of the mitochondrial Sirtuin 3 gene (SIRT3) leading to mitochondrial respiration dysfunction and increased levels of reactive oxygen species. Importantly, restoring the Sirt3 level in TRF2-compromised myotubes fully rescued mitochondrial functions. Finally, targeted ablation of the Terf2 gene in mouse skeletal muscle leads to mitochondrial dysfunction and sirt3 downregulation similarly to those of TRF2-compromised human myotubes. Altogether, these results reveal a TRF2-SIRT3 axis controlling muscle mitochondrial function. We propose that this axis connects developmentally regulated telomere changes to muscle redox metabolism.
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Affiliation(s)
- Jérôme D. Robin
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
- Marseille Medical Genetics (MMG) U1251 Aix Marseille University Marseille France
| | - Maria‐Sol Jacome Burbano
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
| | - Han Peng
- International Research Laboratory in “Hematology, Cancer and Aging” Shanghai Jiao Tong University School of Medicine/Ruijin Hospital/CNRS/Inserm/Nice University Pôle Sino‐Français de Recherche en Sciences du Vivant et Génomique Shanghai Ruijin Hospital Shanghai China
| | - Olivier Croce
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
| | - Jean Luc Thomas
- Neuromuscular Differentiation Group Institut NeuroMyoGene (INMG) UMR5310 Inserm U1217 Ecole Normale Supérieure de Lyon Lyon France
| | | | - Valerie Renault
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
| | - Liudmyla Lototska
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
| | - Mélanie Pousse
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
| | - Florent Tessier
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
| | - Serge Bauwens
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
| | - Waiian Leong
- International Research Laboratory in “Hematology, Cancer and Aging” Shanghai Jiao Tong University School of Medicine/Ruijin Hospital/CNRS/Inserm/Nice University Pôle Sino‐Français de Recherche en Sciences du Vivant et Génomique Shanghai Ruijin Hospital Shanghai China
| | - Sabrina Sacconi
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
- Peripheral Nervous System, Muscle and ALS Neuromuscular & ALS Center of Reference FHU Oncoage Pasteur 2 Nice University Hospital Nice France
| | - Laurent Schaeffer
- Neuromuscular Differentiation Group Institut NeuroMyoGene (INMG) UMR5310 Inserm U1217 Ecole Normale Supérieure de Lyon Lyon France
| | - Frédérique Magdinier
- Marseille Medical Genetics (MMG) U1251 Aix Marseille University Marseille France
| | - Jing Ye
- International Research Laboratory in “Hematology, Cancer and Aging” Shanghai Jiao Tong University School of Medicine/Ruijin Hospital/CNRS/Inserm/Nice University Pôle Sino‐Français de Recherche en Sciences du Vivant et Génomique Shanghai Ruijin Hospital Shanghai China
| | - Eric Gilson
- Université Côte d'Azur CNRS Inserm Institut for Research on Cancer and Aging, Nice (IRCAN) Medical School of Nice Nice France
- International Research Laboratory in “Hematology, Cancer and Aging” Shanghai Jiao Tong University School of Medicine/Ruijin Hospital/CNRS/Inserm/Nice University Pôle Sino‐Français de Recherche en Sciences du Vivant et Génomique Shanghai Ruijin Hospital Shanghai China
- Department of Medical Genetics Archet 2 Hospital FHU Oncoage CHU of Nice Nice France
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36
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Ou HL, Kim CS, Uszkoreit S, Wickström SA, Schumacher B. Somatic Niche Cells Regulate the CEP-1/p53-Mediated DNA Damage Response in Primordial Germ Cells. Dev Cell 2020; 50:167-183.e8. [PMID: 31336098 DOI: 10.1016/j.devcel.2019.06.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/13/2019] [Accepted: 06/17/2019] [Indexed: 12/26/2022]
Abstract
Genome integrity in primordial germ cells (PGCs) is a prerequisite for fertility and species maintenance. In C. elegans, PGCs require global-genome nucleotide excision repair (GG-NER) to remove UV-induced DNA lesions. Failure to remove the lesions leads to the activation of the C. elegans p53, CEP-1, resulting in mitotic arrest of the PGCs. We show that the eIF4E2 translation initiation factor IFE-4 in somatic gonad precursor (SGP) niche cells regulates the CEP-1/p53-mediated DNA damage response (DDR) in PGCs. We determine that the IFE-4 translation target EGL-15/FGFR regulates the non-cell-autonomous DDR that is mediated via FGF-like signaling. Using hair follicle stem cells as a paradigm, we demonstrate that the eIF4E2-mediated niche cell regulation of the p53 response in stem cells is highly conserved in mammals. We thus reveal that the somatic niche regulates the CEP-1/p53-mediated DNA damage checkpoint in PGCs. Our data suggest that the somatic niche impacts the stability of heritable genomes.
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Affiliation(s)
- Hui-Ling Ou
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Christine S Kim
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Paul Gerson Unna Group "Skin Homeostasis and Ageing," Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany
| | - Simon Uszkoreit
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Sara A Wickström
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Paul Gerson Unna Group "Skin Homeostasis and Ageing," Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931 Cologne, Germany; Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, FI-00014 Helsinki, Finland; Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, FI-00014 Helsinki, Finland
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
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37
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Rieckher M, Markaki M, Princz A, Schumacher B, Tavernarakis N. Maintenance of Proteostasis by P Body-Mediated Regulation of eIF4E Availability during Aging in Caenorhabditis elegans. Cell Rep 2020; 25:199-211.e6. [PMID: 30282029 PMCID: PMC6180348 DOI: 10.1016/j.celrep.2018.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/01/2018] [Accepted: 09/05/2018] [Indexed: 11/16/2022] Open
Abstract
Aging is accompanied by a pervasive collapse of proteostasis, while reducing general protein synthesis promotes longevity across taxa. Here, we show that the eIF4E isoform IFE-2 is increasingly sequestered in mRNA processing (P) bodies during aging and upon stress in Caenorhabditis elegans. Loss of the enhancer of mRNA decapping EDC-3 causes further entrapment of IFE-2 in P bodies and lowers protein synthesis rates in somatic tissues. Animals lacking EDC-3 are long lived and stress resistant, congruent with IFE-2-deficient mutants. Notably, neuron-specific expression of EDC-3 is sufficient to reverse lifespan extension, while sequestration of IFE-2 in neuronal P bodies counteracts age-related neuronal decline. The effects of mRNA decapping deficiency on stress resistance and longevity are orchestrated by a multimodal stress response involving the transcription factor SKN-1, which mediates lifespan extension upon reduced protein synthesis. Our findings elucidate a mechanism of proteostasis control during aging through P body-mediated regulation of protein synthesis in the soma.
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Affiliation(s)
- Matthias Rieckher
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Greece; Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, 50931 Cologne, Germany
| | - Maria Markaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Greece
| | - Andrea Princz
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Greece
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, 50931 Cologne, Germany
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Greece; Department of Basic Sciences, School of Medicine, University of Crete, Heraklion 71110, Greece.
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38
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De-Souza EA, Camara H, Salgueiro WG, Moro RP, Knittel TL, Tonon G, Pinto S, Pinca APF, Antebi A, Pasquinelli AE, Massirer KB, Mori MA. RNA interference may result in unexpected phenotypes in Caenorhabditis elegans. Nucleic Acids Res 2019; 47:3957-3969. [PMID: 30838421 PMCID: PMC6486631 DOI: 10.1093/nar/gkz154] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022] Open
Abstract
RNA interference (RNAi) is a valuable technique to determine gene function. In Caenorhabditis elegans, RNAi can be achieved by feeding worms bacteria carrying a plasmid expressing double-stranded RNA (dsRNA) targeting a gene of interest. The most commonly used plasmid vector for this purpose is L4440. However, it has been noticed that sequences within L4440 may elicit unspecific effects. Here, we provide a comprehensive characterization of these effects and their mechanisms and describe new unexpected phenotypes uncovered by the administration of unspecific exogenous dsRNA. An example involves dsRNA produced by the multiple cloning site (MCS) of L4440, which shares complementary sequences with some widely used reporter vectors and induces partial transgene silencing via the canonical and antiviral RNAi pathway. Going beyond transgene silencing, we found that the reduced embryonic viability of mir-35-41(gk262) mutants is partially reversed by exogenous dsRNA via a mechanism that involves canonical RNAi. These results indicate cross-regulation between different small RNA pathways in C. elegans to regulate embryonic viability. Recognition of the possible unspecific effects elicited by RNAi vectors is important for rigorous interpretation of results from RNAi-based experiments.
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Affiliation(s)
- Evandro A De-Souza
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil.,Program in Molecular Biology and Biotechnology, Instituto de Bioquímica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Henrique Camara
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil.,Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Willian G Salgueiro
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Raíssa P Moro
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Thiago L Knittel
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Guilherme Tonon
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Silas Pinto
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil.,Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
| | - Ana Paula F Pinca
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, California 92093-0349, USA
| | - Katlin B Massirer
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil.,Center for Molecular Biology and Genetic Engineering, University of Campinas, CBMEG-UNICAMP, Campinas, São Paulo 13083-875, Brazil.,The Structural Genomics Consortium - UNICAMP, University of Campinas, Campinas, São Paulo 13083-875, Brazil
| | - Marcelo A Mori
- Program in Molecular Biology, Federal University of São Paulo, São Paulo 04044-020, Brazil.,Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, São Paulo 13083-862, Brazil.,Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo 13083-970, Brazil
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39
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Abstract
Ageing appears to be a nearly universal feature of life, ranging from unicellular microorganisms to humans. Longevity depends on the maintenance of cellular functionality, and an organism's ability to respond to stress has been linked to functional maintenance and longevity. Stress response pathways might indeed become therapeutic targets of therapies aimed at extending the healthy lifespan. Various progeroid syndromes have been linked to genome instability, indicating an important causal role of DNA damage accumulation in the ageing process and the development of age-related pathologies. Recently, non-cell-autonomous mechanisms including the systemic consequences of cellular senescence have been implicated in regulating organismal ageing. We discuss here the role of cellular and systemic mechanisms of ageing and their role in ageing-associated diseases.
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Affiliation(s)
- Paulo F L da Silva
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
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40
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Yu W, Huang W, Yang Y, Qiu R, Zeng Y, Hou Y, Sun G, Shi H, Leng S, Feng D, Chen Y, Wang S, Teng X, Yu H, Wang Y. GATA3 recruits UTX for gene transcriptional activation to suppress metastasis of breast cancer. Cell Death Dis 2019; 10:832. [PMID: 31685800 PMCID: PMC6828764 DOI: 10.1038/s41419-019-2062-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/19/2019] [Accepted: 09/06/2019] [Indexed: 12/20/2022]
Abstract
GATA3 has emerged as a prominent transcription factor required for maintaining mammary-gland homeostasis. GATA3 loss is associated with aggressive breast cancer development, but the mechanism by which breast cancer is affected by the loss of GATA3 function remains unclear. Here, we report that GATA3 expression is positively correlated with the expression of UTX, a histone H3K27 demethylase contained in the MLL4 methyltransferase complex, and that GATA3 recruits the chromatin-remodeling MLL4 complex and interacts directly with UTX, ASH2L, and RBBP5. Using RNA sequencing and chromatin immunoprecipitation and sequencing, we demonstrate that the GATA3/UTX complex synergistically regulates a cohort of genes including Dicer and UTX, which are critically involved in the epithelial-to-mesenchymal transition (EMT). Our results further show that the GATA3-UTX-Dicer axis inhibits EMT, invasion, and metastasis of breast cancer cells in vitro and the dissemination of breast cancer in vivo. Our study implicates the GATA3-UTX-Dicer axis in breast cancer metastasis and provides new mechanistic insights into the pathophysiological function of GATA3.
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Affiliation(s)
- Wenqian Yu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China.,Cardiovascular surgery center, Shandong Provincial ENT Hospital affiliated to Shandong University, 250022, Jinan, P.R. China
| | - Wei Huang
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, 100069, Beijing, P.R. China
| | - Yang Yang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China
| | - Rongfang Qiu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China
| | - Yi Zeng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China
| | - Yongqiang Hou
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China
| | - Gancheng Sun
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China
| | - Hang Shi
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China
| | - Shuai Leng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China
| | - Dandan Feng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China
| | - Yang Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China
| | - Shuang Wang
- Cardiovascular surgery center, Shandong Provincial ENT Hospital affiliated to Shandong University, 250022, Jinan, P.R. China
| | - Xu Teng
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, 100069, Beijing, P.R. China
| | - Hefen Yu
- Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, 100069, Beijing, P.R. China
| | - Yan Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, P.R. China. .,Beijing Key Laboratory for Tumor Invasion and Metastasis, Advanced Innovation Center for Human Brain Protection, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, 100069, Beijing, P.R. China.
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41
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Abstract
The field of aging research has progressed significantly over the past decades. Exogenously and endogenously inflicted molecular damage ranging from genotoxic to organellar damage drives the aging process. Repair mechanisms and compensatory responses counteract the detrimental consequences of the various damage types. Here, we discuss recent progress in understanding cellular mechanisms and interconnections between signaling pathways that control longevity. We summarize cell-autonomous and non-cell-autonomous mechanisms that impact the cellular and organismal aging process
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Affiliation(s)
- Robert Bayersdorf
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
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42
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Yang W, Petersen C, Pees B, Zimmermann J, Waschina S, Dirksen P, Rosenstiel P, Tholey A, Leippe M, Dierking K, Kaleta C, Schulenburg H. The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life. Front Microbiol 2019; 10:1793. [PMID: 31440221 PMCID: PMC6693516 DOI: 10.3389/fmicb.2019.01793] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
The biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiota affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode Caenorhabditis elegans as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiota. For this study, we focused on two isolates of the genus Ochrobactrum. These bacteria are known to be abundant in the nematode’s microbiota and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and C. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiota members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes, the affected functions, and ELT-2 target genes. Our analysis further identified a core set of 86 genes that consistently responded to the microbiota members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for C. elegans. This analysis complemented the enrichment analyses by revealing an influence of the Ochrobactrum isolates on C. elegans energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiota isolates on C. elegans life history and thereby provide a framework for further analysis of microbiota-mediated host functions.
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Affiliation(s)
- Wentao Yang
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Barbara Pees
- Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Silvio Waschina
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philipp Dirksen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Research Group Proteomics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Matthias Leippe
- Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
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43
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Bianco JN, Schumacher B. MPK-1/ERK pathway regulates DNA damage response during development through DAF-16/FOXO. Nucleic Acids Res 2019; 46:6129-6139. [PMID: 29788264 PMCID: PMC6159517 DOI: 10.1093/nar/gky404] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/01/2018] [Indexed: 01/25/2023] Open
Abstract
Ultraviolet (UV) induces distorting lesions to the DNA that can lead to stalling of the RNA polymerase II (RNAP II) and that are removed by transcription-coupled nucleotide excision repair (TC-NER). In humans, mutations in the TC-NER genes CSA and CSB lead to severe postnatal developmental defects in Cockayne syndrome patients. In Caenorhabditis elegans, mutations in the TC-NER genes csa-1 and csb-1, lead to developmental growth arrest upon UV treatment. We conducted a genetic suppressor screen in the nematode to identify mutations that could suppress the developmental defects in csb-1 mutants. We found that mutations in the ERK1/2 MAP kinase mpk-1 alleviate the developmental retardation in TC-NER mutants, while constitutive activation of the RAS-MAPK pathway exacerbates the DNA damage-induced growth arrest. We show that MPK-1 act via insulin/insulin-like signaling pathway and regulates the FOXO transcription factor DAF-16 to mediate the developmental DNA damage response.
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Affiliation(s)
- Julien N Bianco
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
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44
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Miles J, Scherz-Shouval R, van Oosten-Hawle P. Expanding the Organismal Proteostasis Network: Linking Systemic Stress Signaling with the Innate Immune Response. Trends Biochem Sci 2019; 44:927-942. [PMID: 31303384 DOI: 10.1016/j.tibs.2019.06.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/31/2022]
Abstract
Stress response pathways regulate proteostasis and mitigate macromolecular damage to promote long-term cellular health. Intercellular signaling is an essential layer of systemic proteostasis in an organism and is facilitated via transcellular signaling molecules that orchestrate the activation of stress responses across tissues and organs. Accumulating evidence indicates that components of the immune response act as signaling factors that regulate the cell-non-autonomous proteostasis network. Here, we review emergent advances in our understanding of cell-non-autonomous regulators of proteostasis networks in multicellular settings, from the model organism, Caenorhabditis elegans, to humans. We further discuss how innate immune responses can be players of the organismal proteostasis network and discuss how both are linked in cancer.
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Affiliation(s)
- Jay Miles
- School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Ruth Scherz-Shouval
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Patricija van Oosten-Hawle
- School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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45
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Lin XX, Sen I, Janssens GE, Zhou X, Fonslow BR, Edgar D, Stroustrup N, Swoboda P, Yates JR, Ruvkun G, Riedel CG. DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity. Nat Commun 2018; 9:4400. [PMID: 30353013 PMCID: PMC6199276 DOI: 10.1038/s41467-018-06624-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 08/24/2018] [Indexed: 01/07/2023] Open
Abstract
The ability to perceive and respond to harmful conditions is crucial for the survival of any organism. The transcription factor DAF-16/FOXO is central to these responses, relaying distress signals into the expression of stress resistance and longevity promoting genes. However, its sufficiency in fulfilling this complex task has remained unclear. Using C. elegans, we show that DAF-16 does not function alone but as part of a transcriptional regulatory module, together with the transcription factor HLH-30/TFEB. Under harmful conditions, both transcription factors translocate into the nucleus, where they often form a complex, co-occupy target promoters, and co-regulate many target genes. Interestingly though, their synergy is stimulus-dependent: They rely on each other, functioning in the same pathway, to promote longevity or resistance to oxidative stress, but they elicit heat stress responses independently, and they even oppose each other during dauer formation. We propose that this module of DAF-16 and HLH-30 acts by combinatorial gene regulation to relay distress signals into the expression of specific target gene sets, ensuring optimal survival under each given threat.
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Affiliation(s)
- Xin-Xuan Lin
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Blickagången 6, 14157, Huddinge, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, Blickagången 16, 14157, Huddinge, Sweden
- European Research Institute for the Biology of Ageing, University of Groningen, Antonius Deusinglaan, 1, 9713AV, Groningen, The Netherlands
| | - Ilke Sen
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Blickagången 6, 14157, Huddinge, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, Blickagången 16, 14157, Huddinge, Sweden
- European Research Institute for the Biology of Ageing, University of Groningen, Antonius Deusinglaan, 1, 9713AV, Groningen, The Netherlands
| | - Georges E Janssens
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Blickagången 6, 14157, Huddinge, Sweden
| | - Xin Zhou
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Blickagången 6, 14157, Huddinge, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, Blickagången 16, 14157, Huddinge, Sweden
| | - Bryan R Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Daniel Edgar
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Blickagången 6, 14157, Huddinge, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, Blickagången 16, 14157, Huddinge, Sweden
| | - Nicholas Stroustrup
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, C/ Dr. Aiguader, 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), C/ Dr. Aiguader, 80, 08003, Barcelona, Spain
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Blickagången 16, 14157, Huddinge, Sweden
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Christian G Riedel
- Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institute, Blickagången 6, 14157, Huddinge, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institute, Blickagången 16, 14157, Huddinge, Sweden.
- European Research Institute for the Biology of Ageing, University of Groningen, Antonius Deusinglaan, 1, 9713AV, Groningen, The Netherlands.
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46
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Gurkar AU, Robinson AR, Cui Y, Li X, Allani SK, Webster A, Muravia M, Fallahi M, Weissbach H, Robbins PD, Wang Y, Kelley EE, Croix CMS, Niedernhofer LJ, Gill MS. Dysregulation of DAF-16/FOXO3A-mediated stress responses accelerates oxidative DNA damage induced aging. Redox Biol 2018; 18:191-199. [PMID: 30031267 PMCID: PMC6076207 DOI: 10.1016/j.redox.2018.06.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/13/2018] [Indexed: 12/21/2022] Open
Abstract
DNA damage is presumed to be one type of stochastic macromolecular damage that contributes to aging, yet little is known about the precise mechanism by which DNA damage drives aging. Here, we attempt to address this gap in knowledge using DNA repair-deficient C. elegans and mice. ERCC1-XPF is a nuclear endonuclease required for genomic stability and loss of ERCC1 in humans and mice accelerates the incidence of age-related pathologies. Like mice, ercc-1 worms are UV sensitive, shorter lived, display premature functional decline and they accumulate spontaneous oxidative DNA lesions (cyclopurines) more rapidly than wild-type worms. We found that ercc-1 worms displayed early activation of DAF-16 relative to wild-type worms, which conferred resistance to multiple stressors and was important for maximal longevity of the mutant worms. However, DAF-16 activity was not maintained over the lifespan of ercc-1 animals and this decline in DAF-16 activation corresponded with a loss of stress resistance, a rise in oxidant levels and increased morbidity, all of which were cep-1/ p53 dependent. A similar early activation of FOXO3A (the mammalian homolog of DAF-16), with increased resistance to oxidative stress, followed by a decline in FOXO3A activity and an increase in oxidant abundance was observed in Ercc1-/- primary mouse embryonic fibroblasts. Likewise, in vivo, ERCC1-deficient mice had transient activation of FOXO3A in early adulthood as did middle-aged wild-type mice, followed by a late life decline. The healthspan and mean lifespan of ERCC1 deficient mice was rescued by inactivation of p53. These data indicate that activation of DAF-16/FOXO3A is a highly conserved response to genotoxic stress that is important for suppressing consequent oxidative stress. Correspondingly, dysregulation of DAF-16/FOXO3A appears to underpin shortened healthspan and lifespan, rather than the increased DNA damage burden itself.
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Affiliation(s)
- Aditi U Gurkar
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, United States
| | - Andria R Robinson
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States
| | - Yuxiang Cui
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Xuesen Li
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, United States
| | - Shailaja K Allani
- Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, FL, United States
| | - Amanda Webster
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, United States
| | - Mariya Muravia
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, United States
| | - Mohammad Fallahi
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, United States
| | - Herbert Weissbach
- Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, FL, United States
| | - Paul D Robbins
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Eric E Kelley
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, United States
| | - Claudette M St Croix
- Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA, United States
| | - Laura J Niedernhofer
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, United States.
| | - Matthew S Gill
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, United States.
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47
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Multilayered Reprogramming in Response to Persistent DNA Damage in C. elegans. Cell Rep 2018; 20:2026-2043. [PMID: 28854356 PMCID: PMC5583510 DOI: 10.1016/j.celrep.2017.08.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/30/2017] [Accepted: 08/04/2017] [Indexed: 11/23/2022] Open
Abstract
DNA damage causally contributes to aging and age-related diseases. Mutations in nucleotide excision repair (NER) genes cause highly complex congenital syndromes characterized by growth retardation, cancer susceptibility, and accelerated aging in humans. Orthologous mutations in Caenorhabditis elegans lead to growth delay, genome instability, and accelerated functional decline, thus allowing investigation of the consequences of persistent DNA damage during development and aging in a simple metazoan model. Here, we conducted proteome, lipidome, and phosphoproteome analysis of NER-deficient animals in response to UV treatment to gain comprehensive insights into the full range of physiological adaptations to unrepaired DNA damage. We derive metabolic changes indicative of a tissue maintenance program and implicate an autophagy-mediated proteostatic response. We assign central roles for the insulin-, EGF-, and AMPK-like signaling pathways in orchestrating the adaptive response to DNA damage. Our results provide insights into the DNA damage responses in the organismal context.
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48
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Bürkle A. In memoriam Olivier Toussaint – Stress-induced premature senescence and the role of DNA damage. Mech Ageing Dev 2018. [DOI: 10.1016/j.mad.2017.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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van Doeselaar S, Burgering BMT. FOXOs Maintaining the Equilibrium for Better or for Worse. Curr Top Dev Biol 2018; 127:49-103. [PMID: 29433740 DOI: 10.1016/bs.ctdb.2017.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A paradigm shift is emerging within the FOXO field and accumulating evidence indicates that we need to reappreciate the role of FOXOs, at least in cancer development. Here, we discuss the possibility that FOXOs are both tumor suppressors as well as promoters of tumor progression. This is mostly dependent on the biological context. Critical to this dichotomous role is the notion that FOXOs are central in preserving cellular homeostasis in redox control, genomic stability, and protein turnover. From this perspective, a paradoxical role in both suppressing and enhancing tumor progression can be reconciled. As many small molecules targeting the PI3K pathway are developed by big pharmaceutical companies and/or are in clinical trial, we will discuss what the consequences may be for the context-dependent role of FOXOs in tumor development in treatment options based on active PI3K signaling in tumors.
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Affiliation(s)
- Sabina van Doeselaar
- Molecular Cancer Research, Center Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Boudewijn M T Burgering
- Molecular Cancer Research, Center Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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50
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DNA damage responses and p53 in the aging process. Blood 2017; 131:488-495. [PMID: 29141944 DOI: 10.1182/blood-2017-07-746396] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/01/2017] [Indexed: 12/18/2022] Open
Abstract
The genome is constantly attacked by genotoxic insults. DNA damage has long been established as a cause of cancer development through its mutagenic consequences. Conversely, radiation therapy and chemotherapy induce DNA damage to drive cells into apoptosis or senescence as outcomes of the DNA damage response (DDR). More recently, DNA damage has been recognized as a causal factor for the aging process. The role of DNA damage in aging and age-related diseases is illustrated by numerous congenital progeroid syndromes that are caused by mutations in genome maintenance pathways. During the past 2 decades, understanding how DDR drives cancer development and contributes to the aging process has progressed rapidly. It turns out that the DDR factor p53 takes center stage during tumor development and also plays an important role in the aging process. Studies in metazoan models ranging from Caenorhabditis elegans to mammals have revealed cell-autonomous and systemic DDR mechanisms that orchestrate adaptive responses that augment maintenance of the aging organism amid gradually accumulating DNA damage.
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